## Changes since v3.7.0 (2025-11-07) ### bug - Fix smaller genomic region being shown when using &tracklist=true URL params (#5388) @cmdcolin - Fix color by CDS / calculation of phase on BED12/bigbed files (#5384) @cmdcolin - Fix hot module reload losing app state (#5374) @cmdcolin - Fix issue where multiple sub-menus could open up at once (#5308) @cmdcolin - Avoid changing displayed regions set when using "Center at feature" in synteny view (#5281) @cmdcolin - Avoid 'polynomial regex' in assembly name parsing (#5258) @cmdcolin - Fix export of SVG hanging if track had error (#5234) @cmdcolin - Reduce coarseStripHTML regex complexity to address codeql warning (#5233) @cmdcolin - Fix click-and-drag starting from a inter-region padding block (#5226) @cmdcolin - Add cancellation stop tokens for linear read arc/cloud displays (#5221) @cmdcolin ### dependencies - Update to jest 30 (#5223) @cmdcolin ### documentation - Add PAG 2026 user tutorial (#5340) @garrettjstevens ### enhancement - Show full dotplot when zoomed all the way out (#5387) @cmdcolin - Switch to pnpm as package manager and add ESM "exports" to packages (#5382) @cmdcolin - Re-organize 'track action' menu items into a submenu (#5378) @cmdcolin - Remove BroadcastChannel from SessionLoader (#5375) @cmdcolin - Allow plugins to make custom radio items for synteny import forms (#5373) @cmdcolin - Allow easily filtering samples in the variant feature details by genotype/dosage (#5366) @cmdcolin - Allow clicking transcript subfeatures of a gene glyph (#5363) @cmdcolin - Add --excludeTracks to jbrowse text-index (#5354) @cmdcolin - Use custom 'jexl' fork with multi-statement evaluation and template strings (#5353) @cmdcolin - Search indexedDB for old sessions when using a local- type URL (#5346) @cmdcolin - Filter out defaults from session snapshots (#5339) @cmdcolin - Add general concept for showing legends on tracks (#5337) @cmdcolin - Improve mouseover and clicking on mismatches/modifications on SNPCoverage (#5336) @cmdcolin - Create layout optimizations for deep RNA-seq data (#5330) @cmdcolin - Filter sashimi arcs by score (#5329) @cmdcolin - Multiple optimizations for alignments tracks (#5326) @cmdcolin - Add WASM code for unzipping in CRAM, BAM, BigWig, Tabix, etc. (#5320) @cmdcolin - Optimizations for multi-wiggle tracks (#5318) @cmdcolin - Add optional directional 'chevrons' to the gene glyphs (#5317) @cmdcolin - Collapse introns transcript selector (#5316) @cmdcolin - Avoid "import form flash" during loading (#5314) @cmdcolin - Avoid drawing tick labels that overlap block boundaries (#5312) @cmdcolin - Create pluggable glyph system for canvas feature renderer (#5311) @cmdcolin - Create optimizations for alignments track (#5310) @cmdcolin - Improve bigwig Y-scalebar label legibility (#5307) @cmdcolin - Make BAM and CRAM adapters use assembly sequence adapter (#5305) @cmdcolin - Add gridlines option for SVG export (#5303) @cmdcolin - Aggregate insertion stats in on SNP coverage track (#5301) @cmdcolin - Add "tiled window manager" to JBrowse apps (#5300) @cmdcolin - Aggregate insertion stats for tooltip (#5294) @cmdcolin - Simplify VCF feature descriptions (#5292) @cmdcolin - If &loc= is not specified in URL bar, then show all regions of the genome (#5289) @cmdcolin - Improve track drag-n-drop re-ordering on linear genome view (#5288) @cmdcolin - Allow rendering inter-chromosomal contacts with Hi-C renderer (#5284) @cmdcolin - Add better source maps in error stack trace on desktop app (#5280) @cmdcolin - Increase lazy loading of some react components (#5278) @cmdcolin - Add ability to click and mouseover RNA-seq junction arcs (#5277) @cmdcolin - Add ability to mouseover and click on 'insertions' on SNPCoverage track (#5276) @cmdcolin - Refactor the renderer and RPC stack (#5270) @cmdcolin - Allow putting helpText on WidgetType (#5268) @cmdcolin - Allow rapid clicking of zoom in and out buttons (#5266) @cmdcolin - Use SanitizedHTML on category names (#5264) @cmdcolin - Improve performance of track list using custom virtualization routines (#5263) @cmdcolin - Add ability to show longest transcript only and easily filter out gene glyphs (#5259) @cmdcolin - Fix scrolling on multivariant display types (#5256) @cmdcolin - Create new 'renderingProps' concept for the 'rendering' react component as a complement to 'renderProps' for renderer (#5255) @cmdcolin - Floating labels optimizations (#5251) @cmdcolin - Optimize the search box using uncontrolled component style (#5250) @cmdcolin - Optimizations for fast updating linear genome view scroll elements (#5249) @cmdcolin - Refactor VcfFeature for speed and clarity (#5247) @cmdcolin - Use numeric encodings for SEQ and CIGAR fields for BAM (#5246) @cmdcolin - Allow drawing transcript subfeature labels on canvas features (#5245) @cmdcolin - Limit showing mismatch mouseovers on alignments tracks (#5241) @cmdcolin - Allow clicking on mismatches and insertions on alignments track to get more info (#5238) @cmdcolin - Add ability to draw hierarchical tree from clustering on multi-sample variant view (#5236) @cmdcolin - Globally stop swipe action from producing back/forward actions on jbrowse-web (#5229) @cmdcolin - Preserve old visualization during block re-rendering (#5227) @cmdcolin - Scroll only the matrix part of the multi-sample variant viewer (#5222) @cmdcolin - Scroll only pileup part of the alignments track (#5220) @cmdcolin - Add mismatches to linked reads display, and make linked read and read arc webworker rendered (#5218) @cmdcolin - Add 'super-compact' display mode for alignments tracks (#5217) @cmdcolin - Optimizations for granular rect layout (#5214) @cmdcolin - Add canvas based renderer for regular gene feature tracks (#5213) @cmdcolin - Add some micro-optimizations for gridlines and scalebar labels (#5210) @cmdcolin - Add some help text to display types (#5207) @cmdcolin - Remove react-dom/server usage in webworker (#5205) @cmdcolin - Vendor @jbrowse/mobx-state-tree (#4938) @cmdcolin - Optimizations to support large tracklists (#4499) @cmdcolin - Save track data method on base track model (#3439) @cmdcolin ### housekeeping - Create simplified browser test suite using puppeteer (#5267) @cmdcolin ### internal - Use mobx-state-tree patches instead of full snapshots for undo manager (#5309) @cmdcolin - Change JBrowse CLI to use 'fetch against the filesystem' with file:/// (#5304) @cmdcolin - Vendor tss-react/mui dependency (#5271) @cmdcolin - Fix `depcheck` warnings (#5257) @cmdcolin - Remove use-query-params library (#5248) @cmdcolin - Use 'gh CLI' for release (#5235) @cmdcolin - Add explicit github workflow permissions (#5232) @cmdcolin - Remove unused makeStyles classes (#5208) @cmdcolin ## Changes since v3.7.0 (2025-11-07) ### bug - Fix smaller genomic region being shown when using &tracklist=true URL params (#5388) @cmdcolin - Fix color by CDS / calculation of phase on BED12/bigbed files (#5384) @cmdcolin - Fix hot module reload losing app state (#5374) @cmdcolin - Fix issue where multiple sub-menus could open up at once (#5308) @cmdcolin - Avoid changing displayed regions set when using "Center at feature" in synteny view (#5281) @cmdcolin - Avoid 'polynomial regex' in assembly name parsing (#5258) @cmdcolin - Fix export of SVG hanging if track had error (#5234) @cmdcolin - Reduce coarseStripHTML regex complexity to address codeql warning (#5233) @cmdcolin - Fix click-and-drag starting from a inter-region padding block (#5226) @cmdcolin - Add cancellation stop tokens for linear read arc/cloud displays (#5221) @cmdcolin ### dependencies - Update to jest 30 (#5223) @cmdcolin ### documentation - Add PAG 2026 user tutorial (#5340) @garrettjstevens ### enhancement - Show full dotplot when zoomed all the way out (#5387) @cmdcolin - Switch to pnpm as package manager and add ESM "exports" to packages (#5382) @cmdcolin - Re-organize 'track action' menu items into a submenu (#5378) @cmdcolin - Remove BroadcastChannel from SessionLoader (#5375) @cmdcolin - Allow plugins to make custom radio items for synteny import forms (#5373) @cmdcolin - Allow easily filtering samples in the variant feature details by genotype/dosage (#5366) @cmdcolin - Allow clicking transcript subfeatures of a gene glyph (#5363) @cmdcolin - Add --excludeTracks to jbrowse text-index (#5354) @cmdcolin - Use custom 'jexl' fork with multi-statement evaluation and template strings (#5353) @cmdcolin - Search indexedDB for old sessions when using a local- type URL (#5346) @cmdcolin - Filter out defaults from session snapshots (#5339) @cmdcolin - Add general concept for showing legends on tracks (#5337) @cmdcolin - Improve mouseover and clicking on mismatches/modifications on SNPCoverage (#5336) @cmdcolin - Create layout optimizations for deep RNA-seq data (#5330) @cmdcolin - Filter sashimi arcs by score (#5329) @cmdcolin - Multiple optimizations for alignments tracks (#5326) @cmdcolin - Add WASM code for unzipping in CRAM, BAM, BigWig, Tabix, etc. (#5320) @cmdcolin - Optimizations for multi-wiggle tracks (#5318) @cmdcolin - Add optional directional 'chevrons' to the gene glyphs (#5317) @cmdcolin - Collapse introns transcript selector (#5316) @cmdcolin - Avoid "import form flash" during loading (#5314) @cmdcolin - Avoid drawing tick labels that overlap block boundaries (#5312) @cmdcolin - Create pluggable glyph system for canvas feature renderer (#5311) @cmdcolin - Create optimizations for alignments track (#5310) @cmdcolin - Improve bigwig Y-scalebar label legibility (#5307) @cmdcolin - Make BAM and CRAM adapters use assembly sequence adapter (#5305) @cmdcolin - Add gridlines option for SVG export (#5303) @cmdcolin - Aggregate insertion stats in on SNP coverage track (#5301) @cmdcolin - Add "tiled window manager" to JBrowse apps (#5300) @cmdcolin - Aggregate insertion stats for tooltip (#5294) @cmdcolin - Simplify VCF feature descriptions (#5292) @cmdcolin - If &loc= is not specified in URL bar, then show all regions of the genome (#5289) @cmdcolin - Improve track drag-n-drop re-ordering on linear genome view (#5288) @cmdcolin - Allow rendering inter-chromosomal contacts with Hi-C renderer (#5284) @cmdcolin - Add better source maps in error stack trace on desktop app (#5280) @cmdcolin - Increase lazy loading of some react components (#5278) @cmdcolin - Add ability to click and mouseover RNA-seq junction arcs (#5277) @cmdcolin - Add ability to mouseover and click on 'insertions' on SNPCoverage track (#5276) @cmdcolin - Refactor the renderer and RPC stack (#5270) @cmdcolin - Allow putting helpText on WidgetType (#5268) @cmdcolin - Allow rapid clicking of zoom in and out buttons (#5266) @cmdcolin - Use SanitizedHTML on category names (#5264) @cmdcolin - Improve performance of track list using custom virtualization routines (#5263) @cmdcolin - Add ability to show longest transcript only and easily filter out gene glyphs (#5259) @cmdcolin - Fix scrolling on multivariant display types (#5256) @cmdcolin - Create new 'renderingProps' concept for the 'rendering' react component as a complement to 'renderProps' for renderer (#5255) @cmdcolin - Floating labels optimizations (#5251) @cmdcolin - Optimize the search box using uncontrolled component style (#5250) @cmdcolin - Optimizations for fast updating linear genome view scroll elements (#5249) @cmdcolin - Refactor VcfFeature for speed and clarity (#5247) @cmdcolin - Use numeric encodings for SEQ and CIGAR fields for BAM (#5246) @cmdcolin - Allow drawing transcript subfeature labels on canvas features (#5245) @cmdcolin - Limit showing mismatch mouseovers on alignments tracks (#5241) @cmdcolin - Allow clicking on mismatches and insertions on alignments track to get more info (#5238) @cmdcolin - Add ability to draw hierarchical tree from clustering on multi-sample variant view (#5236) @cmdcolin - Globally stop swipe action from producing back/forward actions on jbrowse-web (#5229) @cmdcolin - Preserve old visualization during block re-rendering (#5227) @cmdcolin - Scroll only the matrix part of the multi-sample variant viewer (#5222) @cmdcolin - Scroll only pileup part of the alignments track (#5220) @cmdcolin - Add mismatches to linked reads display, and make linked read and read arc webworker rendered (#5218) @cmdcolin - Add 'super-compact' display mode for alignments tracks (#5217) @cmdcolin - Optimizations for granular rect layout (#5214) @cmdcolin - Add canvas based renderer for regular gene feature tracks (#5213) @cmdcolin - Add some micro-optimizations for gridlines and scalebar labels (#5210) @cmdcolin - Add some help text to display types (#5207) @cmdcolin - Remove react-dom/server usage in webworker (#5205) @cmdcolin - Vendor @jbrowse/mobx-state-tree (#4938) @cmdcolin - Optimizations to support large tracklists (#4499) @cmdcolin - Save track data method on base track model (#3439) @cmdcolin ### housekeeping - Create simplified browser test suite using puppeteer (#5267) @cmdcolin ### internal - Use mobx-state-tree patches instead of full snapshots for undo manager (#5309) @cmdcolin - Change JBrowse CLI to use 'fetch against the filesystem' with file:/// (#5304) @cmdcolin - Vendor tss-react/mui dependency (#5271) @cmdcolin - Fix `depcheck` warnings (#5257) @cmdcolin - Remove use-query-params library (#5248) @cmdcolin - Use 'gh CLI' for release (#5235) @cmdcolin - Add explicit github workflow permissions (#5232) @cmdcolin - Remove unused makeStyles classes (#5208) @cmdcolin ## Changes since v3.7.0 (2025-11-07) ### bug - Fix smaller genomic region being shown when using &tracklist=true URL params (#5388) @cmdcolin - Fix color by CDS / calculation of phase on BED12/bigbed files (#5384) @cmdcolin - Fix hot module reload losing app state (#5374) @cmdcolin - Fix issue where multiple sub-menus could open up at once (#5308) @cmdcolin - Avoid changing displayed regions set when using "Center at feature" in synteny view (#5281) @cmdcolin - Avoid 'polynomial regex' in assembly name parsing (#5258) @cmdcolin - Fix export of SVG hanging if track had error (#5234) @cmdcolin - Reduce coarseStripHTML regex complexity to address codeql warning (#5233) @cmdcolin - Fix click-and-drag starting from a inter-region padding block (#5226) @cmdcolin - Add cancellation stop tokens for linear read arc/cloud displays (#5221) @cmdcolin ### dependencies - Update to jest 30 (#5223) @cmdcolin ### documentation - Add PAG 2026 user tutorial (#5340) @garrettjstevens ### enhancement - Show full dotplot when zoomed all the way out (#5387) @cmdcolin - Switch to pnpm as package manager and add ESM "exports" to packages (#5382) @cmdcolin - Re-organize 'track action' menu items into a submenu (#5378) @cmdcolin - Remove BroadcastChannel from SessionLoader (#5375) @cmdcolin - Allow plugins to make custom radio items for synteny import forms (#5373) @cmdcolin - Allow easily filtering samples in the variant feature details by genotype/dosage (#5366) @cmdcolin - Allow clicking transcript subfeatures of a gene glyph (#5363) @cmdcolin - Add --excludeTracks to jbrowse text-index (#5354) @cmdcolin - Use custom 'jexl' fork with multi-statement evaluation and template strings (#5353) @cmdcolin - Search indexedDB for old sessions when using a local- type URL (#5346) @cmdcolin - Filter out defaults from session snapshots (#5339) @cmdcolin - Add general concept for showing legends on tracks (#5337) @cmdcolin - Improve mouseover and clicking on mismatches/modifications on SNPCoverage (#5336) @cmdcolin - Create layout optimizations for deep RNA-seq data (#5330) @cmdcolin - Filter sashimi arcs by score (#5329) @cmdcolin - Multiple optimizations for alignments tracks (#5326) @cmdcolin - Add WASM code for unzipping in CRAM, BAM, BigWig, Tabix, etc. (#5320) @cmdcolin - Optimizations for multi-wiggle tracks (#5318) @cmdcolin - Add optional directional 'chevrons' to the gene glyphs (#5317) @cmdcolin - Collapse introns transcript selector (#5316) @cmdcolin - Avoid "import form flash" during loading (#5314) @cmdcolin - Avoid drawing tick labels that overlap block boundaries (#5312) @cmdcolin - Create pluggable glyph system for canvas feature renderer (#5311) @cmdcolin - Create optimizations for alignments track (#5310) @cmdcolin - Improve bigwig Y-scalebar label legibility (#5307) @cmdcolin - Make BAM and CRAM adapters use assembly sequence adapter (#5305) @cmdcolin - Add gridlines option for SVG export (#5303) @cmdcolin - Aggregate insertion stats in on SNP coverage track (#5301) @cmdcolin - Add "tiled window manager" to JBrowse apps (#5300) @cmdcolin - Aggregate insertion stats for tooltip (#5294) @cmdcolin - Simplify VCF feature descriptions (#5292) @cmdcolin - If &loc= is not specified in URL bar, then show all regions of the genome (#5289) @cmdcolin - Improve track drag-n-drop re-ordering on linear genome view (#5288) @cmdcolin - Allow rendering inter-chromosomal contacts with Hi-C renderer (#5284) @cmdcolin - Add better source maps in error stack trace on desktop app (#5280) @cmdcolin - Increase lazy loading of some react components (#5278) @cmdcolin - Add ability to click and mouseover RNA-seq junction arcs (#5277) @cmdcolin - Add ability to mouseover and click on 'insertions' on SNPCoverage track (#5276) @cmdcolin - Refactor the renderer and RPC stack (#5270) @cmdcolin - Allow putting helpText on WidgetType (#5268) @cmdcolin - Allow rapid clicking of zoom in and out buttons (#5266) @cmdcolin - Use SanitizedHTML on category names (#5264) @cmdcolin - Improve performance of track list using custom virtualization routines (#5263) @cmdcolin - Add ability to show longest transcript only and easily filter out gene glyphs (#5259) @cmdcolin - Fix scrolling on multivariant display types (#5256) @cmdcolin - Create new 'renderingProps' concept for the 'rendering' react component as a complement to 'renderProps' for renderer (#5255) @cmdcolin - Floating labels optimizations (#5251) @cmdcolin - Optimize the search box using uncontrolled component style (#5250) @cmdcolin - Optimizations for fast updating linear genome view scroll elements (#5249) @cmdcolin - Refactor VcfFeature for speed and clarity (#5247) @cmdcolin - Use numeric encodings for SEQ and CIGAR fields for BAM (#5246) @cmdcolin - Allow drawing transcript subfeature labels on canvas features (#5245) @cmdcolin - Limit showing mismatch mouseovers on alignments tracks (#5241) @cmdcolin - Allow clicking on mismatches and insertions on alignments track to get more info (#5238) @cmdcolin - Add ability to draw hierarchical tree from clustering on multi-sample variant view (#5236) @cmdcolin - Globally stop swipe action from producing back/forward actions on jbrowse-web (#5229) @cmdcolin - Preserve old visualization during block re-rendering (#5227) @cmdcolin - Scroll only the matrix part of the multi-sample variant viewer (#5222) @cmdcolin - Scroll only pileup part of the alignments track (#5220) @cmdcolin - Add mismatches to linked reads display, and make linked read and read arc webworker rendered (#5218) @cmdcolin - Add 'super-compact' display mode for alignments tracks (#5217) @cmdcolin - Optimizations for granular rect layout (#5214) @cmdcolin - Add canvas based renderer for regular gene feature tracks (#5213) @cmdcolin - Add some micro-optimizations for gridlines and scalebar labels (#5210) @cmdcolin - Add some help text to display types (#5207) @cmdcolin - Remove react-dom/server usage in webworker (#5205) @cmdcolin - Vendor @jbrowse/mobx-state-tree (#4938) @cmdcolin - Optimizations to support large tracklists (#4499) @cmdcolin - Save track data method on base track model (#3439) @cmdcolin ### housekeeping - Create simplified browser test suite using puppeteer (#5267) @cmdcolin ### internal - Use mobx-state-tree patches instead of full snapshots for undo manager (#5309) @cmdcolin - Change JBrowse CLI to use 'fetch against the filesystem' with file:/// (#5304) @cmdcolin - Vendor tss-react/mui dependency (#5271) @cmdcolin - Fix `depcheck` warnings (#5257) @cmdcolin - Remove use-query-params library (#5248) @cmdcolin - Use 'gh CLI' for release (#5235) @cmdcolin - Add explicit github workflow permissions (#5232) @cmdcolin - Remove unused makeStyles classes (#5208) @cmdcolin ## Changes since v3.7.0 (2025-11-07) ### bug - Fix smaller genomic region being shown when using &tracklist=true URL params (#5388) @cmdcolin - Fix color by CDS / calculation of phase on BED12/bigbed files (#5384) @cmdcolin - Fix hot module reload losing app state (#5374) @cmdcolin - Fix issue where multiple sub-menus could open up at once (#5308) @cmdcolin - Avoid changing displayed regions set when using "Center at feature" in synteny view (#5281) @cmdcolin - Avoid 'polynomial regex' in assembly name parsing (#5258) @cmdcolin - Fix export of SVG hanging if track had error (#5234) @cmdcolin - Reduce coarseStripHTML regex complexity to address codeql warning (#5233) @cmdcolin - Fix click-and-drag starting from a inter-region padding block (#5226) @cmdcolin - Add cancellation stop tokens for linear read arc/cloud displays (#5221) @cmdcolin ### dependencies - Update to jest 30 (#5223) @cmdcolin ### documentation - Add PAG 2026 user tutorial (#5340) @garrettjstevens ### enhancement - Show full dotplot when zoomed all the way out (#5387) @cmdcolin - Switch to pnpm as package manager and add ESM "exports" to packages (#5382) @cmdcolin - Re-organize 'track action' menu items into a submenu (#5378) @cmdcolin - Remove BroadcastChannel from SessionLoader (#5375) @cmdcolin - Allow plugins to make custom radio items for synteny import forms (#5373) @cmdcolin - Allow easily filtering samples in the variant feature details by genotype/dosage (#5366) @cmdcolin - Allow clicking transcript subfeatures of a gene glyph (#5363) @cmdcolin - Add --excludeTracks to jbrowse text-index (#5354) @cmdcolin - Use custom 'jexl' fork with multi-statement evaluation and template strings (#5353) @cmdcolin - Search indexedDB for old sessions when using a local- type URL (#5346) @cmdcolin - Filter out defaults from session snapshots (#5339) @cmdcolin - Add general concept for showing legends on tracks (#5337) @cmdcolin - Improve mouseover and clicking on mismatches/modifications on SNPCoverage (#5336) @cmdcolin - Create layout optimizations for deep RNA-seq data (#5330) @cmdcolin - Filter sashimi arcs by score (#5329) @cmdcolin - Multiple optimizations for alignments tracks (#5326) @cmdcolin - Add WASM code for unzipping in CRAM, BAM, BigWig, Tabix, etc. (#5320) @cmdcolin - Optimizations for multi-wiggle tracks (#5318) @cmdcolin - Add optional directional 'chevrons' to the gene glyphs (#5317) @cmdcolin - Collapse introns transcript selector (#5316) @cmdcolin - Avoid "import form flash" during loading (#5314) @cmdcolin - Avoid drawing tick labels that overlap block boundaries (#5312) @cmdcolin - Create pluggable glyph system for canvas feature renderer (#5311) @cmdcolin - Create optimizations for alignments track (#5310) @cmdcolin - Improve bigwig Y-scalebar label legibility (#5307) @cmdcolin - Make BAM and CRAM adapters use assembly sequence adapter (#5305) @cmdcolin - Add gridlines option for SVG export (#5303) @cmdcolin - Aggregate insertion stats in on SNP coverage track (#5301) @cmdcolin - Add "tiled window manager" to JBrowse apps (#5300) @cmdcolin - Aggregate insertion stats for tooltip (#5294) @cmdcolin - Simplify VCF feature descriptions (#5292) @cmdcolin - If &loc= is not specified in URL bar, then show all regions of the genome (#5289) @cmdcolin - Improve track drag-n-drop re-ordering on linear genome view (#5288) @cmdcolin - Allow rendering inter-chromosomal contacts with Hi-C renderer (#5284) @cmdcolin - Add better source maps in error stack trace on desktop app (#5280) @cmdcolin - Increase lazy loading of some react components (#5278) @cmdcolin - Add ability to click and mouseover RNA-seq junction arcs (#5277) @cmdcolin - Add ability to mouseover and click on 'insertions' on SNPCoverage track (#5276) @cmdcolin - Refactor the renderer and RPC stack (#5270) @cmdcolin - Allow putting helpText on WidgetType (#5268) @cmdcolin - Allow rapid clicking of zoom in and out buttons (#5266) @cmdcolin - Use SanitizedHTML on category names (#5264) @cmdcolin - Improve performance of track list using custom virtualization routines (#5263) @cmdcolin - Add ability to show longest transcript only and easily filter out gene glyphs (#5259) @cmdcolin - Fix scrolling on multivariant display types (#5256) @cmdcolin - Create new 'renderingProps' concept for the 'rendering' react component as a complement to 'renderProps' for renderer (#5255) @cmdcolin - Floating labels optimizations (#5251) @cmdcolin - Optimize the search box using uncontrolled component style (#5250) @cmdcolin - Optimizations for fast updating linear genome view scroll elements (#5249) @cmdcolin - Refactor VcfFeature for speed and clarity (#5247) @cmdcolin - Use numeric encodings for SEQ and CIGAR fields for BAM (#5246) @cmdcolin - Allow drawing transcript subfeature labels on canvas features (#5245) @cmdcolin - Limit showing mismatch mouseovers on alignments tracks (#5241) @cmdcolin - Allow clicking on mismatches and insertions on alignments track to get more info (#5238) @cmdcolin - Add ability to draw hierarchical tree from clustering on multi-sample variant view (#5236) @cmdcolin - Globally stop swipe action from producing back/forward actions on jbrowse-web (#5229) @cmdcolin - Preserve old visualization during block re-rendering (#5227) @cmdcolin - Scroll only the matrix part of the multi-sample variant viewer (#5222) @cmdcolin - Scroll only pileup part of the alignments track (#5220) @cmdcolin - Add mismatches to linked reads display, and make linked read and read arc webworker rendered (#5218) @cmdcolin - Add 'super-compact' display mode for alignments tracks (#5217) @cmdcolin - Optimizations for granular rect layout (#5214) @cmdcolin - Add canvas based renderer for regular gene feature tracks (#5213) @cmdcolin - Add some micro-optimizations for gridlines and scalebar labels (#5210) @cmdcolin - Add some help text to display types (#5207) @cmdcolin - Remove react-dom/server usage in webworker (#5205) @cmdcolin - Vendor @jbrowse/mobx-state-tree (#4938) @cmdcolin - Optimizations to support large tracklists (#4499) @cmdcolin - Save track data method on base track model (#3439) @cmdcolin ### housekeeping - Create simplified browser test suite using puppeteer (#5267) @cmdcolin ### internal - Use mobx-state-tree patches instead of full snapshots for undo manager (#5309) @cmdcolin - Change JBrowse CLI to use 'fetch against the filesystem' with file:/// (#5304) @cmdcolin - Vendor tss-react/mui dependency (#5271) @cmdcolin - Fix `depcheck` warnings (#5257) @cmdcolin - Remove use-query-params library (#5248) @cmdcolin - Use 'gh CLI' for release (#5235) @cmdcolin - Add explicit github workflow permissions (#5232) @cmdcolin - Remove unused makeStyles classes (#5208) @cmdcolin ## 3.7.0 (2025-11-07) #### :rocket: Enhancement - `core` - [#5201](https://github.com/GMOD/jbrowse-components/pull/5201) Add 'bulk operations' to the multi-wiggle color editor ([@cmdcolin](https://github.com/cmdcolin)) - [#5197](https://github.com/GMOD/jbrowse-components/pull/5197) Ability to make help text on menu items ([@cmdcolin](https://github.com/cmdcolin)) - [#5183](https://github.com/GMOD/jbrowse-components/pull/5183) Add ability to link supplementary alignments and pairs ([@cmdcolin](https://github.com/cmdcolin)) - [#5136](https://github.com/GMOD/jbrowse-components/pull/5136) Add ability to mouseover alignments tracks ([@cmdcolin](https://github.com/cmdcolin)) - [#4967](https://github.com/GMOD/jbrowse-components/pull/4967) Add ability to connect to genark and UCSC browsers to jbrowse desktop ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#5195](https://github.com/GMOD/jbrowse-components/pull/5195) Add ability to adjust alpha, min alignment length, color scheme and option to diagonalize synteny plots ([@cmdcolin](https://github.com/cmdcolin)) - [#5196](https://github.com/GMOD/jbrowse-components/pull/5196) Optimize gridlines component ([@cmdcolin](https://github.com/cmdcolin)) - [#5188](https://github.com/GMOD/jbrowse-components/pull/5188) Add searchable header bar to breakpoint split view ([@cmdcolin](https://github.com/cmdcolin)) - [#5186](https://github.com/GMOD/jbrowse-components/pull/5186) Fix the display of 'duplex' sequence modifications on BAM files and default to only showing mods >=10% ([@cmdcolin](https://github.com/cmdcolin)) - [#5182](https://github.com/GMOD/jbrowse-components/pull/5182) Add deletions and mismatches to the pileup mouseover ([@cmdcolin](https://github.com/cmdcolin)) - [#5178](https://github.com/GMOD/jbrowse-components/pull/5178) Add CDS protein numbering to glyphs ([@cmdcolin](https://github.com/cmdcolin)) - [#5169](https://github.com/GMOD/jbrowse-components/pull/5169) Use more accurate alpha blending for synteny view ([@cmdcolin](https://github.com/cmdcolin)) - [#5162](https://github.com/GMOD/jbrowse-components/pull/5162) Add some support for SVLEN to infer the END of a variant from VCF 4.5 ([@cmdcolin](https://github.com/cmdcolin)) - [#5122](https://github.com/GMOD/jbrowse-components/pull/5122) Link to "Genomes" in jbrowse website header bar ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - [#5177](https://github.com/GMOD/jbrowse-components/pull/5177) Fix incorrect coloring for multi-sample variant renderer in some cases ([@cmdcolin](https://github.com/cmdcolin)) - [#5173](https://github.com/GMOD/jbrowse-components/pull/5173) Add lint fixes for eslint-plugin-react-hooks v7 ([@cmdcolin](https://github.com/cmdcolin)) - [#5174](https://github.com/GMOD/jbrowse-components/pull/5174) Fix some loading messages ([@cmdcolin](https://github.com/cmdcolin)) - [#5166](https://github.com/GMOD/jbrowse-components/pull/5166) Fix menu zindex for some situations ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#5175](https://github.com/GMOD/jbrowse-components/pull/5175) Fix for tracks from wrong assembly showing up in track list when using connections ([@cmdcolin](https://github.com/cmdcolin)) - [#5170](https://github.com/GMOD/jbrowse-components/pull/5170) Update gff-nostream dependency to fix features not found errors ([@cmdcolin](https://github.com/cmdcolin)) - [#5169](https://github.com/GMOD/jbrowse-components/pull/5169) Use more accurate alpha blending for synteny view ([@cmdcolin](https://github.com/cmdcolin)) - [#5164](https://github.com/GMOD/jbrowse-components/pull/5164) Fix SV inspector data grid filtering synchronization with circular view ([@cmdcolin](https://github.com/cmdcolin)) - [#5161](https://github.com/GMOD/jbrowse-components/pull/5161) Add missing "tmp" dependency to `@jbrowse/cli` package.json ([@garrettjstevens](https://github.com/garrettjstevens)) #### :house: Internal - `core` - [#5173](https://github.com/GMOD/jbrowse-components/pull/5173) Add lint fixes for eslint-plugin-react-hooks v7 ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#5158](https://github.com/GMOD/jbrowse-components/pull/5158) Use actions-up to bump actions ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) Done in 2.38s. ## 3.6.5 (2025-09-11) #### :rocket: Enhancement - [#5142](https://github.com/GMOD/jbrowse-components/pull/5142) Load jbrowse config passed as CLI arg to jbrowse desktop, and support .jbrowse file extension ([@amorison](https://github.com/amorison)) - [#5144](https://github.com/GMOD/jbrowse-components/pull/5144) Convert GC content calculation to rolling average for speed improvement ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - [#5155](https://github.com/GMOD/jbrowse-components/pull/5155) Avoid multiple context submenus from being visible at once ([@cmdcolin](https://github.com/cmdcolin)) - [#5128](https://github.com/GMOD/jbrowse-components/pull/5128) Fix the calculation of the width of view containers ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#5140](https://github.com/GMOD/jbrowse-components/pull/5140) Destroy old root model on pluginManager reload ([@garrettjstevens](https://github.com/garrettjstevens)) - [#5133](https://github.com/GMOD/jbrowse-components/pull/5133) Fix pin track function being missing from track menu ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - [#5140](https://github.com/GMOD/jbrowse-components/pull/5140) Destroy old root model on pluginManager reload ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 3 - Adrien Morison ([@amorison](https://github.com/amorison)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) Done in 1.40s. ## 3.6.4 (2025-07-21) #### :rocket: Enhancement - `core`, `web-core` - [#5101](https://github.com/GMOD/jbrowse-components/pull/5101) Add concept of loading a JBrowse 2 config.json as a connection, and add extension point to allow plugins to lazy load configs ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#5116](https://github.com/GMOD/jbrowse-components/pull/5116) Add padding if selecting search result from table ([@garrettjstevens](https://github.com/garrettjstevens)) - `product-core` - [#5114](https://github.com/GMOD/jbrowse-components/pull/5114) Add locstrings to synteny mouseovers ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - [#5120](https://github.com/GMOD/jbrowse-components/pull/5120) Generalize parse line by line function to fix bed, gff3, and other types of files with no trailing newline ([@cmdcolin](https://github.com/cmdcolin)) - [#5111](https://github.com/GMOD/jbrowse-components/pull/5111) Fix issue where multiple cascading submenus could be opened at once ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#5118](https://github.com/GMOD/jbrowse-components/pull/5118) Avoid clearing click-and-drag rubberband boundaries onMouseOut to fix "Zoom to region", bookmark region, etc. ([@cmdcolin](https://github.com/cmdcolin)) - [#5115](https://github.com/GMOD/jbrowse-components/pull/5115) Fix 'Add track widget' bug when changing input filename ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) Done in 1.54s. Done in 0.81s. Done in 0.54s. Done in 0.53s. ## 3.6.0 (2025-07-10) #### :rocket: Enhancement - Other - [#5102](https://github.com/GMOD/jbrowse-components/pull/5102) Refactor CLI to use built-in nodejs parseArgs ([@cmdcolin](https://github.com/cmdcolin)) - [#5090](https://github.com/GMOD/jbrowse-components/pull/5090) Optimize some MM tag parsing for performance and readability ([@cmdcolin](https://github.com/cmdcolin)) - [#5087](https://github.com/GMOD/jbrowse-components/pull/5087) Better usage of dark mode on sequence track ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#5095](https://github.com/GMOD/jbrowse-components/pull/5095) Fix alpha rendering of SVG renderer box stroke/fill ([@cmdcolin](https://github.com/cmdcolin)) - [#5086](https://github.com/GMOD/jbrowse-components/pull/5086) Add status message reporting for synteny view loading ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#5100](https://github.com/GMOD/jbrowse-components/pull/5100) Fix adding .pif file from dotplot and linear synteny import form ([@cmdcolin](https://github.com/cmdcolin)) - [#5098](https://github.com/GMOD/jbrowse-components/pull/5098) Also migrate the linear-comparative-view rubberband tooltip to default MUI tooltip to avoid potential UI hangs ([@cmdcolin](https://github.com/cmdcolin)) - [#5097](https://github.com/GMOD/jbrowse-components/pull/5097) Fix make pif on large files throwing ENOBUFS error in certain cases ([@cmdcolin](https://github.com/cmdcolin)) - [#5089](https://github.com/GMOD/jbrowse-components/pull/5089) Additional type check to catch non-string MM tags from older Cell Ranger version BAM files ([@haessar](https://github.com/haessar)) - [#5085](https://github.com/GMOD/jbrowse-components/pull/5085) Fix rubberband getting stuck under certain conditions ([@cmdcolin](https://github.com/cmdcolin)) - [#5080](https://github.com/GMOD/jbrowse-components/pull/5080) Fix crash on multi-wiggle importer on jbrowse-web ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#5095](https://github.com/GMOD/jbrowse-components/pull/5095) Fix alpha rendering of SVG renderer box stroke/fill ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#5099](https://github.com/GMOD/jbrowse-components/pull/5099) Update readme with short description of what JBrowse 2 is, new links, and publications ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `__mocks__`, `app-core`, `core` - [#5077](https://github.com/GMOD/jbrowse-components/pull/5077) Bump generic-filehandle with mock for test environment ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Will Haese-Hill ([@haessar](https://github.com/haessar)) Done in 1.34s. ## 3.5.1 (2025-06-05) #### :rocket: Enhancement - Other - [#5064](https://github.com/GMOD/jbrowse-components/pull/5064) Optimize fetching many small sequences from IndexedFasta (e.g. MSA datasets) ([@cmdcolin](https://github.com/cmdcolin)) - [#5059](https://github.com/GMOD/jbrowse-components/pull/5059) Canonicalize refNames in search results ([@cmdcolin](https://github.com/cmdcolin)) - [#5056](https://github.com/GMOD/jbrowse-components/pull/5056) Use assembly displayName on synteny header and ruler ([@garrettjstevens](https://github.com/garrettjstevens)) - [#5050](https://github.com/GMOD/jbrowse-components/pull/5050) Use standard sessionId for linear synteny view to reduce data re-fetching ([@cmdcolin](https://github.com/cmdcolin)) - `app-core`, `core`, `embedded-core` - [#5063](https://github.com/GMOD/jbrowse-components/pull/5063) Improve usability of dropdown menus by making submenus not disappear immediately onMouseLeave ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#5049](https://github.com/GMOD/jbrowse-components/pull/5049) Add react compiler ([@cmdcolin](https://github.com/cmdcolin)) - `app-core`, `core` - [#5044](https://github.com/GMOD/jbrowse-components/pull/5044) Allow plugins to register entries onto the root configuration ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#5062](https://github.com/GMOD/jbrowse-components/pull/5062) Fix useSWR usage from plugins ([@cmdcolin](https://github.com/cmdcolin)) - [#5053](https://github.com/GMOD/jbrowse-components/pull/5053) Fix @jbrowse/img using a no-op css import ([@cmdcolin](https://github.com/cmdcolin)) - [#5051](https://github.com/GMOD/jbrowse-components/pull/5051) Fix race condition with text search using useEffect cleanup ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#5058](https://github.com/GMOD/jbrowse-components/pull/5058) Improve speed of navigation for fragmented assemblies ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#5047](https://github.com/GMOD/jbrowse-components/pull/5047) Reduce the embedded website tutorial ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - Other - [#5057](https://github.com/GMOD/jbrowse-components/pull/5057) Reduce S3 uploads per-branch ([@cmdcolin](https://github.com/cmdcolin)) - [#5054](https://github.com/GMOD/jbrowse-components/pull/5054) Add ability to make commits to update docs only and avoid running CI ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#5061](https://github.com/GMOD/jbrowse-components/pull/5061) Modularize some integration tests for launching views ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) Done in 1.94s. ## 3.5.0 (2025-05-27) #### :rocket: Enhancement - [#5042](https://github.com/GMOD/jbrowse-components/pull/5042) Avoid inferring CDS subfeatures from non-coding gene pred features ([@cmdcolin](https://github.com/cmdcolin)) - [#5035](https://github.com/GMOD/jbrowse-components/pull/5035) Use trash icon for uninstall in plugin store, and add version number string ([@cmdcolin](https://github.com/cmdcolin)) - [#4735](https://github.com/GMOD/jbrowse-components/pull/4735) Remove jbrowse-web start screen ([@cmdcolin](https://github.com/cmdcolin)) - [#5025](https://github.com/GMOD/jbrowse-components/pull/5025) Allow hiding insertion and deletion in synteny view to help chain file visualization ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#5037](https://github.com/GMOD/jbrowse-components/pull/5037) Check that breakpoint split view is ready before fetching to avoid crash/large data fetching ([@cmdcolin](https://github.com/cmdcolin)) - [#5033](https://github.com/GMOD/jbrowse-components/pull/5033) Bump @gmod/bbi to fix loading bigwig files from bigtools ([@cmdcolin](https://github.com/cmdcolin)) - [#5024](https://github.com/GMOD/jbrowse-components/pull/5024) Fix lines crossing over view headers in breakpoint split view by only setting sticky view headers on top-level views ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#5029](https://github.com/GMOD/jbrowse-components/pull/5029) Fix data grid re-exports ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - [#5039](https://github.com/GMOD/jbrowse-components/pull/5039) Add titleNode prop to @jbrowse/core/ui/Dialog ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#5036](https://github.com/GMOD/jbrowse-components/pull/5036) Remove the async keyword from BaseLinearDisplayModel ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) Done in 1.78s. ## 3.4.0 (2025-05-13) #### :rocket: Enhancement - `core` - [#5018](https://github.com/GMOD/jbrowse-components/pull/5018) Avoid serializing large features to sessions to fix quota exceeded errors in localstorage ([@cmdcolin](https://github.com/cmdcolin)) - [#5010](https://github.com/GMOD/jbrowse-components/pull/5010) Add mouseover metadata for fields in the base feature widget ([@cmdcolin](https://github.com/cmdcolin)) - [#4998](https://github.com/GMOD/jbrowse-components/pull/4998) Add padding to the genomic window of search result hits ([@cmdcolin](https://github.com/cmdcolin)) - [#4995](https://github.com/GMOD/jbrowse-components/pull/4995) Add uFuzzy to improve gene name search ([@cmdcolin](https://github.com/cmdcolin)) - [#4983](https://github.com/GMOD/jbrowse-components/pull/4983) Update some data parser packages for ESM compat ([@cmdcolin](https://github.com/cmdcolin)) - [#4980](https://github.com/GMOD/jbrowse-components/pull/4980) Synthesize displayId if none provided in display config ([@cmdcolin](https://github.com/cmdcolin)) - [#4972](https://github.com/GMOD/jbrowse-components/pull/4972) Support cytoband bed files starting with "#" ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#5008](https://github.com/GMOD/jbrowse-components/pull/5008) Allow parsing non-indexed BED files larger than 512MB ([@cmdcolin](https://github.com/cmdcolin)) - [#4997](https://github.com/GMOD/jbrowse-components/pull/4997) Better message for "quota exceeded" message from localstorage ([@cmdcolin](https://github.com/cmdcolin)) - [#4974](https://github.com/GMOD/jbrowse-components/pull/4974) Minor optimizations in multi-sample variant rendering ([@cmdcolin](https://github.com/cmdcolin)) - [#4973](https://github.com/GMOD/jbrowse-components/pull/4973) Add basic cytoband for Drosophila ([@cmdcolin](https://github.com/cmdcolin)) - [#4970](https://github.com/GMOD/jbrowse-components/pull/4970) Dynamically toggle wheel-scroll normalization to improve touchpad pinch-to-zoom usage ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - [#5013](https://github.com/GMOD/jbrowse-components/pull/5013) Fix UCSC chain parsing which have header lines ([@cmdcolin](https://github.com/cmdcolin)) - [#4993](https://github.com/GMOD/jbrowse-components/pull/4993) Fix re-export of @mui/material/styles, and re-export theme ([@cmdcolin](https://github.com/cmdcolin)) - [#4968](https://github.com/GMOD/jbrowse-components/pull/4968) Fix theme augmentation for primary/secondary colors in v3.3.0 ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#5004](https://github.com/GMOD/jbrowse-components/pull/5004) Fix modifications rendering broken in v3.2.0 ([@cmdcolin](https://github.com/cmdcolin)) - [#4992](https://github.com/GMOD/jbrowse-components/pull/4992) Fix mouseover for some variable width bigwig features ([@cmdcolin](https://github.com/cmdcolin)) - [#4984](https://github.com/GMOD/jbrowse-components/pull/4984) Avoid rendering 'yellow' for low scores in wiggle density renderings with 'log-scale' enabled ([@cmdcolin](https://github.com/cmdcolin)) - [#4969](https://github.com/GMOD/jbrowse-components/pull/4969) Avoid aggregating bigbed features with geneName === 'none' ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#5005](https://github.com/GMOD/jbrowse-components/pull/5005) Updated screenshots in gallery ([@cmdcolin](https://github.com/cmdcolin)) - [#5001](https://github.com/GMOD/jbrowse-components/pull/5001) Improve website docs with grammarly suggestions ([@cmdcolin](https://github.com/cmdcolin)) - [#4982](https://github.com/GMOD/jbrowse-components/pull/4982) Add example of disabling side-scroll/zoom in embedded lgv ([@cmdcolin](https://github.com/cmdcolin)) - [#4977](https://github.com/GMOD/jbrowse-components/pull/4977) Fix `addToExtensionPoint` example in docs ([@garrettjstevens](https://github.com/garrettjstevens)) #### :house: Internal - `core`, `product-core` - [#5011](https://github.com/GMOD/jbrowse-components/pull/5011) Remove some unused functions on the session model ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#5003](https://github.com/GMOD/jbrowse-components/pull/5003) Fix typescript on renderToAbstractCanvas ([@cmdcolin](https://github.com/cmdcolin)) - [#4994](https://github.com/GMOD/jbrowse-components/pull/4994) Refactor some ReExport code ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) Done in 1.68s. ## 3.3.0 (2025-04-18) #### :rocket: Enhancement - `core` - [#4956](https://github.com/GMOD/jbrowse-components/pull/4956) Add simplified display of REF/ALT to help with long strings produced by e.g. Cactus VCF ([@cmdcolin](https://github.com/cmdcolin)) - [#4954](https://github.com/GMOD/jbrowse-components/pull/4954) Add genotype frequency table to variant feature details ([@cmdcolin](https://github.com/cmdcolin)) - [#4952](https://github.com/GMOD/jbrowse-components/pull/4952) Add 'genotype' column to the Variant sample grid ([@cmdcolin](https://github.com/cmdcolin)) - [#4944](https://github.com/GMOD/jbrowse-components/pull/4944) Show ALT allele description on multi-variant mouseover ([@cmdcolin](https://github.com/cmdcolin)) - [#4922](https://github.com/GMOD/jbrowse-components/pull/4922) Add Multi-variant SV display ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#4950](https://github.com/GMOD/jbrowse-components/pull/4950) Add ability to use jexl filters on multi-sample variant displays ([@cmdcolin](https://github.com/cmdcolin)) - [#4934](https://github.com/GMOD/jbrowse-components/pull/4934) Add alpha-transparency to help show overlapping SVs in the Multi-sample variant display ([@cmdcolin](https://github.com/cmdcolin)) - [#4931](https://github.com/GMOD/jbrowse-components/pull/4931) Show target zoom level in tooltip on slider ([@cmdcolin](https://github.com/cmdcolin)) - [#4930](https://github.com/GMOD/jbrowse-components/pull/4930) Upload last release build to https://jbrowse.org/code/jb2/latest ([@cmdcolin](https://github.com/cmdcolin)) - `app-core`, `core`, `embedded-core`, `product-core`, `sv-core`, `web-core` - [#4933](https://github.com/GMOD/jbrowse-components/pull/4933) Upgrade to MUI v6 -> MUI v7 ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#4929](https://github.com/GMOD/jbrowse-components/pull/4929) Fix broken bigbed features when there is gene level aggregation ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#4923](https://github.com/GMOD/jbrowse-components/pull/4923) Fix dark stock theme showing bad colors ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - `core` - [#4949](https://github.com/GMOD/jbrowse-components/pull/4949) Controlling navigation of embedded component - storybook examples ([@cmdcolin](https://github.com/cmdcolin)) - [#4924](https://github.com/GMOD/jbrowse-components/pull/4924) Add config docs for pre-processors with simplified config snapshots ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#4925](https://github.com/GMOD/jbrowse-components/pull/4925) Update docs with phased VCF tutorial ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - [#4926](https://github.com/GMOD/jbrowse-components/pull/4926) Skip running hydration for server side rendering ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.41s. ## 3.2.0 (2025-03-22) #### :rocket: Enhancement - `core` - [#4919](https://github.com/GMOD/jbrowse-components/pull/4919) Add in-app clustering method for multi-wiggle tracks ([@cmdcolin](https://github.com/cmdcolin)) - [#4909](https://github.com/GMOD/jbrowse-components/pull/4909) Add ability to load refNameAliases from chromAliases.bb file ([@cmdcolin](https://github.com/cmdcolin)) - [#4906](https://github.com/GMOD/jbrowse-components/pull/4906) Add in-app clustering method for genotype matrix ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#4914](https://github.com/GMOD/jbrowse-components/pull/4914) Allow looking up header column by name for RefNameAliases ([@cmdcolin](https://github.com/cmdcolin)) - [#4910](https://github.com/GMOD/jbrowse-components/pull/4910) Allow refNameColumn in RefNameAliasAdapter to override the default displayed refnames ([@cmdcolin](https://github.com/cmdcolin)) - [#4907](https://github.com/GMOD/jbrowse-components/pull/4907) Simplified snapshot API for initial navigation of LGV ([@cmdcolin](https://github.com/cmdcolin)) - `app-core`, `core`, `product-core`, `web-core` - [#4899](https://github.com/GMOD/jbrowse-components/pull/4899) Add aborting to multi-variant rendering, multi-wiggle rendering ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - [#4920](https://github.com/GMOD/jbrowse-components/pull/4920) Fix issue where multi-level linear synteny view would show a blank tracklist ([@cmdcolin](https://github.com/cmdcolin)) - [#4913](https://github.com/GMOD/jbrowse-components/pull/4913) Fix parent aggregation in BigBed files using larger request window ([@cmdcolin](https://github.com/cmdcolin)) - [#4905](https://github.com/GMOD/jbrowse-components/pull/4905) Fix bug where applying genotype clustering twice produces randomness ([@cmdcolin](https://github.com/cmdcolin)) - [#4897](https://github.com/GMOD/jbrowse-components/pull/4897) Fix clustering for certain sets of bigwig files ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.00s. ## 3.1.0 (2025-03-14) #### :rocket: Enhancement - Other - [#4876](https://github.com/GMOD/jbrowse-components/pull/4876) Allow inferring default values of adapter urls to simplify config.json ([@cmdcolin](https://github.com/cmdcolin)) - [#4875](https://github.com/GMOD/jbrowse-components/pull/4875) Add sample data from HGSVCv3 to 1000 genomes demo and config_demo ([@cmdcolin](https://github.com/cmdcolin)) - [#4880](https://github.com/GMOD/jbrowse-components/pull/4880) Allow selecting track error messages with click and drag ([@cmdcolin](https://github.com/cmdcolin)) - [#4882](https://github.com/GMOD/jbrowse-components/pull/4882) Allow clustering multi-wiggle tracks on the fly ([@cmdcolin](https://github.com/cmdcolin)) - [#4874](https://github.com/GMOD/jbrowse-components/pull/4874) Use a '012' matrix to improve clustering of genotypes ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#4871](https://github.com/GMOD/jbrowse-components/pull/4871) Add deletion, insertion, skip, softclip, hardclip to theme ([@cmdcolin](https://github.com/cmdcolin)) - `app-core`, `core`, `product-core` - [#4237](https://github.com/GMOD/jbrowse-components/pull/4237) Add ability for views to pin elements, such as headers and tracks ([@garrettjstevens](https://github.com/garrettjstevens)) #### :bug: Bug Fix - `core` - [#4867](https://github.com/GMOD/jbrowse-components/pull/4867) Fix web worker usage of lollipop renderer ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#4883](https://github.com/GMOD/jbrowse-components/pull/4883) Bump @gmod/bam for CSI index fix ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) Done in 1.07s. ## 3.0.5 (2025-03-04) #### :bug: Bug Fix - [#4864](https://github.com/GMOD/jbrowse-components/pull/4864) Bump trix to fix bug fetching some search results ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.24s. ## 3.0.4 (2025-03-01) #### :rocket: Enhancement - Other - [#4856](https://github.com/GMOD/jbrowse-components/pull/4856) Add status callback while parsing .delta (MUMmer), .chain (liftover) and PIF files ([@cmdcolin](https://github.com/cmdcolin)) - [#4855](https://github.com/GMOD/jbrowse-components/pull/4855) Handle case insensitive UTR ([@cmdcolin](https://github.com/cmdcolin)) - [#4853](https://github.com/GMOD/jbrowse-components/pull/4853) Split VCF adapter ([@cmdcolin](https://github.com/cmdcolin)) - [#4848](https://github.com/GMOD/jbrowse-components/pull/4848) Allow clicking feature even if there is a slight mouse drag ([@cmdcolin](https://github.com/cmdcolin)) - [#4847](https://github.com/GMOD/jbrowse-components/pull/4847) Add mouseover color and resize handle to variant matrix view ([@cmdcolin](https://github.com/cmdcolin)) - [#4846](https://github.com/GMOD/jbrowse-components/pull/4846) Increase color clarity in the multi-variant viewer ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#4854](https://github.com/GMOD/jbrowse-components/pull/4854) Add status callback for parsing PAF, BLAST tabular, MashMap files ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - [#4862](https://github.com/GMOD/jbrowse-components/pull/4862) Fix name indexing failure on jbrowse desktop ([@cmdcolin](https://github.com/cmdcolin)) - [#4851](https://github.com/GMOD/jbrowse-components/pull/4851) Fix NCBI sequence aliases refNameAliases adapter for some sequence_report.tsv files ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#4849](https://github.com/GMOD/jbrowse-components/pull/4849) Fix height of Hi-C track, and add adjust-to-height ([@cmdcolin](https://github.com/cmdcolin)) - [#4845](https://github.com/GMOD/jbrowse-components/pull/4845) Fix retrieval of VCF metadata for tooltips in VCF feature details ([@cmdcolin](https://github.com/cmdcolin)) - [#4842](https://github.com/GMOD/jbrowse-components/pull/4842) Fix occasional 1px gap in sequence track ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - [#4843](https://github.com/GMOD/jbrowse-components/pull/4843) Remove usage of some deprecated APIs ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.14s. Done in 0.44s. ## 3.0.2 (2025-02-13) #### :rocket: Enhancement - `core` - [#4834](https://github.com/GMOD/jbrowse-components/pull/4834) Update ReExports for @jbrowse/core/BaseFeatureDetails ([@cmdcolin](https://github.com/cmdcolin)) - [#4818](https://github.com/GMOD/jbrowse-components/pull/4818) Improve status updating for BamAdapter, CramAdapter ([@cmdcolin](https://github.com/cmdcolin)) - [#4811](https://github.com/GMOD/jbrowse-components/pull/4811) Improvements to the sesson/config warning dialogs ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#4829](https://github.com/GMOD/jbrowse-components/pull/4829) Less gappyness at SVG features block boundaries ([@cmdcolin](https://github.com/cmdcolin)) - [#4828](https://github.com/GMOD/jbrowse-components/pull/4828) Additional ?hubURL compat ([@cmdcolin](https://github.com/cmdcolin)) - [#4827](https://github.com/GMOD/jbrowse-components/pull/4827) Improve status updating for BedTabixAdapter, Gff3TabixAdapter, VcfTabixAdapter, BigBedAdapter ([@cmdcolin](https://github.com/cmdcolin)) - [#4825](https://github.com/GMOD/jbrowse-components/pull/4825) Handle multiple jobs with the same name ([@garrettjstevens](https://github.com/garrettjstevens)) - [#4826](https://github.com/GMOD/jbrowse-components/pull/4826) Calculate most frequent non-ref allele for multi-variant renderer ([@cmdcolin](https://github.com/cmdcolin)) - [#4824](https://github.com/GMOD/jbrowse-components/pull/4824) Aggregate transcript level features in GTF based on "gene_name" field ([@cmdcolin](https://github.com/cmdcolin)) - [#4810](https://github.com/GMOD/jbrowse-components/pull/4810) Ensure embedded users get the latest semver @gmod/vcf for multi-variant fixes ([@cmdcolin](https://github.com/cmdcolin)) - `app-core`, `core` - [#4819](https://github.com/GMOD/jbrowse-components/pull/4819) Use assembly "displayName" field on View titles ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `sv-core` - [#4837](https://github.com/GMOD/jbrowse-components/pull/4837) Update @gmod/cram for fixed decoding of some CRAM files ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#4808](https://github.com/GMOD/jbrowse-components/pull/4808) Fix random palette color generation for multi-variant colors ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#4838](https://github.com/GMOD/jbrowse-components/pull/4838) 2024 year in review blog post ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - [#4835](https://github.com/GMOD/jbrowse-components/pull/4835) Move plugin devtools to it's own repo ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) Done in 1.91s. Done in 0.69s. ## 3.0.0 (2025-01-29) #### :boom: Breaking Change - `core` - [#4716](https://github.com/GMOD/jbrowse-components/pull/4716) Update to generic-filehandle2 ([@cmdcolin](https://github.com/cmdcolin)) - `__mocks__`, `app-core`, `core`, `embedded-core`, `product-core`, `sv-core` - [#4702](https://github.com/GMOD/jbrowse-components/pull/4702) Update to react 19 ([@cmdcolin](https://github.com/cmdcolin)) #### :rocket: Enhancement - Other - [#4789](https://github.com/GMOD/jbrowse-components/pull/4789) Allow user to edit region size as 'Custom zoom' ([@cmdcolin](https://github.com/cmdcolin)) - [#4796](https://github.com/GMOD/jbrowse-components/pull/4796) Make any bigType track open as BigBedAdapter in ucsc connections ([@cmdcolin](https://github.com/cmdcolin)) - [#4788](https://github.com/GMOD/jbrowse-components/pull/4788) Allow supplying a tsv of sample metadata with VCF for multi-variant views ([@cmdcolin](https://github.com/cmdcolin)) - [#4782](https://github.com/GMOD/jbrowse-components/pull/4782) Add track filetype guesser for BedGraph ([@cmdcolin](https://github.com/cmdcolin)) - [#4774](https://github.com/GMOD/jbrowse-components/pull/4774) Restore concept of linking synteny views ([@cmdcolin](https://github.com/cmdcolin)) - [#4770](https://github.com/GMOD/jbrowse-components/pull/4770) Add turbo-zoom buttons ([@cmdcolin](https://github.com/cmdcolin)) - [#4756](https://github.com/GMOD/jbrowse-components/pull/4756) Improved mouseover on alignment squiggles in breakpoint split view ([@cmdcolin](https://github.com/cmdcolin)) - [#4736](https://github.com/GMOD/jbrowse-components/pull/4736) Bulk delete session tracks ([@cmdcolin](https://github.com/cmdcolin)) - [#4733](https://github.com/GMOD/jbrowse-components/pull/4733) Add option to 'Hide small indels (less than 10bp)' ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `web-core` - [#4799](https://github.com/GMOD/jbrowse-components/pull/4799) Add genotype to multi-variant mouseover ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `product-core` - [#4798](https://github.com/GMOD/jbrowse-components/pull/4798) Add more track metadata to UCSC assembly hub loading ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#4795](https://github.com/GMOD/jbrowse-components/pull/4795) Improved rendering of phased VCF and polyploid VCF in multi-variant view ([@cmdcolin](https://github.com/cmdcolin)) - [#4792](https://github.com/GMOD/jbrowse-components/pull/4792) Allow uploading a sampleTsv file with per-sample metadata for VCF files ([@cmdcolin](https://github.com/cmdcolin)) - [#4786](https://github.com/GMOD/jbrowse-components/pull/4786) Allow opening "synteny tracks" from the default Add track workflow ([@cmdcolin](https://github.com/cmdcolin)) - [#4785](https://github.com/GMOD/jbrowse-components/pull/4785) Allow opening BedGraph et al in the default Add track workflow ([@cmdcolin](https://github.com/cmdcolin)) - [#4784](https://github.com/GMOD/jbrowse-components/pull/4784) Improve UI for choosing query and target assemblies in the "New track" workflow for synteny tracks ([@cmdcolin](https://github.com/cmdcolin)) - [#4767](https://github.com/GMOD/jbrowse-components/pull/4767) Improve load time when multiple tracks use same data file ([@cmdcolin](https://github.com/cmdcolin)) - [#4750](https://github.com/GMOD/jbrowse-components/pull/4750) Add some more lazy loading for smaller bundle size ([@cmdcolin](https://github.com/cmdcolin)) - `sv-core` - [#4753](https://github.com/GMOD/jbrowse-components/pull/4753) Allow launching a single level breakpoint split view focused on the breakends ([@cmdcolin](https://github.com/cmdcolin)) - `web-core` - [#4745](https://github.com/GMOD/jbrowse-components/pull/4745) Add ability to load a ?hubURL= from URL bar ([@cmdcolin](https://github.com/cmdcolin)) - `app-core`, `core` - [#4729](https://github.com/GMOD/jbrowse-components/pull/4729) Update cram-js to avoid requesting file size for more CORS compatibility ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#4778](https://github.com/GMOD/jbrowse-components/pull/4778) Fix GC content calculation consistency across blocks ([@cmdcolin](https://github.com/cmdcolin)) - [#4773](https://github.com/GMOD/jbrowse-components/pull/4773) Fix "Color by CDS" for BED12 features ([@cmdcolin](https://github.com/cmdcolin)) - [#4771](https://github.com/GMOD/jbrowse-components/pull/4771) Fix generating categories for composite tracks in UCSC hubs ([@cmdcolin](https://github.com/cmdcolin)) - [#4769](https://github.com/GMOD/jbrowse-components/pull/4769) Fix facet filter crash ([@cmdcolin](https://github.com/cmdcolin)) - [#4765](https://github.com/GMOD/jbrowse-components/pull/4765) Fix repeat masker track BED interpretation ([@cmdcolin](https://github.com/cmdcolin)) - [#4764](https://github.com/GMOD/jbrowse-components/pull/4764) Fix modifications coverage calculations ([@cmdcolin](https://github.com/cmdcolin)) - [#4731](https://github.com/GMOD/jbrowse-components/pull/4731) Fix naming of subtracks produced by "group by tag" operation ([@cmdcolin](https://github.com/cmdcolin)) - [#4732](https://github.com/GMOD/jbrowse-components/pull/4732) Fix persisting alignments "color by" and "filter by" settings in snapshots/session shares/page reloads ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#4776](https://github.com/GMOD/jbrowse-components/pull/4776) Fix maximum recursion error in linear synteny view import form ([@cmdcolin](https://github.com/cmdcolin)) - [#4768](https://github.com/GMOD/jbrowse-components/pull/4768) Fix navigation via CIGAR string alignment in synteny view ([@cmdcolin](https://github.com/cmdcolin)) - [#4766](https://github.com/GMOD/jbrowse-components/pull/4766) Fix some bed12 transcripts displaying as bedMethyl features ([@cmdcolin](https://github.com/cmdcolin)) - [#4727](https://github.com/GMOD/jbrowse-components/pull/4727) Fix type confusion where sequence feature details crashes for empty subfeatures ([@cmdcolin](https://github.com/cmdcolin)) - [#4725](https://github.com/GMOD/jbrowse-components/pull/4725) Avoid error on closing draggable dialog and a couple more refactors ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - [#4791](https://github.com/GMOD/jbrowse-components/pull/4791) Fix storybook vcf failing to load in dev server ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Kim Rutherford ([@kimrutherford](https://github.com/kimrutherford)) Done in 2.19s. ## 2.18.0 (2024-12-10) #### :rocket: Enhancement - `core`, `product-core`, `sv-core` - [#4511](https://github.com/GMOD/jbrowse-components/pull/4511) Add 'matrix' display for multi-sample VCFs ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#4692](https://github.com/GMOD/jbrowse-components/pull/4692) Rename some session options on desktop "File" menu ([@cmdcolin](https://github.com/cmdcolin)) - [#4703](https://github.com/GMOD/jbrowse-components/pull/4703) Add mobx transaction to multi-level synteny zoom ([@cmdcolin](https://github.com/cmdcolin)) - [#4696](https://github.com/GMOD/jbrowse-components/pull/4696) BED optimizations for GWAS type data ([@cmdcolin](https://github.com/cmdcolin)) - [#4693](https://github.com/GMOD/jbrowse-components/pull/4693) Add mate.name to LGVSyntenyDisplay feature mouseovers ([@cmdcolin](https://github.com/cmdcolin)) - [#4694](https://github.com/GMOD/jbrowse-components/pull/4694) Allow opening bedpe files from users tracks in SV inspector ([@cmdcolin](https://github.com/cmdcolin)) - [#4672](https://github.com/GMOD/jbrowse-components/pull/4672) Add BedGraphAdapter and BedGraphTabixAdapter ([@cmdcolin](https://github.com/cmdcolin)) - `app-core`, `core`, `product-core`, `web-core` - [#4074](https://github.com/GMOD/jbrowse-components/pull/4074) Autosave sessions in jbrowse-web IndexedDB database to make it easier to access old sessions ([@cmdcolin](https://github.com/cmdcolin)) - `app-core`, `core`, `embedded-core`, `product-core`, `sv-core`, `text-indexing`, `web-core` - [#4682](https://github.com/GMOD/jbrowse-components/pull/4682) SV inspector improvements (x-data-grid, opening track data, re-navigate breakpoint split view, support INV/DEL/more) ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `product-core` - [#4178](https://github.com/GMOD/jbrowse-components/pull/4178) Add ability to use colorBy and filterBy for alignments track configs, and group by strand ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `product-core`, `text-indexing` - [#4663](https://github.com/GMOD/jbrowse-components/pull/4663) Replace AbortSignal with "stop token" to rescue some aborting behavior ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - [#4708](https://github.com/GMOD/jbrowse-components/pull/4708) Avoid full length sequence fetch on SNP coverage calculation ([@cmdcolin](https://github.com/cmdcolin)) - [#4676](https://github.com/GMOD/jbrowse-components/pull/4676) Fix MCScanAnchorsAdapter rendering in linear genome view ([@cmdcolin](https://github.com/cmdcolin)) - [#4670](https://github.com/GMOD/jbrowse-components/pull/4670) Fix GC-content track regression in v2.17.0 ([@cmdcolin](https://github.com/cmdcolin)) - [#4667](https://github.com/GMOD/jbrowse-components/pull/4667) Reduce self-pairing for some paired-end read data in breakpoint split view ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `__mocks__`, `app-core`, `core`, `embedded-core`, `product-core`, `sv-core`, `text-indexing`, `web-core` - [#4680](https://github.com/GMOD/jbrowse-components/pull/4680) Add eslint-plugin-import for sort ordering ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#4675](https://github.com/GMOD/jbrowse-components/pull/4675) Add fix for potential hydration mismatch errors ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.52s. ## 2.17.0 (2024-11-18) #### :rocket: Enhancement - `core` - [#4662](https://github.com/GMOD/jbrowse-components/pull/4662) Add better handling for bedMethyl files ([@cmdcolin](https://github.com/cmdcolin)) - [#4652](https://github.com/GMOD/jbrowse-components/pull/4652) Reduce re-rendering on quantitative and snpcoverage track height adjustments ([@cmdcolin](https://github.com/cmdcolin)) - [#4651](https://github.com/GMOD/jbrowse-components/pull/4651) Add mismatches cache to improve performance on ultra-long reads ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#4649](https://github.com/GMOD/jbrowse-components/pull/4649) Add support for displaying SNPs in "no_ref" CRAM files ([@cmdcolin](https://github.com/cmdcolin)) - [#4627](https://github.com/GMOD/jbrowse-components/pull/4627) Create BLAST tabular adapter ([@garrettjstevens](https://github.com/garrettjstevens)) #### :bug: Bug Fix - Other - [#4647](https://github.com/GMOD/jbrowse-components/pull/4647) Improved rendering of modifications ([@cmdcolin](https://github.com/cmdcolin)) - [#4646](https://github.com/GMOD/jbrowse-components/pull/4646) Fix mouseover pixelation on linear synteny view ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#4639](https://github.com/GMOD/jbrowse-components/pull/4639) Fix RNA-seq stranded arc coloring, change the color of RNA-seq introns, and improve compact rendering ([@cmdcolin](https://github.com/cmdcolin)) - [#4638](https://github.com/GMOD/jbrowse-components/pull/4638) Fix rendering of UCSC repeatmasker BigBed and BED files ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - [#4648](https://github.com/GMOD/jbrowse-components/pull/4648) Run codemod fix for some MUI deprecated props ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) Done in 1.81s. ## 2.16.1 (2024-11-03) #### :rocket: Enhancement - `app-core`, `core`, `product-core`, `text-indexing` - [#4624](https://github.com/GMOD/jbrowse-components/pull/4624) Add utility links to synteny feature details to allow centering a view on a feature ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#4628](https://github.com/GMOD/jbrowse-components/pull/4628) Allow configuring Hi-C normalization and default resolution multiplier ([@cmdcolin](https://github.com/cmdcolin)) - [#4619](https://github.com/GMOD/jbrowse-components/pull/4619) Add resolutionMultiplier config slot to BigWigAdapter ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - [#4634](https://github.com/GMOD/jbrowse-components/pull/4634) Fix opening local files in the multi-wiggle add track selector ([@cmdcolin](https://github.com/cmdcolin)) - [#4633](https://github.com/GMOD/jbrowse-components/pull/4633) Fix "Add track" select box not going away after selecting element ([@cmdcolin](https://github.com/cmdcolin)) - [#4632](https://github.com/GMOD/jbrowse-components/pull/4632) Standardize modification colors between alignments track coverage and pileup subtracks ([@cmdcolin](https://github.com/cmdcolin)) - [#4631](https://github.com/GMOD/jbrowse-components/pull/4631) Fix config description of assembly name ordering for synteny data adapters ([@cmdcolin](https://github.com/cmdcolin)) - [#4630](https://github.com/GMOD/jbrowse-components/pull/4630) Fix MM tag modifications from particular BAM file failing to render on the negative strand ([@cmdcolin](https://github.com/cmdcolin)) - [#4626](https://github.com/GMOD/jbrowse-components/pull/4626) Fix dark redraw on selected features after vertical resize of the synteny canvas ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.20s. ## 2.16.0 (2024-10-23) #### :rocket: Enhancement - Other - [#4615](https://github.com/GMOD/jbrowse-components/pull/4615) Add configuration of transcriptTypes and containerTypes to the svg feature rendering ([@cmdcolin](https://github.com/cmdcolin)) - `app-core`, `core` - [#4430](https://github.com/GMOD/jbrowse-components/pull/4430) Multi-level synteny rendering ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#4593](https://github.com/GMOD/jbrowse-components/pull/4593) Fix navigating to a refname result that is also indexed in search track index ([@cmdcolin](https://github.com/cmdcolin)) - [#4612](https://github.com/GMOD/jbrowse-components/pull/4612) Fix error with tooltips in embedded components in vite dev mode ([@cmdcolin](https://github.com/cmdcolin)) - [#4602](https://github.com/GMOD/jbrowse-components/pull/4602) Fix decoding of CRAM ML tag ([@cmdcolin](https://github.com/cmdcolin)) - [#4594](https://github.com/GMOD/jbrowse-components/pull/4594) Fix highlight button causing issues clicking underlying track features ([@cmdcolin](https://github.com/cmdcolin)) - [#4586](https://github.com/GMOD/jbrowse-components/pull/4586) Update electron-builder to fix broken desktop builds ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#4600](https://github.com/GMOD/jbrowse-components/pull/4600) Fix check for "hasSubSubfeatures" in svg feature rendering ([@cmdcolin](https://github.com/cmdcolin)) - [#4590](https://github.com/GMOD/jbrowse-components/pull/4590) Fix opening .jbrowse files on desktop ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#4607](https://github.com/GMOD/jbrowse-components/pull/4607) Add tiberius sample dataset and updated gencode and ncbi GFF gene sets ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - Other - [#4607](https://github.com/GMOD/jbrowse-components/pull/4607) Add tiberius sample dataset and updated gencode and ncbi GFF gene sets ([@cmdcolin](https://github.com/cmdcolin)) - `app-core`, `core`, `embedded-core`, `product-core`, `web-core` - [#4606](https://github.com/GMOD/jbrowse-components/pull/4606) Remove react-error-boundary ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.02s. ## 2.15.4 (2024-09-20) #### :bug: Bug Fix - Other - [#4582](https://github.com/GMOD/jbrowse-components/pull/4582) Fix text indexing on Windows ([@cmdcolin](https://github.com/cmdcolin)) - `text-indexing` - [#4580](https://github.com/GMOD/jbrowse-components/pull/4580) Fix indexing plaintext gff/vcf on desktop ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.22s. Done in 0.57s. ## 2.15.2 (2024-09-18) #### :rocket: Enhancement - [#4573](https://github.com/GMOD/jbrowse-components/pull/4573) Add pif.gz option to synteny import form ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - [#4571](https://github.com/GMOD/jbrowse-components/pull/4571) Fix code signing on the windows for jbrowse desktop ([@cmdcolin](https://github.com/cmdcolin)) - [#4566](https://github.com/GMOD/jbrowse-components/pull/4566) Fix handling of "." in VCF ALT field ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - [#4569](https://github.com/GMOD/jbrowse-components/pull/4569) Refactor GFF3 parser to avoid returning internal \_linehash variable ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.30s. ## 2.15.1 (2024-09-12) #### :rocket: Enhancement - `core`, `sv-core` - [#4561](https://github.com/GMOD/jbrowse-components/pull/4561) Create notion of launching a single-row breakpoint split view ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#4556](https://github.com/GMOD/jbrowse-components/pull/4556) Add dropdown menu from bookmark label clicks ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#4554](https://github.com/GMOD/jbrowse-components/pull/4554) Fix the ability to sort menu items by priority for CascadingMenu ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#4560](https://github.com/GMOD/jbrowse-components/pull/4560) Fix coloring on circular chord renderings ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#4553](https://github.com/GMOD/jbrowse-components/pull/4553) Fix performance regression since v2.14.0 in assembly loading ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - [#4548](https://github.com/GMOD/jbrowse-components/pull/4548) Create BaseTooltip component in @jbrowse/core/ui ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#4547](https://github.com/GMOD/jbrowse-components/pull/4547) Avoid stream polyfill for GFF3/GTF parsing ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.16s. Done in 1.26s. ## 2.14.0 (2024-08-28) #### :rocket: Enhancement - `core` - [#4532](https://github.com/GMOD/jbrowse-components/pull/4532) De-duplicate snackbar messages ([@cmdcolin](https://github.com/cmdcolin)) - [#4516](https://github.com/GMOD/jbrowse-components/pull/4516) Add NCBI sequence_report.tsv alias adapter, with ability to recode NCBI fasta files to use UCSC style names ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#4533](https://github.com/GMOD/jbrowse-components/pull/4533) Allow setting sequenceType='pep' in ReferenceSequenceTrack configuration ([@cmdcolin](https://github.com/cmdcolin)) - [#4531](https://github.com/GMOD/jbrowse-components/pull/4531) Add UnindexedFastaAdapter for fetching small plaintext FASTA files ([@cmdcolin](https://github.com/cmdcolin)) - [#4528](https://github.com/GMOD/jbrowse-components/pull/4528) Add description config slot to reference sequence track ([@cmdcolin](https://github.com/cmdcolin)) - `app-core`, `core` - [#4523](https://github.com/GMOD/jbrowse-components/pull/4523) Allow plaintext GTF and VCF files greater than 512Mb ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `product-core` - [#4519](https://github.com/GMOD/jbrowse-components/pull/4519) Add "Group by" method for alignments tracks ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - [#4535](https://github.com/GMOD/jbrowse-components/pull/4535) Fix crash after navToLocString in some cases ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - Other - [#4530](https://github.com/GMOD/jbrowse-components/pull/4530) Consolidate gff3 adapter featureData routine, avoid Number-ifying null phase ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#4518](https://github.com/GMOD/jbrowse-components/pull/4518) Don't send displayModel to "rendering" components on server side ([@cmdcolin](https://github.com/cmdcolin)) - `__mocks__`, `app-core`, `core`, `embedded-core`, `product-core`, `text-indexing`, `web-core` - [#4513](https://github.com/GMOD/jbrowse-components/pull/4513) Add new eslint rules (no-unnecessary-condition, no-unused-expressions, etc) and tsconfig noUncheckedIndexedAccess ([@cmdcolin](https://github.com/cmdcolin)) - `app-core`, `core`, `embedded-core`, `product-core`, `text-indexing`, `web-core` - [#4510](https://github.com/GMOD/jbrowse-components/pull/4510) Add biome lint fixes ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `product-core`, `text-indexing` - [#4508](https://github.com/GMOD/jbrowse-components/pull/4508) Use @mui/x-charts-vendor for d3 upgrade ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) Done in 1.30s. ## 2.13.1 (2024-07-31) #### :rocket: Enhancement - [#4497](https://github.com/GMOD/jbrowse-components/pull/4497) Add ability to toggle "Show track outlines" ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - [#4501](https://github.com/GMOD/jbrowse-components/pull/4501) Fix opening track selector in linear synteny view causing crash in v2.13.0 ([@cmdcolin](https://github.com/cmdcolin)) - [#4495](https://github.com/GMOD/jbrowse-components/pull/4495) Fix log scale for some types of signal tracks ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.30s. ## 2.13.0 (2024-07-25) #### :rocket: Enhancement - [#4494](https://github.com/GMOD/jbrowse-components/pull/4494) Add assembly name to scalebar in synteny views ([@cmdcolin](https://github.com/cmdcolin)) - [#4480](https://github.com/GMOD/jbrowse-components/pull/4480) Changes default height for SVG rendering to maxHeight to fix blank track effect on slow CPU ([@carolinebridge](https://github.com/carolinebridge)) - [#4478](https://github.com/GMOD/jbrowse-components/pull/4478) Add ability to use CSI indexes in @jbrowse/img ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - [#4483](https://github.com/GMOD/jbrowse-components/pull/4483) Fix configuration settings for track sorting in the track selector ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#4476](https://github.com/GMOD/jbrowse-components/pull/4476) Fix config editor crash in vite usage of embedded components in dev mode ([@cmdcolin](https://github.com/cmdcolin)) - [#4473](https://github.com/GMOD/jbrowse-components/pull/4473) Fix 'Show no tracks active button' checkbox not working ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - `core` - [#4481](https://github.com/GMOD/jbrowse-components/pull/4481) Add SARS-CoV2 demo to test_data ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#4487](https://github.com/GMOD/jbrowse-components/pull/4487) Update faq.md with compression explanation ([@Maarten-vd-Sande](https://github.com/Maarten-vd-Sande)) #### :house: Internal - `core` - [#4493](https://github.com/GMOD/jbrowse-components/pull/4493) Remove prop-types from re-exports ([@cmdcolin](https://github.com/cmdcolin)) - [#4492](https://github.com/GMOD/jbrowse-components/pull/4492) Change abortable-promise-cache to @gmod/abortable-promise-cache ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#4488](https://github.com/GMOD/jbrowse-components/pull/4488) Fix autogen docs build ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 - Caroline Bridge ([@carolinebridge](https://github.com/carolinebridge)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - [@Maarten-vd-Sande](https://github.com/Maarten-vd-Sande) Done in 1.66s. ## 2.12.3 (2024-06-27) #### :rocket: Enhancement - [#4465](https://github.com/GMOD/jbrowse-components/pull/4465) Add `contig` to the default dontRedispatch list for Gff3TabixAdapter ([@cmdcolin](https://github.com/cmdcolin)) - [#4464](https://github.com/GMOD/jbrowse-components/pull/4464) Bump generic-filehandle to put URL in error messages ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - [#4469](https://github.com/GMOD/jbrowse-components/pull/4469) Fix error launching session on desktop in v2.12.2 ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#4466](https://github.com/GMOD/jbrowse-components/pull/4466) Add demo of using farm-fe bundler for embedded components ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.30s. Done in 0.74s. Done in 0.81s. ## 2.12.0 (2024-06-20) #### :rocket: Enhancement - Other - [#4459](https://github.com/GMOD/jbrowse-components/pull/4459) Allow using keyboard shortcut for devtools in production desktop builds ([@cmdcolin](https://github.com/cmdcolin)) - [#4455](https://github.com/GMOD/jbrowse-components/pull/4455) Add slot.type to configuration editor elements ([@cmdcolin](https://github.com/cmdcolin)) - [#4427](https://github.com/GMOD/jbrowse-components/pull/4427) Add ctrl+wheel scroll to zoom both top and bottom of synteny view ([@cmdcolin](https://github.com/cmdcolin)) - [#4425](https://github.com/GMOD/jbrowse-components/pull/4425) Add ability to dismiss dotplot warnings ([@cmdcolin](https://github.com/cmdcolin)) - [#4422](https://github.com/GMOD/jbrowse-components/pull/4422) Make initial linear synteny view import form submit show all regions by default ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#4456](https://github.com/GMOD/jbrowse-components/pull/4456) Add aggregation to BigBedAdapter to group bigGenePred transcripts ([@cmdcolin](https://github.com/cmdcolin)) - [#4448](https://github.com/GMOD/jbrowse-components/pull/4448) Adds genomic coordinates back into the sequence panel accounting for strand direction ([@carolinebridge](https://github.com/carolinebridge)) - [#4423](https://github.com/GMOD/jbrowse-components/pull/4423) Speed up large displayedRegions sets by converting MST array of Region[] into a types.frozen ([@cmdcolin](https://github.com/cmdcolin)) - [#4399](https://github.com/GMOD/jbrowse-components/pull/4399) Allow viewing coordinates in sequence feature display panel ([@cmdcolin](https://github.com/cmdcolin)) - `app-core` - [#4443](https://github.com/GMOD/jbrowse-components/pull/4443) Allow drawer widget to be "popped out" into a dialog box ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `product-core` - [#3992](https://github.com/GMOD/jbrowse-components/pull/3992) Add ability to get refNames for a track in the "About track" panel ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#4458](https://github.com/GMOD/jbrowse-components/pull/4458) Fix sandbox error on AppImage startup on certain linux systems ([@cmdcolin](https://github.com/cmdcolin)) - [#4441](https://github.com/GMOD/jbrowse-components/pull/4441) Fix sorting data grid on multi-wiggle 'Edit colors/arrangement' dialog ([@cmdcolin](https://github.com/cmdcolin)) - [#4439](https://github.com/GMOD/jbrowse-components/pull/4439) Fix blank lines in multi-wiggle add track workflow causing crash ([@cmdcolin](https://github.com/cmdcolin)) - [#4438](https://github.com/GMOD/jbrowse-components/pull/4438) Fix cursor:pointer style on an alignments feature detail clickable link ([@cmdcolin](https://github.com/cmdcolin)) - [#4436](https://github.com/GMOD/jbrowse-components/pull/4436) Fix "Open synteny view at this position" when file contains CIGAR X/= operators ([@cmdcolin](https://github.com/cmdcolin)) - [#4426](https://github.com/GMOD/jbrowse-components/pull/4426) Fix side scroll in linear synteny view causing the browser "back" action ([@cmdcolin](https://github.com/cmdcolin)) - [#4417](https://github.com/GMOD/jbrowse-components/pull/4417) Fix error message shown on chromosomes with missing data for plaintext GFF3 ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#4442](https://github.com/GMOD/jbrowse-components/pull/4442) Fix unstable dialog width in "About track" dialog for multi-quantitative tracks ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - [#4445](https://github.com/GMOD/jbrowse-components/pull/4445) Update oclif/test and oclif/core ([@cmdcolin](https://github.com/cmdcolin)) - [#4440](https://github.com/GMOD/jbrowse-components/pull/4440) Use ref instead of deprecated findDOMNode for draggable dialog ([@cmdcolin](https://github.com/cmdcolin)) - [#4429](https://github.com/GMOD/jbrowse-components/pull/4429) Remove normalize-wheel library ([@cmdcolin](https://github.com/cmdcolin)) - [#4400](https://github.com/GMOD/jbrowse-components/pull/4400) Remove node-polyfill-webpack-plugin ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 - Caroline Bridge ([@carolinebridge](https://github.com/carolinebridge)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.71s. ## 2.11.2 (2024-06-03) #### :rocket: Enhancement - Other - [#4406](https://github.com/GMOD/jbrowse-components/pull/4406) Allow loading plaintext GFF3 files larger than 512Mb ([@cmdcolin](https://github.com/cmdcolin)) - [#4398](https://github.com/GMOD/jbrowse-components/pull/4398) Adds a context menu option to zoom to a feature ([@carolinebridge](https://github.com/carolinebridge)) - `core` - [#4405](https://github.com/GMOD/jbrowse-components/pull/4405) Include a raw version of function names in error message stack traces ([@cmdcolin](https://github.com/cmdcolin)) - [#4393](https://github.com/GMOD/jbrowse-components/pull/4393) Allow users to configure filters and set them at runtime via a editable dialog ([@cmdcolin](https://github.com/cmdcolin)) - [#4395](https://github.com/GMOD/jbrowse-components/pull/4395) Remove x-data-grid resize bar workaround ([@cmdcolin](https://github.com/cmdcolin)) - [#4389](https://github.com/GMOD/jbrowse-components/pull/4389) Improve return type of `intersection2` ([@garrettjstevens](https://github.com/garrettjstevens)) #### :bug: Bug Fix - [#4407](https://github.com/GMOD/jbrowse-components/pull/4407) Fix custom theme being applied in renderings in desktop ([@cmdcolin](https://github.com/cmdcolin)) - [#4402](https://github.com/GMOD/jbrowse-components/pull/4402) Fix for rendering of softclipping when there are insertions in the sequence ([@cmdcolin](https://github.com/cmdcolin)) - [#4385](https://github.com/GMOD/jbrowse-components/pull/4385) Fix ability to choose line plot bigwig coloring ([@cmdcolin](https://github.com/cmdcolin)) - [#4386](https://github.com/GMOD/jbrowse-components/pull/4386) Fix ability to add custom frame colors ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 3 - Caroline Bridge ([@carolinebridge](https://github.com/carolinebridge)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) Done in 1.23s. ## 2.11.1 (2024-05-11) #### :rocket: Enhancement - `core` - [#4354](https://github.com/GMOD/jbrowse-components/pull/4354) Allow capitalizing CDS sequences and lowercasing introns in sequence feature panel ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#4351](https://github.com/GMOD/jbrowse-components/pull/4351) Store and retrieve user track selector settings in local storage ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - [#4381](https://github.com/GMOD/jbrowse-components/pull/4381) Replace all rgba(...) color strings with rgb(...) in SVG exports to fix usage in illustrator/inkscape ([@cmdcolin](https://github.com/cmdcolin)) - [#4364](https://github.com/GMOD/jbrowse-components/pull/4364) Fix tooltips creating a scrollbar when overflowing off the screen in Chrome ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#4366](https://github.com/GMOD/jbrowse-components/pull/4366) Fix for regex sequence search on reverse strand features ([@cmdcolin](https://github.com/cmdcolin)) - [#4362](https://github.com/GMOD/jbrowse-components/pull/4362) Auto-detect file format better when importing BED or TSV bookmarks ([@cmdcolin](https://github.com/cmdcolin)) - [#4357](https://github.com/GMOD/jbrowse-components/pull/4357) Fix bookmark showing up on wrong assembly/crashing ([@cmdcolin](https://github.com/cmdcolin)) - [#4353](https://github.com/GMOD/jbrowse-components/pull/4353) Remove snap package ([@cmdcolin](https://github.com/cmdcolin)) - `app-core` - [#4350](https://github.com/GMOD/jbrowse-components/pull/4350) Fix Fab positioning on @jbrowse/react-app ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.13s. ## 2.11.0 (2024-04-16) #### :rocket: Enhancement - `core` - [#4341](https://github.com/GMOD/jbrowse-components/pull/4341) Improve error dialog stack trace display and fix usage on https sites ([@cmdcolin](https://github.com/cmdcolin)) - [#4340](https://github.com/GMOD/jbrowse-components/pull/4340) Change email on error message dialog ([@cmdcolin](https://github.com/cmdcolin)) - [#4288](https://github.com/GMOD/jbrowse-components/pull/4288) Create GCContentTrack type ([@cmdcolin](https://github.com/cmdcolin)) - [#4312](https://github.com/GMOD/jbrowse-components/pull/4312) Update @mui/x-data-grid 6->7 ([@cmdcolin](https://github.com/cmdcolin)) - [#4280](https://github.com/GMOD/jbrowse-components/pull/4280) Add JSON.parse utility to the "jexl function library" ([@cmdcolin](https://github.com/cmdcolin)) - [#4276](https://github.com/GMOD/jbrowse-components/pull/4276) Add retry method to share link dialog in case of error ([@cmdcolin](https://github.com/cmdcolin)) - [#4266](https://github.com/GMOD/jbrowse-components/pull/4266) Add bookmark highlight to overview scale bar ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Other - [#4335](https://github.com/GMOD/jbrowse-components/pull/4335) Add ability to create multiple highlights on the linear genome view ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - [#4287](https://github.com/GMOD/jbrowse-components/pull/4287) Fix snap package and also add deb package ([@cmdcolin](https://github.com/cmdcolin)) - [#4034](https://github.com/GMOD/jbrowse-components/pull/4034) Subtler minicontrols focus ([@cmdcolin](https://github.com/cmdcolin)) - `app-core`, `product-core` - [#4337](https://github.com/GMOD/jbrowse-components/pull/4337) Allow moving tracks and views up/down/to top/to bottom, and better click and drag track re-ordering ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `product-core` - [#4336](https://github.com/GMOD/jbrowse-components/pull/4336) Add new Hi-C color schemes with log scale mode ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `web-core` - [#4284](https://github.com/GMOD/jbrowse-components/pull/4284) Allow getting stack trace error dialog from session.notify errors ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#4318](https://github.com/GMOD/jbrowse-components/pull/4318) Use node-fetch-native to fix warning from JBrowse CLI on node 21+ ([@cmdcolin](https://github.com/cmdcolin)) - [#4319](https://github.com/GMOD/jbrowse-components/pull/4319) Fix Hi-C rendering for some high resolution files ([@cmdcolin](https://github.com/cmdcolin)) - [#4314](https://github.com/GMOD/jbrowse-components/pull/4314) Fix loading of BED12 data from a plaintext BED with column headers ([@cmdcolin](https://github.com/cmdcolin)) - [#4293](https://github.com/GMOD/jbrowse-components/pull/4293) Fix alignment curves showing up in inkscape for breakpoint svg ([@cmdcolin](https://github.com/cmdcolin)) - [#4287](https://github.com/GMOD/jbrowse-components/pull/4287) Fix snap package and also add deb package ([@cmdcolin](https://github.com/cmdcolin)) - [#4277](https://github.com/GMOD/jbrowse-components/pull/4277) Fix usage of --assemblyNames in `jbrowse add-connection` ([@cmdcolin](https://github.com/cmdcolin)) - [#4275](https://github.com/GMOD/jbrowse-components/pull/4275) Fixes bug on URL highlight param in which refName aliases were not working ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - `text-indexing` - [#4269](https://github.com/GMOD/jbrowse-components/pull/4269) Avoid crash on badly encoded GFF attributes ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 - Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) Done in 1.85s. ## 2.10.3 (2024-03-06) #### :rocket: Enhancement - Other - [#4257](https://github.com/GMOD/jbrowse-components/pull/4257) Smaller sequence track size ([@cmdcolin](https://github.com/cmdcolin)) - [#4256](https://github.com/GMOD/jbrowse-components/pull/4256) Update deps including electron 28->29 ([@cmdcolin](https://github.com/cmdcolin)) - [#4234](https://github.com/GMOD/jbrowse-components/pull/4234) Adds URL query param for highlight on LGV ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - `core`, `product-core` - [#4255](https://github.com/GMOD/jbrowse-components/pull/4255) Allow getting stack trace from track errors ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - [#4254](https://github.com/GMOD/jbrowse-components/pull/4254) Throw if no sequenceAdapter supplied to CramAdapter ([@cmdcolin](https://github.com/cmdcolin)) - [#4250](https://github.com/GMOD/jbrowse-components/pull/4250) Fix the viewport calculations for when URL params includes &tracklist=true ([@cmdcolin](https://github.com/cmdcolin)) - [#4232](https://github.com/GMOD/jbrowse-components/pull/4232) Fix for missing INFO.STRANDS tag for TRA features in breakpoint split view ([@cmdcolin](https://github.com/cmdcolin)) - [#4224](https://github.com/GMOD/jbrowse-components/pull/4224) Fix parsing of BAM and CRAM refNames that contain a colon ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#4240](https://github.com/GMOD/jbrowse-components/pull/4240) Small fixes to embedding tutorial docs ([@kwentine](https://github.com/kwentine)) - [#4223](https://github.com/GMOD/jbrowse-components/pull/4223) Add FAQ section about faceted track selector ([@Maarten-vd-Sande](https://github.com/Maarten-vd-Sande)) #### Committers: 5 - Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - Quentin Agren ([@kwentine](https://github.com/kwentine)) - [@Maarten-vd-Sande](https://github.com/Maarten-vd-Sande) Done in 1.56s. ## 2.10.2 (2024-02-19) #### :rocket: Enhancement - Other - [#4219](https://github.com/GMOD/jbrowse-components/pull/4219) Add ability to render only snpcoverage in jbrowse-img ([@cmdcolin](https://github.com/cmdcolin)) - [#4196](https://github.com/GMOD/jbrowse-components/pull/4196) Allow adding &tracklist=true to URL bar to open the track selector, &nav=false to hide linear genome view header ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#4215](https://github.com/GMOD/jbrowse-components/pull/4215) Launch breakpoint split view directly from alignments feature details ([@cmdcolin](https://github.com/cmdcolin)) - [#4184](https://github.com/GMOD/jbrowse-components/pull/4184) Add ability to get stack trace for error messages in the UI ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#4220](https://github.com/GMOD/jbrowse-components/pull/4220) Fix hydration error from translocation features in plaintext VCF adapter ([@cmdcolin](https://github.com/cmdcolin)) - [#4217](https://github.com/GMOD/jbrowse-components/pull/4217) Fix breakpoint split view SVG export occasionally having wrong clipping ([@cmdcolin](https://github.com/cmdcolin)) - [#4213](https://github.com/GMOD/jbrowse-components/pull/4213) Fix issue with tagFilter \* in alignments track ([@cmdcolin](https://github.com/cmdcolin)) - [#4208](https://github.com/GMOD/jbrowse-components/pull/4208) Fix @jbrowse/img under node environment ([@cmdcolin](https://github.com/cmdcolin)) - [#4146](https://github.com/GMOD/jbrowse-components/pull/4146) Remove --tracks and --view options from set-default-session CLI ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#4190](https://github.com/GMOD/jbrowse-components/pull/4190) Remove text selection on sequence track with user-select: none ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `product-core` - [#4177](https://github.com/GMOD/jbrowse-components/pull/4177) Fix session tracks being displayed in the tracklist on @jbrowse/react-linear-genome-view ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#4166](https://github.com/GMOD/jbrowse-components/pull/4166) Year in review blog post ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.42s. ## 2.10.1 (2024-01-09) #### :rocket: Enhancement - `core` - [#4155](https://github.com/GMOD/jbrowse-components/pull/4155) Remove react-svg-tooltip library ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#4152](https://github.com/GMOD/jbrowse-components/pull/4152) Add directional feet to breakends in linear arc display ([@cmdcolin](https://github.com/cmdcolin)) - [#4143](https://github.com/GMOD/jbrowse-components/pull/4143) Add webpack build for @jbrowse/react-app ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#4158](https://github.com/GMOD/jbrowse-components/pull/4158) Fix subfeature refNames on BED and BEDTabix parsers ([@cmdcolin](https://github.com/cmdcolin)) - [#4154](https://github.com/GMOD/jbrowse-components/pull/4154) Fix metadata facet filters being blank ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#4147](https://github.com/GMOD/jbrowse-components/pull/4147) Fix bad svg output in v2.10.0 in cases where feature names have angle brackets ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#4142](https://github.com/GMOD/jbrowse-components/pull/4142) Update 03_assemblies.md ([@dtdoering](https://github.com/dtdoering)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Drew T. Doering ([@dtdoering](https://github.com/dtdoering)) Done in 3.10s. ## 2.10.0 (2023-12-15) #### :rocket: Enhancement - `core` - [#4138](https://github.com/GMOD/jbrowse-components/pull/4138) Speed up large FromConfigAdapter usages with alternative adapter id calculation ([@cmdcolin](https://github.com/cmdcolin)) - [#4114](https://github.com/GMOD/jbrowse-components/pull/4114) Improve pluginManager.jexl typescript definition ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#4135](https://github.com/GMOD/jbrowse-components/pull/4135) Split "recently used tracks" local storage keys by view assemblies ([@cmdcolin](https://github.com/cmdcolin)) - [#4003](https://github.com/GMOD/jbrowse-components/pull/4003) Adds the ability to highlight regions using the bookmarks widget ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - [#4123](https://github.com/GMOD/jbrowse-components/pull/4123) Remove session.notify after using the Add track workflow ([@cmdcolin](https://github.com/cmdcolin)) - [#3859](https://github.com/GMOD/jbrowse-components/pull/3859) Add new pairwise indexed PAF adapter format with CLI creation workflow ([@cmdcolin](https://github.com/cmdcolin)) - [#4109](https://github.com/GMOD/jbrowse-components/pull/4109) Allow right clicking synteny features ([@cmdcolin](https://github.com/cmdcolin)) - [#4110](https://github.com/GMOD/jbrowse-components/pull/4110) Scroll both panels of the linear synteny view when side scrolling the middle panel ([@cmdcolin](https://github.com/cmdcolin)) - [#4108](https://github.com/GMOD/jbrowse-components/pull/4108) Convert to floating-ui for tooltips for small speedup ([@cmdcolin](https://github.com/cmdcolin)) - [#4107](https://github.com/GMOD/jbrowse-components/pull/4107) Refactors and bundle size improvements ([@cmdcolin](https://github.com/cmdcolin)) - `app-core`, `core` - [#4134](https://github.com/GMOD/jbrowse-components/pull/4134) Add ability to click and drag synteny area of synteny view to side scroll ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#4137](https://github.com/GMOD/jbrowse-components/pull/4137) Fix dotplot axis ticks going out of bounds ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#4136](https://github.com/GMOD/jbrowse-components/pull/4136) Fix "Export SVG" feature in next 14 ([@cmdcolin](https://github.com/cmdcolin)) - [#4125](https://github.com/GMOD/jbrowse-components/pull/4125) Fix internet accounts not being shown in file selector after page refresh and hide HTTP basic internet accounts ([@cmdcolin](https://github.com/cmdcolin)) - `app-core`, `embedded-core` - [#4121](https://github.com/GMOD/jbrowse-components/pull/4121) Fix view menu checkboxes not responding in some cases ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - `app-core`, `product-core`, `web-core` - [#4106](https://github.com/GMOD/jbrowse-components/pull/4106) Add links between autogen docs ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - [#4103](https://github.com/GMOD/jbrowse-components/pull/4103) Add mastodon account to website links ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 - Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 2.06s. ## 2.9.0 (2023-11-30) #### :rocket: Enhancement - Other - [#4070](https://github.com/GMOD/jbrowse-components/pull/4070) Add support for single file hubs ([@cmdcolin](https://github.com/cmdcolin)) - [#4096](https://github.com/GMOD/jbrowse-components/pull/4096) Allow searching by gene name using linear synteny view ([@cmdcolin](https://github.com/cmdcolin)) - [#4068](https://github.com/GMOD/jbrowse-components/pull/4068) Allow searching the text-index by gene name from the URL bar ([@cmdcolin](https://github.com/cmdcolin)) - [#3948](https://github.com/GMOD/jbrowse-components/pull/3948) Make the default setting for the dotplot/synteny views use 'Existing tracks' by default ([@cmdcolin](https://github.com/cmdcolin)) - [#4039](https://github.com/GMOD/jbrowse-components/pull/4039) Adds "Favorites" and "Recently used" track categories to the track selector ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - [#4067](https://github.com/GMOD/jbrowse-components/pull/4067) Add arc plugin to @jbrowse/react-linear-genome-view core plugins ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `product-core` - [#4091](https://github.com/GMOD/jbrowse-components/pull/4091) Allow hiding subfeatures in the feature details panel ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - [#4094](https://github.com/GMOD/jbrowse-components/pull/4094) Refactor faceted track selector to use more MST state ([@cmdcolin](https://github.com/cmdcolin)) - [#4086](https://github.com/GMOD/jbrowse-components/pull/4086) Fix issue where --load inPlace and --force can sometimes remove file unexpectedly ([@cmdcolin](https://github.com/cmdcolin)) - [#4059](https://github.com/GMOD/jbrowse-components/pull/4059) Fix missing icons on some cascading menus ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Other - [#4095](https://github.com/GMOD/jbrowse-components/pull/4095) Fix faceted metadata header names colliding with non-metadata header names ([@cmdcolin](https://github.com/cmdcolin)) - [#4071](https://github.com/GMOD/jbrowse-components/pull/4071) Fix Mac auto-updates fetching non-existent zip ([@cmdcolin](https://github.com/cmdcolin)) - [#4062](https://github.com/GMOD/jbrowse-components/pull/4062) Fix duplicate key error in hierarchical track selector from using connections ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 - Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.41s. ## 2.8.0 (2023-11-09) #### :rocket: Enhancement - Other - [#4045](https://github.com/GMOD/jbrowse-components/pull/4045) Create multi-region arc display type for variant tracks ([@cmdcolin](https://github.com/cmdcolin)) - [#4050](https://github.com/GMOD/jbrowse-components/pull/4050) Allow specifying alternative config.json path via global variable ([@cmdcolin](https://github.com/cmdcolin)) - [#4046](https://github.com/GMOD/jbrowse-components/pull/4046) Show last autosave on jbrowse-web start screen ([@cmdcolin](https://github.com/cmdcolin)) - [#4044](https://github.com/GMOD/jbrowse-components/pull/4044) Speed up "multi-region" navigation in search box ([@cmdcolin](https://github.com/cmdcolin)) - [#4032](https://github.com/GMOD/jbrowse-components/pull/4032) Add `jbrowse sort-gff` subcommand ([@cmdcolin](https://github.com/cmdcolin)) - `product-core` - [#4040](https://github.com/GMOD/jbrowse-components/pull/4040) Strip baseUri in 'About track' copy config ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#4035](https://github.com/GMOD/jbrowse-components/pull/4035) Prompt to horizontally flip view when launching linear synteny view on inverted feature ([@cmdcolin](https://github.com/cmdcolin)) - `app-core` - [#4024](https://github.com/GMOD/jbrowse-components/pull/4024) Add right-handed arrow to view title to emphasize the focused view ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) #### :bug: Bug Fix - [#4052](https://github.com/GMOD/jbrowse-components/pull/4052) Fix browser back button behavior in jbrowse-web ([@cmdcolin](https://github.com/cmdcolin)) - [#4043](https://github.com/GMOD/jbrowse-components/pull/4043) Fix crash in "Open session" widget for sessions that have 'track-less views' ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#4027](https://github.com/GMOD/jbrowse-components/pull/4027) Add office hours and community meetings ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 - Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 2.23s. ## 2.7.2 (2023-10-27) #### :rocket: Enhancement - `core` - [#3923](https://github.com/GMOD/jbrowse-components/pull/3923) Proposal: Add "extendWorker" extension point ([@garrettjstevens](https://github.com/garrettjstevens)) - Other - [#4020](https://github.com/GMOD/jbrowse-components/pull/4020) Allow configuring LGV trackLabels setting via config ([@cmdcolin](https://github.com/cmdcolin)) - [#3999](https://github.com/GMOD/jbrowse-components/pull/3999) Example of using customElement + ShadowDOM for @jbrowse/react-linear-genome-view ([@AcaDemIQ](https://github.com/AcaDemIQ)) - [#4015](https://github.com/GMOD/jbrowse-components/pull/4015) Create MacOS universal build of jbrowse-desktop to help M1 macs ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `product-core` - [#4013](https://github.com/GMOD/jbrowse-components/pull/4013) Create concept of global hovered state ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - [#4016](https://github.com/GMOD/jbrowse-components/pull/4016) Fix mouseover tooltip getting stuck after region select popup in dotplot ([@cmdcolin](https://github.com/cmdcolin)) - [#4007](https://github.com/GMOD/jbrowse-components/pull/4007) Update cram-js for bzip2 fix ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - [#4005](https://github.com/GMOD/jbrowse-components/pull/4005) Refactors and typescript improvements for jbrowse-web loader ([@cmdcolin](https://github.com/cmdcolin)) - `app-core`, `core` - [#3994](https://github.com/GMOD/jbrowse-components/pull/3994) Refactors for app-core view container ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 - Alexey Mukhin ([@AcaDemIQ](https://github.com/AcaDemIQ)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) Done in 1.56s. ## 2.7.1 (2023-10-18) #### :rocket: Enhancement - Other - [#3986](https://github.com/GMOD/jbrowse-components/pull/3986) Allow editing step size and window size of GC content adapter ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3982](https://github.com/GMOD/jbrowse-components/pull/3982) Allow rendering semi-circles in the arc renderer + SVG rendering of arcs ([@cmdcolin](https://github.com/cmdcolin)) - `__mocks__`, `core` - [#3981](https://github.com/GMOD/jbrowse-components/pull/3981) Auto-create HTML links for URLs, and strip HTML tags where they can't be rendered ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#3991](https://github.com/GMOD/jbrowse-components/pull/3991) Remove some non-functioning options from top level menu in @jbrowse/react-app ([@cmdcolin](https://github.com/cmdcolin)) - [#3980](https://github.com/GMOD/jbrowse-components/pull/3980) Downgrade electron 26->25 to fix screen blanking ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3971](https://github.com/GMOD/jbrowse-components/pull/3971) Fix rendering multi-quantitative tracks when blank data is present ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.65s. ## 2.7.0 (2023-10-04) #### :rocket: Enhancement - Other - [#3956](https://github.com/GMOD/jbrowse-components/pull/3956) Make faceted track selector facet filters responsive to adjacent filter selections ([@cmdcolin](https://github.com/cmdcolin)) - [#3953](https://github.com/GMOD/jbrowse-components/pull/3953) Report JSON parse error when failing to load JSON file on desktop ([@cmdcolin](https://github.com/cmdcolin)) - [#3951](https://github.com/GMOD/jbrowse-components/pull/3951) Add jobs widget to jbrowse-web ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - [#3900](https://github.com/GMOD/jbrowse-components/pull/3900) Make bookmarks persistent across sessions with local storage ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - [#3896](https://github.com/GMOD/jbrowse-components/pull/3896) Upgrade oclif to v3 to avoid deprecation warnings ([@garrettjstevens](https://github.com/garrettjstevens)) - [#3907](https://github.com/GMOD/jbrowse-components/pull/3907) Change the config.json missing screen to an "It worked!" message ([@cmdcolin](https://github.com/cmdcolin)) - [#3901](https://github.com/GMOD/jbrowse-components/pull/3901) Use shortened VCF feature description for some types of insertions and deletions ([@cmdcolin](https://github.com/cmdcolin)) - [#3840](https://github.com/GMOD/jbrowse-components/pull/3840) Adds custom filtering option to alignments tracks ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - [#3832](https://github.com/GMOD/jbrowse-components/pull/3832) Adds keyboard shortcuts for panning and zooming on a focused view ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - `core` - [#3954](https://github.com/GMOD/jbrowse-components/pull/3954) Add column resizing for jbrowse-desktop start screen recent sessions panel ([@cmdcolin](https://github.com/cmdcolin)) - [#3938](https://github.com/GMOD/jbrowse-components/pull/3938) Adds code improvements to GridBookmarkWidget ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - [#3914](https://github.com/GMOD/jbrowse-components/pull/3914) Swap out NPM `color` library for `colord` library ([@cmdcolin](https://github.com/cmdcolin)) - `app-core`, `core`, `embedded-core` - [#3931](https://github.com/GMOD/jbrowse-components/pull/3931) Add eslint-plugin-fast-refresh ([@cmdcolin](https://github.com/cmdcolin)) - `app-core` - [#3916](https://github.com/GMOD/jbrowse-components/pull/3916) Use theme.secondary.main instead of theme.secondary.light on focusedView ([@cmdcolin](https://github.com/cmdcolin)) - `app-core`, `core`, `embedded-core`, `product-core`, `text-indexing`, `web-core` - [#3502](https://github.com/GMOD/jbrowse-components/pull/3502) Update to react v18, mobx-react v9 ([@cmdcolin](https://github.com/cmdcolin)) - [#3885](https://github.com/GMOD/jbrowse-components/pull/3885) Eject react-script config from jbrowse-web and jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) - `app-core`, `core`, `web-core` - [#3831](https://github.com/GMOD/jbrowse-components/pull/3831) Adds session model reference to view in focus ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) #### :bug: Bug Fix - `app-core`, `core` - [#3959](https://github.com/GMOD/jbrowse-components/pull/3959) Remove type `any` from return value of getContainingView, getSession ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#3946](https://github.com/GMOD/jbrowse-components/pull/3946) Fix setting multiple hierarchical defaultCollapsed config options at initialization ([@cmdcolin](https://github.com/cmdcolin)) - [#3937](https://github.com/GMOD/jbrowse-components/pull/3937) Fix dev mode error from LGV overview scalebar ([@cmdcolin](https://github.com/cmdcolin)) - [#3925](https://github.com/GMOD/jbrowse-components/pull/3925) Reduce amount of canvas commands issued to the dotplot renderer ([@cmdcolin](https://github.com/cmdcolin)) - [#3924](https://github.com/GMOD/jbrowse-components/pull/3924) Fix incorrect tick mark label on dotplot axes happening in some cases ([@cmdcolin](https://github.com/cmdcolin)) - [#3921](https://github.com/GMOD/jbrowse-components/pull/3921) Fix hydration warning by only rendering the SvgFeature "selected feature" and "mouseover" client side ([@cmdcolin](https://github.com/cmdcolin)) - [#3910](https://github.com/GMOD/jbrowse-components/pull/3910) Fix feature label offsets in SVG exports with main thread RPC ([@cmdcolin](https://github.com/cmdcolin)) - [#3905](https://github.com/GMOD/jbrowse-components/pull/3905) Fix alignments track infinite loading when applying same "Color by" or "Sort by" setting twice ([@cmdcolin](https://github.com/cmdcolin)) - [#3904](https://github.com/GMOD/jbrowse-components/pull/3904) Fix "Color by"->"Mapping quality" for CRAM files ([@cmdcolin](https://github.com/cmdcolin)) - [#3902](https://github.com/GMOD/jbrowse-components/pull/3902) Fix ability to use plaintext bed in add-track CLI ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3929](https://github.com/GMOD/jbrowse-components/pull/3929) Fix mouse getting out of sync while dragging resize handle ([@cmdcolin](https://github.com/cmdcolin)) - [#3912](https://github.com/GMOD/jbrowse-components/pull/3912) Avoid undefined getConf on assembly.configuration safeReference ([@cmdcolin](https://github.com/cmdcolin)) - [#3887](https://github.com/GMOD/jbrowse-components/pull/3887) Add forwardRef to wrapped re-exported lazy components ([@garrettjstevens](https://github.com/garrettjstevens)) - [#3866](https://github.com/GMOD/jbrowse-components/pull/3866) Fix calculation of width of "view container title" ([@cmdcolin](https://github.com/cmdcolin)) - [#3865](https://github.com/GMOD/jbrowse-components/pull/3865) Strip alpha from colors for improved SVG export compatibility ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#3957](https://github.com/GMOD/jbrowse-components/pull/3957) Add error handler example for embedded components ([@cmdcolin](https://github.com/cmdcolin)) - [#3913](https://github.com/GMOD/jbrowse-components/pull/3913) Add color scheme for pathogenicity for ClinVar config_demo track ([@scottcain](https://github.com/scottcain)) - [#3881](https://github.com/GMOD/jbrowse-components/pull/3881) Improve some of the extension point documentation ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `app-core`, `core`, `embedded-core` - [#3931](https://github.com/GMOD/jbrowse-components/pull/3931) Add eslint-plugin-fast-refresh ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3920](https://github.com/GMOD/jbrowse-components/pull/3920) Remove some unused "renameReference" code in static/dynamic blocks ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#3882](https://github.com/GMOD/jbrowse-components/pull/3882) Minor refactors and typescripting improvements ([@cmdcolin](https://github.com/cmdcolin)) - `app-core`, `core`, `embedded-core`, `product-core`, `web-core` - [#3855](https://github.com/GMOD/jbrowse-components/pull/3855) Replace shortid with vendored nanoid ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 4 - Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - Scott Cain ([@scottcain](https://github.com/scottcain)) Done in 2.80s. #### :rocket: Enhancement - Other - [#3830](https://github.com/GMOD/jbrowse-components/pull/3830) Refactors LGV synteny and pileup with shared mixins ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - [#3811](https://github.com/GMOD/jbrowse-components/pull/3811) Add ability to show/hide all tracks in category ([@cmdcolin](https://github.com/cmdcolin)) - `app-core` - [#3810](https://github.com/GMOD/jbrowse-components/pull/3810) Add sorting and collapsing options to the hierarchical track selector ([@cmdcolin](https://github.com/cmdcolin)) - [#3827](https://github.com/GMOD/jbrowse-components/pull/3827) Add check for document.activeElement == INPUT before undo/redo ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - [#3839](https://github.com/GMOD/jbrowse-components/pull/3839) Fix bug where multi-quantitative tracks plotted incorrectly for some bigwigs with empty regions ([@cmdcolin](https://github.com/cmdcolin)) - [#3837](https://github.com/GMOD/jbrowse-components/pull/3837) Fix text layout in dotplots with long coordinate strings ([@cmdcolin](https://github.com/cmdcolin)) - [#3825](https://github.com/GMOD/jbrowse-components/pull/3825) Fix SVG export compatibility by removing rgba strings ([@cmdcolin](https://github.com/cmdcolin)) - [#3814](https://github.com/GMOD/jbrowse-components/pull/3814) Fix suspense fallback to track container for lazy loaded display components ([@cmdcolin](https://github.com/cmdcolin)) - [#3808](https://github.com/GMOD/jbrowse-components/pull/3808) Fix track ordering of hierarchical track selector to more closely match the config.json ([@cmdcolin](https://github.com/cmdcolin)) - [#3806](https://github.com/GMOD/jbrowse-components/pull/3806) Fix a bug on the BookmarkWidget mui data grid where labels were not saving ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - [#3804](https://github.com/GMOD/jbrowse-components/pull/3804) Fix version missing from about menu in @jbrowse/react-app ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - [#3818](https://github.com/GMOD/jbrowse-components/pull/3818) Miscellaneous plugin store code refactoring ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 - Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Robert Buels ([@rbuels](https://github.com/rbuels)) Done in 1.50s. #### :rocket: Enhancement - [#3796](https://github.com/GMOD/jbrowse-components/pull/3796) Allow workers to load CJS plugins ([@garrettjstevens](https://github.com/garrettjstevens)) - [#3783](https://github.com/GMOD/jbrowse-components/pull/3783) Add ability for track selector button in synteny view to select individual views ([@cmdcolin](https://github.com/cmdcolin)) - [#3452](https://github.com/GMOD/jbrowse-components/pull/3452) Use notarytool for macOS desktop signing ([@cmdcolin](https://github.com/cmdcolin)) - [#3766](https://github.com/GMOD/jbrowse-components/pull/3766) Add nextjs circular genome view demo ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#3798](https://github.com/GMOD/jbrowse-components/pull/3798) Fix VCF feature starting at 1-based 1 ([@cmdcolin](https://github.com/cmdcolin)) - [#3775](https://github.com/GMOD/jbrowse-components/pull/3775) Fix stranded RNA-seq rendering and rename option Color by -> "First-of-pair strand" ([@cmdcolin](https://github.com/cmdcolin)) - [#3758](https://github.com/GMOD/jbrowse-components/pull/3758) Adds safety checks on AlignmentsDisplay properties to avoid undefined rendering ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - [#3770](https://github.com/GMOD/jbrowse-components/pull/3770) Fix potential issue with display searchFeatureByID being undefined ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3784](https://github.com/GMOD/jbrowse-components/pull/3784) Fix synteny rubberband tooltips when views are exactly the same ([@cmdcolin](https://github.com/cmdcolin)) - [#3782](https://github.com/GMOD/jbrowse-components/pull/3782) Fix crash on color picker component using debounce on color property ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - [#3767](https://github.com/GMOD/jbrowse-components/pull/3767) Check session tracks for text search adapters ([@garrettjstevens](https://github.com/garrettjstevens)) - `app-core`, `core`, `embedded-core`, `product-core`, `text-indexing`, `web-core` - [#3771](https://github.com/GMOD/jbrowse-components/pull/3771) Use inlineSourceMaps for tsc builds and other misc changes ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - Other - [#3794](https://github.com/GMOD/jbrowse-components/pull/3794) Move embedded demos to individual repos ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `product-core` - [#3786](https://github.com/GMOD/jbrowse-components/pull/3786) Centralize rpcWorker in product-core ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 - Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) Done in 1.55s. #### :rocket: Enhancement - Other - [#3743](https://github.com/GMOD/jbrowse-components/pull/3743) Create mixin for shared code between LinearWiggleDisplay and MultiWiggleLinearDisplay ([@cmdcolin](https://github.com/cmdcolin)) - [#3711](https://github.com/GMOD/jbrowse-components/pull/3711) Allow synteny data adapters to open files larger than 512Mb ([@cmdcolin](https://github.com/cmdcolin)) - [#3639](https://github.com/GMOD/jbrowse-components/pull/3639) Add button to bookmark in jbrowse-web share dialog ([@cmdcolin](https://github.com/cmdcolin)) - [#3631](https://github.com/GMOD/jbrowse-components/pull/3631) Add BEDPE add track workflow, avoid showing "Add track" when disabled ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - [#3700](https://github.com/GMOD/jbrowse-components/pull/3700) Render alignment track arcs instantly after bpPerPx change ([@cmdcolin](https://github.com/cmdcolin)) - [#3695](https://github.com/GMOD/jbrowse-components/pull/3695) Reduce re-drawing on alignments track paired read arcs/cloud display types ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3725](https://github.com/GMOD/jbrowse-components/pull/3725) Filter tracks that match all view.assemblyNames in multi-assembly track selector modes ([@cmdcolin](https://github.com/cmdcolin)) - [#3531](https://github.com/GMOD/jbrowse-components/pull/3531) Add @jbrowse/react-app embedded component ([@cmdcolin](https://github.com/cmdcolin)) - [#3653](https://github.com/GMOD/jbrowse-components/pull/3653) Evaluate extension point on track config pre-process snapshot ([@cmdcolin](https://github.com/cmdcolin)) - [#3706](https://github.com/GMOD/jbrowse-components/pull/3706) Miscellaneous alignments arc/cloud fixes ([@cmdcolin](https://github.com/cmdcolin)) - [#3698](https://github.com/GMOD/jbrowse-components/pull/3698) Add column resizers to the variant ANN/CSQ panels ([@cmdcolin](https://github.com/cmdcolin)) - `app-core`, `product-core`, `web-core` - [#3531](https://github.com/GMOD/jbrowse-components/pull/3531) Add @jbrowse/react-app embedded component ([@cmdcolin](https://github.com/cmdcolin)) - `__mocks__` - [#3707](https://github.com/GMOD/jbrowse-components/pull/3707) Improved read cloud display for long reads with inversions ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - [#3749](https://github.com/GMOD/jbrowse-components/pull/3749) Avoid re-prompting a user login when refresh token is processed ([@cmdcolin](https://github.com/cmdcolin)) - [#3572](https://github.com/GMOD/jbrowse-components/pull/3572) Add OAuth and HTTP BasicAuth servers for local testing, fix some OAuth flows ([@garrettjstevens](https://github.com/garrettjstevens)) - [#3708](https://github.com/GMOD/jbrowse-components/pull/3708) Add removable-media to jbrowse desktop snap ([@cmdcolin](https://github.com/cmdcolin)) - [#3687](https://github.com/GMOD/jbrowse-components/pull/3687) Take into account ML tag when showing MM tag on alignments, misc refactoring ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#3747](https://github.com/GMOD/jbrowse-components/pull/3747) Fix blank lines in GFF crashing text-index ([@cmdcolin](https://github.com/cmdcolin)) - [#3739](https://github.com/GMOD/jbrowse-components/pull/3739) Fix specifying the assemblyNames config slot on add-connection CLI ([@cmdcolin](https://github.com/cmdcolin)) - [#3631](https://github.com/GMOD/jbrowse-components/pull/3631) Add BEDPE add track workflow, avoid showing "Add track" when disabled ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - [#3667](https://github.com/GMOD/jbrowse-components/pull/3667) Fix horizontal flip functionality for Hi-C display ([@studentshivang](https://github.com/studentshivang)) - [#3703](https://github.com/GMOD/jbrowse-components/pull/3703) Fix rendering error in alignments tracks when filtering by tag in CRAM file ([@Lilas-w](https://github.com/Lilas-w)) - [#3694](https://github.com/GMOD/jbrowse-components/pull/3694) Fix ability to filter certain fields in BAM/CRAM files ([@cmdcolin](https://github.com/cmdcolin)) - [#3691](https://github.com/GMOD/jbrowse-components/pull/3691) Fix breakpoint split view alignment connections not pointing at right position in v2.5.0 ([@cmdcolin](https://github.com/cmdcolin)) - [#3686](https://github.com/GMOD/jbrowse-components/pull/3686) Fix jbrowse create/jbrowse upgrade CLI intermittent failures ([@cmdcolin](https://github.com/cmdcolin)) - `product-core`, `web-core` - [#3738](https://github.com/GMOD/jbrowse-components/pull/3738) Don't throw on UCSC connection containing assemblies not matching connection->assemblyNames config ([@cmdcolin](https://github.com/cmdcolin)) - `app-core`, `core`, `embedded-core` - [#3731](https://github.com/GMOD/jbrowse-components/pull/3731) Fix view menu going off screen in some cases ([@cmdcolin](https://github.com/cmdcolin)) - `app-core` - [#3713](https://github.com/GMOD/jbrowse-components/pull/3713) Fix centering of the ImportForm on SV inspector ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - Other - [#3752](https://github.com/GMOD/jbrowse-components/pull/3752) Add storybook example for fetching features currently in view ([@cmdcolin](https://github.com/cmdcolin)) - [#3732](https://github.com/GMOD/jbrowse-components/pull/3732) Add JBrowse R shiny app demo ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - [#3693](https://github.com/GMOD/jbrowse-components/pull/3693) Remove package table from release blogposts ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `embedded-core`, `product-core` - [#3704](https://github.com/GMOD/jbrowse-components/pull/3704) Organize autogenerated docs into categories ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `app-core`, `core`, `product-core`, `text-indexing` - [#3740](https://github.com/GMOD/jbrowse-components/pull/3740) Bump electron, proxy-agent, fontsource-roboto, etc. and update SnackbarMessage from typed array to object ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3741](https://github.com/GMOD/jbrowse-components/pull/3741) Distinguish between SessionWithConnections and SessionWithConnectionEditing ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#3734](https://github.com/GMOD/jbrowse-components/pull/3734) PileupRenderer refactor ([@cmdcolin](https://github.com/cmdcolin)) - `app-core`, `core`, `product-core`, `web-core` - [#3717](https://github.com/GMOD/jbrowse-components/pull/3717) More modularizing of shared app code ([@cmdcolin](https://github.com/cmdcolin)) - `product-core` - [#3709](https://github.com/GMOD/jbrowse-components/pull/3709) Silence console warn in CopyAndDelete test ([@cmdcolin](https://github.com/cmdcolin)) - `app-core`, `core`, `embedded-core`, `product-core`, `text-indexing` - [#3701](https://github.com/GMOD/jbrowse-components/pull/3701) Create app-core and embedded-core packages ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `product-core` - [#3661](https://github.com/GMOD/jbrowse-components/pull/3661) Create packages/product-core containing shared code between the various products ([@rbuels](https://github.com/rbuels)) #### Committers: 6 - Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - Robert Buels ([@rbuels](https://github.com/rbuels)) - Shivang Dwivedi ([@studentshivang](https://github.com/studentshivang)) - [@Lilas-w](https://github.com/Lilas-w) Done in 2.84s. ## 2.5.0 (2023-05-04)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - Other - [#3675](https://github.com/GMOD/jbrowse-components/pull/3675) Use react-popper for tooltips in DotplotView ([@cmdcolin](https://github.com/cmdcolin)) - [#3637](https://github.com/GMOD/jbrowse-components/pull/3637) Fix renderDelay not being applied to dynamicBlocks ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3677](https://github.com/GMOD/jbrowse-components/pull/3677) Adjust RefNameAutocomplete width calculation to avoid ellipses ([@cmdcolin](https://github.com/cmdcolin)) - [#3660](https://github.com/GMOD/jbrowse-components/pull/3660) Bump x-data-grid dependency, refactors for BaseFeatureDetails, add GridToolbar ([@cmdcolin](https://github.com/cmdcolin)) - [#3626](https://github.com/GMOD/jbrowse-components/pull/3626) Update to mui x-data-grid 6 ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - [#3681](https://github.com/GMOD/jbrowse-components/pull/3681) Guard against undefined in CoreGetFeatureDetails ([@cmdcolin](https://github.com/cmdcolin)) - [#3662](https://github.com/GMOD/jbrowse-components/pull/3662) Fix empty feature sequence on top-level gene feature ([@cmdcolin](https://github.com/cmdcolin)) - [#3666](https://github.com/GMOD/jbrowse-components/pull/3666) Fix text boxes being too small in Dialog boxes ([@cmdcolin](https://github.com/cmdcolin)) - [#3642](https://github.com/GMOD/jbrowse-components/pull/3642) Fix error handling of feature detail formatter jexl callbacks ([@cmdcolin](https://github.com/cmdcolin)) - [#3621](https://github.com/GMOD/jbrowse-components/pull/3621) Update plugin rollup polyfill package ([@garrettjstevens](https://github.com/garrettjstevens)) - [#3620](https://github.com/GMOD/jbrowse-components/pull/3620) Fix potential crashes where alignment SEQ field may be empty, simplify some display model code ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#3670](https://github.com/GMOD/jbrowse-components/pull/3670) Only double-click zoom if not clicking on feature ([@cmdcolin](https://github.com/cmdcolin)) - [#3652](https://github.com/GMOD/jbrowse-components/pull/3652) Fix text being invisible on overview scalebar when cytobands shown ([@cmdcolin](https://github.com/cmdcolin)) - [#3632](https://github.com/GMOD/jbrowse-components/pull/3632) Fix mouse click-and-drag behavior in the alternative "cursor mode" for the dotplot view ([@cmdcolin](https://github.com/cmdcolin)) - [#3625](https://github.com/GMOD/jbrowse-components/pull/3625) Fix UCSC trackhub assembly aliases matching ([@andrzejgrzelak](https://github.com/andrzejgrzelak)) - `__mocks__`, `core` - [#3630](https://github.com/GMOD/jbrowse-components/pull/3630) Fix flakiness of connection test ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - Other - [#3676](https://github.com/GMOD/jbrowse-components/pull/3676) Refactor circular genome view storybook ([@cmdcolin](https://github.com/cmdcolin)) - [#3671](https://github.com/GMOD/jbrowse-components/pull/3671) Fix website documentation sidebar on browsers with prefers-reduced-motion ([@cmdcolin](https://github.com/cmdcolin)) - [#3654](https://github.com/GMOD/jbrowse-components/pull/3654) Add some docs for configuring defaultSession ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3646](https://github.com/GMOD/jbrowse-components/pull/3646) Refactor linear genome view storybook ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - [#3647](https://github.com/GMOD/jbrowse-components/pull/3647) Refactoring navToMultiple, navToLocString, and related ([@cmdcolin](https://github.com/cmdcolin)) - [#3629](https://github.com/GMOD/jbrowse-components/pull/3629) Typescript checking for config slot names ([@rbuels](https://github.com/rbuels)) - [#3618](https://github.com/GMOD/jbrowse-components/pull/3618) Rename APIs for feature density stats and quantitative stats ([@cmdcolin](https://github.com/cmdcolin)) - [#3615](https://github.com/GMOD/jbrowse-components/pull/3615) Add check for default export to plugin loader ([@rbuels](https://github.com/rbuels)) #### Committers: 4 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - Robert Buels ([@rbuels](https://github.com/rbuels)) - [@andrzejgrzelak](https://github.com/andrzejgrzelak) ## 2.4.2 (2023-03-27)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-hic | | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - `core` - [#3604](https://github.com/GMOD/jbrowse-components/pull/3604) Alignments tags description in feature details on mouseover ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#3586](https://github.com/GMOD/jbrowse-components/pull/3586) Add authorization(internetAccount) support for Trix index files ([@andrzejgrzelak](https://github.com/andrzejgrzelak)) #### :bug: Bug Fix - Other - [#3610](https://github.com/GMOD/jbrowse-components/pull/3610) Avoid cutting off import form of spreadsheet view, fix overflowed text in table header ([@cmdcolin](https://github.com/cmdcolin)) - [#3600](https://github.com/GMOD/jbrowse-components/pull/3600) Fix using the force load button after a stats timeout ([@cmdcolin](https://github.com/cmdcolin)) - [#3592](https://github.com/GMOD/jbrowse-components/pull/3592) Fix shading on synteny features after mouseout ([@cmdcolin](https://github.com/cmdcolin)) - `__mocks__`, `core` - [#3608](https://github.com/GMOD/jbrowse-components/pull/3608) Fix subfeatures formatter not being applied to feature detail panel ([@cmdcolin](https://github.com/cmdcolin)) - [#3607](https://github.com/GMOD/jbrowse-components/pull/3607) Avoid "ResizeObserver" loop warning during development ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3593](https://github.com/GMOD/jbrowse-components/pull/3593) Fix gene without subfeatures not being displayed in sequence feature details ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - [#3611](https://github.com/GMOD/jbrowse-components/pull/3611) Use local data instead of remote data for LGV component test ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - [@andrzejgrzelak](https://github.com/andrzejgrzelak) ## 2.4.1 (2023-03-14)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/text-indexing | | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-authentication | https://www.npmjs.com/package/@jbrowse/plugin-authentication | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-jobs-management | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-text-indexing | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - `core` - [#3534](https://github.com/GMOD/jbrowse-components/pull/3534) Improve visibility of SNPs on alignments track ([@cmdcolin](https://github.com/cmdcolin)) - [#3561](https://github.com/GMOD/jbrowse-components/pull/3561) Add scroll zoom, d-pad, and more click+drag options to dotplot ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#3574](https://github.com/GMOD/jbrowse-components/pull/3574) Add ability to load all built-in synteny data sources from @jbrowse/cli ([@cmdcolin](https://github.com/cmdcolin)) - [#3564](https://github.com/GMOD/jbrowse-components/pull/3564) Use double-click to zoom in on particular offset in LGV, and make ctrl+scroll also zoom in on particular offset ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - [#3578](https://github.com/GMOD/jbrowse-components/pull/3578) Fix selected synteny feature getting unselected after scroll ([@cmdcolin](https://github.com/cmdcolin)) - [#3566](https://github.com/GMOD/jbrowse-components/pull/3566) Fix use of "show all regions with data" feature in SV inspector with TRA entries (with CHR2 from INFO) ([@cmdcolin](https://github.com/cmdcolin)) - [#3558](https://github.com/GMOD/jbrowse-components/pull/3558) Fix visual effect from using the overview scalebar click and dragging backwards ([@cmdcolin](https://github.com/cmdcolin)) - [#3556](https://github.com/GMOD/jbrowse-components/pull/3556) Fix infinite loading state when no synteny features are visible in synteny view ([@cmdcolin](https://github.com/cmdcolin)) - [#3551](https://github.com/GMOD/jbrowse-components/pull/3551) Fix bad layout on tabix tracks that have Unicode characters ([@cmdcolin](https://github.com/cmdcolin)) - [#3548](https://github.com/GMOD/jbrowse-components/pull/3548) Fix upper case querying of jbrowse 1 text search store ([@cmdcolin](https://github.com/cmdcolin)) - [#3545](https://github.com/GMOD/jbrowse-components/pull/3545) Fix issue where clearing search box on LGV import form turns search box into loading bar ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#3571](https://github.com/GMOD/jbrowse-components/pull/3571) Fixing link to PAG 2023 tutorial ([@scottcain](https://github.com/scottcain)) #### :house: Internal - Other - [#3567](https://github.com/GMOD/jbrowse-components/pull/3567) Update github actions workflows to newer versions ([@cmdcolin](https://github.com/cmdcolin)) - `__mocks__`, `core`, `text-indexing` - [#3557](https://github.com/GMOD/jbrowse-components/pull/3557) Add additional lint rules from typescript-eslint and eslint-plugin-unicorn ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Scott Cain ([@scottcain](https://github.com/scottcain)) ## 2.4.0 (2023-02-24)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-authentication | https://www.npmjs.com/package/@jbrowse/plugin-authentication | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-jobs-management | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-menus | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - Other - [#3527](https://github.com/GMOD/jbrowse-components/pull/3527) Breakpoint split view SVG export ([@cmdcolin](https://github.com/cmdcolin)) - [#3510](https://github.com/GMOD/jbrowse-components/pull/3510) Allow configuring default display height ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3513](https://github.com/GMOD/jbrowse-components/pull/3513) Add ability to open refNameAliases+cytobands in "Open sequence" start screen on desktop ([@cmdcolin](https://github.com/cmdcolin)) - [#3512](https://github.com/GMOD/jbrowse-components/pull/3512) SVG export of linear synteny view, dotplot, and circular views ([@cmdcolin](https://github.com/cmdcolin)) - [#3467](https://github.com/GMOD/jbrowse-components/pull/3467) Create dark theme and allow user to toggle different themes from preferences dialog ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - [#3525](https://github.com/GMOD/jbrowse-components/pull/3525) Fix missing grid ticks in dotplot ([@cmdcolin](https://github.com/cmdcolin)) - [#3524](https://github.com/GMOD/jbrowse-components/pull/3524) Fix loading session shares that have a plus sign in the sessionId ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#3532](https://github.com/GMOD/jbrowse-components/pull/3532) Check website links in CI ([@cmdcolin](https://github.com/cmdcolin)) - [#3507](https://github.com/GMOD/jbrowse-components/pull/3507) Fix mygene.info demo track ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) ## 2.3.4 (2023-02-01)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - `core` - [#3494](https://github.com/GMOD/jbrowse-components/pull/3494) Use transitionDuration 0 as defaultProp in theme for both popovers and menus ([@cmdcolin](https://github.com/cmdcolin)) - [#3488](https://github.com/GMOD/jbrowse-components/pull/3488) Render HTML in faceted track selector for track data/metadata ([@cmdcolin](https://github.com/cmdcolin)) - [#3483](https://github.com/GMOD/jbrowse-components/pull/3483) Add anchorOrigin/transformOrigin to default menu component ([@cmdcolin](https://github.com/cmdcolin)) - [#3470](https://github.com/GMOD/jbrowse-components/pull/3470) Variant sample grid auto-size columns and resizer ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#3304](https://github.com/GMOD/jbrowse-components/pull/3304) Faceted/data grid style track selector ([@cmdcolin](https://github.com/cmdcolin)) - [#3477](https://github.com/GMOD/jbrowse-components/pull/3477) Larger margins to add track workflow to visually clarify next button behavior ([@cmdcolin](https://github.com/cmdcolin)) - [#3475](https://github.com/GMOD/jbrowse-components/pull/3475) Bypass plugins.json download if unneeded during app startup ([@cmdcolin](https://github.com/cmdcolin)) - [#3458](https://github.com/GMOD/jbrowse-components/pull/3458) Improve auto-update of sequence track height when toggling forward/reverse/translation settings ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - [#3482](https://github.com/GMOD/jbrowse-components/pull/3482) Fix loading external plugins in embedded linear-genome-view demo ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#3457](https://github.com/GMOD/jbrowse-components/pull/3457) Fix synteny view not drawing after horizontal flip in v2.3.3 ([@cmdcolin](https://github.com/cmdcolin)) - [#3459](https://github.com/GMOD/jbrowse-components/pull/3459) Booleanize localstorage settings from older versions of LGV to avoid crash ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#3487](https://github.com/GMOD/jbrowse-components/pull/3487) Storybook 7 ([@cmdcolin](https://github.com/cmdcolin)) - [#3464](https://github.com/GMOD/jbrowse-components/pull/3464) Add source file to config/state model docs ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) ## 2.3.3 (2023-01-11)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/text-indexing | | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-authentication | https://www.npmjs.com/package/@jbrowse/plugin-authentication | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gccontent | https://www.npmjs.com/package/@jbrowse/plugin-gccontent | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-jobs-management | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-text-indexing | | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - `core` - [#3440](https://github.com/GMOD/jbrowse-components/pull/3440) "Show all regions" for dotplot and synteny views and refactor synteny rendering RPC to optimize scrolling ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#3451](https://github.com/GMOD/jbrowse-components/pull/3451) Fix auto-updates on desktop not working since v2.2.2 ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3428](https://github.com/GMOD/jbrowse-components/pull/3428) Add missing dependencies to embedded component package.json's ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#3448](https://github.com/GMOD/jbrowse-components/pull/3448) Typescriptify some docusaurus website code ([@cmdcolin](https://github.com/cmdcolin)) - [#3444](https://github.com/GMOD/jbrowse-components/pull/3444) Human vs mouse synteny demo ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - [#3445](https://github.com/GMOD/jbrowse-components/pull/3445) Typescriptify more tests ([@cmdcolin](https://github.com/cmdcolin)) - [#3443](https://github.com/GMOD/jbrowse-components/pull/3443) Restore console mocks after running ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) ## 2.3.2 (2022-12-20)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gccontent | https://www.npmjs.com/package/@jbrowse/plugin-gccontent | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - `core` - [#3422](https://github.com/GMOD/jbrowse-components/pull/3422) Auto-adjust height of reference sequence track to current settings ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#3421](https://github.com/GMOD/jbrowse-components/pull/3421) Add ability to revcomp sequence in the "Get sequence" dialog ([@cmdcolin](https://github.com/cmdcolin)) - [#3413](https://github.com/GMOD/jbrowse-components/pull/3413) Add a "base" set of tracks and assemblies for the embedded demos ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - [#3419](https://github.com/GMOD/jbrowse-components/pull/3419) Fix rendering base-level alignments on synteny visualizations, especially in inverted regions ([@cmdcolin](https://github.com/cmdcolin)) - [#3416](https://github.com/GMOD/jbrowse-components/pull/3416) Fix rendering alignment arcs on files that need refname renaming and add jitter setting ([@cmdcolin](https://github.com/cmdcolin)) - [#3415](https://github.com/GMOD/jbrowse-components/pull/3415) Fix circular view being rendered as a blank area if tab is opened in the background ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin))
Packages in this release

| Package | Download | | ----------------------------------- | ----------------------------------------------------------------- | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |

## 2.3.0 (2022-12-15)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/text-indexing | | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-authentication | https://www.npmjs.com/package/@jbrowse/plugin-authentication | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gccontent | https://www.npmjs.com/package/@jbrowse/plugin-gccontent | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-jobs-management | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-menus | | | @jbrowse/plugin-protein | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-text-indexing | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - Other - [#3403](https://github.com/GMOD/jbrowse-components/pull/3403) Reduce overplotting on dotplot grid lines and other misc improvements ([@cmdcolin](https://github.com/cmdcolin)) - [#3381](https://github.com/GMOD/jbrowse-components/pull/3381) Add method for cache busting requests to the config file in jbrowse-web ([@cmdcolin](https://github.com/cmdcolin)) - [#3384](https://github.com/GMOD/jbrowse-components/pull/3384) Add method to more easily create compact view of alignments ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3391](https://github.com/GMOD/jbrowse-components/pull/3391) Allow arc display to connect to "unpaired" positions using RNEXT/PNEXT or SA tag ([@cmdcolin](https://github.com/cmdcolin)) - [#3387](https://github.com/GMOD/jbrowse-components/pull/3387) Small UI tweaks for add track workflow ([@cmdcolin](https://github.com/cmdcolin)) - [#3358](https://github.com/GMOD/jbrowse-components/pull/3358) Create new "arc" display type to show long range connections between paired-end and split-reads ([@cmdcolin](https://github.com/cmdcolin)) - `text-indexing` - [#3385](https://github.com/GMOD/jbrowse-components/pull/3385) Optimize prefix size for text indexing automatically ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#3407](https://github.com/GMOD/jbrowse-components/pull/3407) Remove trackhub registry plugin from core plugins, moved to plugin store ([@cmdcolin](https://github.com/cmdcolin)) - [#3406](https://github.com/GMOD/jbrowse-components/pull/3406) Fix loading connection tracks from connections that don't specify assemblyNames in config ([@cmdcolin](https://github.com/cmdcolin)) - [#3390](https://github.com/GMOD/jbrowse-components/pull/3390) Fix positioning within large alignments for query->target LGV synteny navigation ([@cmdcolin](https://github.com/cmdcolin)) - [#3388](https://github.com/GMOD/jbrowse-components/pull/3388) Fix search result that matches synonyms that matches multiple locations ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3404](https://github.com/GMOD/jbrowse-components/pull/3404) Fix double-render of some synteny features ([@cmdcolin](https://github.com/cmdcolin)) - [#3401](https://github.com/GMOD/jbrowse-components/pull/3401) Remove y-scalebar rendering placeholder values in blank and loading states ([@cmdcolin](https://github.com/cmdcolin)) - [#3389](https://github.com/GMOD/jbrowse-components/pull/3389) Fix issue where snackbar would not show up when same error message is triggered multiple times ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - `core` - [#3396](https://github.com/GMOD/jbrowse-components/pull/3396) Use prettier to word wrap markdown prose ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#3383](https://github.com/GMOD/jbrowse-components/pull/3383) Add note to user guide about variant callers that can be used for SV inspector ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `__mocks__`, `core`, `text-indexing` - [#3400](https://github.com/GMOD/jbrowse-components/pull/3400) Reduce peerDependency warnings from installing dev environment ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3394](https://github.com/GMOD/jbrowse-components/pull/3394) Simplify RPC watchWorker ([@cmdcolin](https://github.com/cmdcolin)) - [#3386](https://github.com/GMOD/jbrowse-components/pull/3386) Fix warning when rendering circular chord displays with web worker RPC ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) ## 2.2.2 (2022-12-06)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/text-indexing | | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-authentication | https://www.npmjs.com/package/@jbrowse/plugin-authentication | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gccontent | https://www.npmjs.com/package/@jbrowse/plugin-gccontent | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-jobs-management | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-protein | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-text-indexing | | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - Other - [#3350](https://github.com/GMOD/jbrowse-components/pull/3350) Retain feature labels in compact display mode for SVG features, and allow turning off keeping feature description without feature label ([@cmdcolin](https://github.com/cmdcolin)) - [#3357](https://github.com/GMOD/jbrowse-components/pull/3357) Allow holding shift key to create rubberband selection on LGV ([@cmdcolin](https://github.com/cmdcolin)) - [#3363](https://github.com/GMOD/jbrowse-components/pull/3363) Create remove-track CLI command ([@cmdcolin](https://github.com/cmdcolin)) - [#3341](https://github.com/GMOD/jbrowse-components/pull/3341) Add BEDPE adapter type ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3359](https://github.com/GMOD/jbrowse-components/pull/3359) Fix typos in codebase using typos-cli ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#3377](https://github.com/GMOD/jbrowse-components/pull/3377) Fix rendering and clicking synteny features when using MainThreadRpc ([@cmdcolin](https://github.com/cmdcolin)) - [#3375](https://github.com/GMOD/jbrowse-components/pull/3375) Fix `jbrowse upgrade` CLI command overwriting config.json with --branch or --nightly options ([@cmdcolin](https://github.com/cmdcolin)) - [#3370](https://github.com/GMOD/jbrowse-components/pull/3370) Fix error with SNPCoverage not rendering MM tag modifications in some cases ([@cmdcolin](https://github.com/cmdcolin)) - [#3366](https://github.com/GMOD/jbrowse-components/pull/3366) Fix ability to use LGV synteny track on inverted alignments ([@cmdcolin](https://github.com/cmdcolin)) - [#3348](https://github.com/GMOD/jbrowse-components/pull/3348) Fix for breakpoint split view and circular view issues with `` type entries in v2.2.1 ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3369](https://github.com/GMOD/jbrowse-components/pull/3369) Fix uncaught promise errors and add lint rule for catching these ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#3347](https://github.com/GMOD/jbrowse-components/pull/3347) Reduce number of quickstart guides ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - [#3368](https://github.com/GMOD/jbrowse-components/pull/3368) Create base "Dialog" component to standardize dialogs across codebase ([@cmdcolin](https://github.com/cmdcolin)) - `text-indexing` - [#3344](https://github.com/GMOD/jbrowse-components/pull/3344) fix yarn build error in Windows ([@Lilas-w](https://github.com/Lilas-w)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - [@Lilas-w](https://github.com/Lilas-w) ## 2.2.1 (2022-11-21)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-authentication | https://www.npmjs.com/package/@jbrowse/plugin-authentication | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gccontent | https://www.npmjs.com/package/@jbrowse/plugin-gccontent | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - Other - [#3277](https://github.com/GMOD/jbrowse-components/pull/3277) Create new "Add track workflow" that allows pasting JSON track configs ([@cmdcolin](https://github.com/cmdcolin)) - [#3328](https://github.com/GMOD/jbrowse-components/pull/3328) Add GC content display type to the reference sequence track ([@cmdcolin](https://github.com/cmdcolin)) - [#3316](https://github.com/GMOD/jbrowse-components/pull/3316) Add LGV typescripting to @jbrowse/react-linear-genome-view ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3298](https://github.com/GMOD/jbrowse-components/pull/3298) Add authentication plugin to embedded components ([@garrettjstevens](https://github.com/garrettjstevens)) - [#3329](https://github.com/GMOD/jbrowse-components/pull/3329) Add ability to minimize/collapse tracks and views and move views up/down in view stack ([@cmdcolin](https://github.com/cmdcolin)) - [#3308](https://github.com/GMOD/jbrowse-components/pull/3308) Add ability to display synteny track in a normal LGV showing regions of synteny as features ([@cmdcolin](https://github.com/cmdcolin)) - [#3317](https://github.com/GMOD/jbrowse-components/pull/3317) Move ErrorBoundary so that tracks/views that have crashed can be closed more easily ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#3342](https://github.com/GMOD/jbrowse-components/pull/3342) Fix CRAM mismatches calculation regression in v2.2.0 ([@cmdcolin](https://github.com/cmdcolin)) - [#3319](https://github.com/GMOD/jbrowse-components/pull/3319) Fix pileup "sort by" setting being lost on zoom level change ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3340](https://github.com/GMOD/jbrowse-components/pull/3340) Fix linear genome view import form going into infinite loading state changing assemblies with same refnames ([@cmdcolin](https://github.com/cmdcolin)) - [#3339](https://github.com/GMOD/jbrowse-components/pull/3339) Fix force flag for drawing large regions and node-fetch polyfill for node 18 fix in @jbrowse/img ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) ## 2.2.0 (2022-11-04)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/text-indexing | | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-authentication | https://www.npmjs.com/package/@jbrowse/plugin-authentication | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-jobs-management | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-menus | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-text-indexing | | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - Other - [#3296](https://github.com/GMOD/jbrowse-components/pull/3296) Add option to use OAuth "state" param in internet accounts ([@garrettjstevens](https://github.com/garrettjstevens)) - [#3285](https://github.com/GMOD/jbrowse-components/pull/3285) Use typescript version of @gmod/cram ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3299](https://github.com/GMOD/jbrowse-components/pull/3299) Add ability to open a synteny track directly from the dotplot/linear synteny view import forms ([@cmdcolin](https://github.com/cmdcolin)) - [#3287](https://github.com/GMOD/jbrowse-components/pull/3287) Lazy-load assemblies on demand instead of all at app startup ([@cmdcolin](https://github.com/cmdcolin)) - [#3279](https://github.com/GMOD/jbrowse-components/pull/3279) Remove unnecessary expanded region query and small refactors ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - [#3309](https://github.com/GMOD/jbrowse-components/pull/3309) Fix animated "Loading..." message keyframes ([@cmdcolin](https://github.com/cmdcolin)) - [#3306](https://github.com/GMOD/jbrowse-components/pull/3306) Fix the RefNameAutocomplete displaying a stale value for chromosome names ([@cmdcolin](https://github.com/cmdcolin)) - [#3302](https://github.com/GMOD/jbrowse-components/pull/3302) Improve rubberband zooming across elided regions ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#3293](https://github.com/GMOD/jbrowse-components/pull/3293) Fix CRAM plotting for data files that encode insertions in uncommon way ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - `core`, `text-indexing` - [#3278](https://github.com/GMOD/jbrowse-components/pull/3278) Auto-generate docs ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - [#3310](https://github.com/GMOD/jbrowse-components/pull/3310) Remove CacheProvider emotion cache ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - Scott Cain ([@scottcain](https://github.com/scottcain)) ## 2.1.7 (2022-10-20)
Packages in this release

| Package | Download | | ----------------------------------- | ----------------------------------------------------------------- | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |

#### :bug: Bug Fix - [#3282](https://github.com/GMOD/jbrowse-components/pull/3282) Fix for embedded build with webpack 4 failing with v2.1.6 ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) ## 2.1.6 (2022-10-19)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/text-indexing | | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-jobs-management | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-protein | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-text-indexing | | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | jbrowse-predefined-sessions | | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - Other - [#3272](https://github.com/GMOD/jbrowse-components/pull/3272) Disable resolution of Derives_from fields in GFF3 parsing, fixes TAIR gff ([@cmdcolin](https://github.com/cmdcolin)) - [#3254](https://github.com/GMOD/jbrowse-components/pull/3254) Use tick labels that correspond to the overview's larger zoom level ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3230](https://github.com/GMOD/jbrowse-components/pull/3230) Add ability to customize About dialog with callbacks and optionally hide links to data ([@cmdcolin](https://github.com/cmdcolin)) - [#3275](https://github.com/GMOD/jbrowse-components/pull/3275) Add help dialog for feature sequence panel ([@cmdcolin](https://github.com/cmdcolin)) - [#3250](https://github.com/GMOD/jbrowse-components/pull/3250) Handle alternate line endings ([@garrettjstevens](https://github.com/garrettjstevens)) - [#3252](https://github.com/GMOD/jbrowse-components/pull/3252) Fix gene sequence fetching in embedded, and allow fetching genomic sequence for other feature types ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `text-indexing` - [#3276](https://github.com/GMOD/jbrowse-components/pull/3276) Allow using web worker RPC on embedded LGV ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - [#3266](https://github.com/GMOD/jbrowse-components/pull/3266) Fix relative path loading of plugins ([@cmdcolin](https://github.com/cmdcolin)) - [#3269](https://github.com/GMOD/jbrowse-components/pull/3269) Fix ability to rename session in web/desktop ([@cmdcolin](https://github.com/cmdcolin)) - [#3256](https://github.com/GMOD/jbrowse-components/pull/3256) Fix tracks hanging in safari and polyfill for bigwig tracks ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#3274](https://github.com/GMOD/jbrowse-components/pull/3274) Update bbi-js for bugfix on webpack 4 ([@cmdcolin](https://github.com/cmdcolin)) - [#3259](https://github.com/GMOD/jbrowse-components/pull/3259) Fix issue with breakpoint split view using view before initialized ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#3255](https://github.com/GMOD/jbrowse-components/pull/3255) Add more docs about color callbacks ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - [#3261](https://github.com/GMOD/jbrowse-components/pull/3261) Fix for flaky test ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - Scott Cain ([@scottcain](https://github.com/scottcain)) ## 2.1.5 (2022-10-03)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-jobs-management | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-menus | | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - Other - [#3200](https://github.com/GMOD/jbrowse-components/pull/3200) Use Alert component for track messages ([@garrettjstevens](https://github.com/garrettjstevens)) - [#3229](https://github.com/GMOD/jbrowse-components/pull/3229) Allow user to select local assembly to add tracks to for trackhub registry ([@cmdcolin](https://github.com/cmdcolin)) - [#3220](https://github.com/GMOD/jbrowse-components/pull/3220) Improve error reporting on SV inspector/spreadsheet view on import form ([@cmdcolin](https://github.com/cmdcolin)) - [#3198](https://github.com/GMOD/jbrowse-components/pull/3198) Improve error reporting on jbrowse-web start screen when user attempts to open a broken recent session ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - `core` - [#3223](https://github.com/GMOD/jbrowse-components/pull/3223) Allow adding session tracks to embedded react component along with disableAddTracks option if unwanted ([@cmdcolin](https://github.com/cmdcolin)) - [#3227](https://github.com/GMOD/jbrowse-components/pull/3227) Add infrastructure for creating linear-genome-view sub-classes ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - [#3215](https://github.com/GMOD/jbrowse-components/pull/3215) Add error boundary on view, track, and drawer widget ([@cmdcolin](https://github.com/cmdcolin)) - [#3216](https://github.com/GMOD/jbrowse-components/pull/3216) Add ability to set number of bp to fetch up/down stream/inside intron in feature details ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#3241](https://github.com/GMOD/jbrowse-components/pull/3241) Fix local session failing to load copying between tabs in some cases ([@cmdcolin](https://github.com/cmdcolin)) - [#3234](https://github.com/GMOD/jbrowse-components/pull/3234) Fix circular embedded view failing to load in v2.1.3 and v2.1.4 ([@cmdcolin](https://github.com/cmdcolin)) - [#3233](https://github.com/GMOD/jbrowse-components/pull/3233) Fix legend being cutoff on multiwiggle tracks with wide window ([@cmdcolin](https://github.com/cmdcolin)) - [#3217](https://github.com/GMOD/jbrowse-components/pull/3217) Fix loading tracks from connection using assembly alias ([@cmdcolin](https://github.com/cmdcolin)) - [#3214](https://github.com/GMOD/jbrowse-components/pull/3214) Fix trackhub registry failing to load in 2.x.y versions of jbrowse ([@cmdcolin](https://github.com/cmdcolin)) - [#3204](https://github.com/GMOD/jbrowse-components/pull/3204) Fix authentication configuration on jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3231](https://github.com/GMOD/jbrowse-components/pull/3231) Fix theme coloring for components that use overrides e.g. accordion summary ([@garrettjstevens](https://github.com/garrettjstevens)) #### :memo: Documentation - [#3193](https://github.com/GMOD/jbrowse-components/pull/3193) Add desktop specific plugin tutorial ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) #### :house: Internal - Other - [#3243](https://github.com/GMOD/jbrowse-components/pull/3243) Add component test for circular genome view ([@cmdcolin](https://github.com/cmdcolin)) - [#3242](https://github.com/GMOD/jbrowse-components/pull/3242) Fix flaky test in plugins/linear-genome-view ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3228](https://github.com/GMOD/jbrowse-components/pull/3228) Improve TypeScript for queueDialog ([@garrettjstevens](https://github.com/garrettjstevens)) - [#3224](https://github.com/GMOD/jbrowse-components/pull/3224) More typescripting of plain js files ([@cmdcolin](https://github.com/cmdcolin)) - [#3207](https://github.com/GMOD/jbrowse-components/pull/3207) Hardcoded block width of 800px on static blocks ([@cmdcolin](https://github.com/cmdcolin)) - [#3197](https://github.com/GMOD/jbrowse-components/pull/3197) Use "temporaryAssemblies" to store read vs ref assemblies, and allow selecting "sessionAssemblies" in dropdown ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 - Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) ## 2.1.4 (2022-09-16)
Packages in this release

| Package | Download | | ----------------------------------- | ----------------------------------------------------------------- | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |

#### :bug: Bug Fix - [#3191](https://github.com/GMOD/jbrowse-components/pull/3191) Fix the UMD build of the react embedded components ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) ## 2.1.3 (2022-09-15)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - Other - [#3188](https://github.com/GMOD/jbrowse-components/pull/3188) Add 'Open saved session' button to start screen on desktop ([@cmdcolin](https://github.com/cmdcolin)) - [#3187](https://github.com/GMOD/jbrowse-components/pull/3187) Add mouseover tooltip descriptions to the header of the VariantFeatureDetails sample/genotype table ([@cmdcolin](https://github.com/cmdcolin)) - [#3179](https://github.com/GMOD/jbrowse-components/pull/3179) Add extendSession extension point to web and desktop ([@garrettjstevens](https://github.com/garrettjstevens)) - [#3178](https://github.com/GMOD/jbrowse-components/pull/3178) Allow X/Y assemblies of dotplot or top/bottom selection of synteny views to be either query or target ([@cmdcolin](https://github.com/cmdcolin)) - [#3173](https://github.com/GMOD/jbrowse-components/pull/3173) Add ability for CLI to recognize plaintext BED files ([@cmdcolin](https://github.com/cmdcolin)) - [#3162](https://github.com/GMOD/jbrowse-components/pull/3162) Add about dialog with version number for embedded components ([@cmdcolin](https://github.com/cmdcolin)) - [#3163](https://github.com/GMOD/jbrowse-components/pull/3163) Note for user to wait before re-launching app on desktop update ([@cmdcolin](https://github.com/cmdcolin)) - [#3179](https://github.com/GMOD/jbrowse-components/pull/3179) Add extendSession extension point to web and desktop ([@garrettjstevens](https://github.com/garrettjstevens)) - [#3178](https://github.com/GMOD/jbrowse-components/pull/3178) Allow X/Y assemblies of dotplot or top/bottom selection of synteny views to be either query or target ([@cmdcolin](https://github.com/cmdcolin)) - [#3173](https://github.com/GMOD/jbrowse-components/pull/3173) Add ability for CLI to recognize plaintext BED files ([@cmdcolin](https://github.com/cmdcolin)) - [#3162](https://github.com/GMOD/jbrowse-components/pull/3162) Add about dialog with version number for embedded components ([@cmdcolin](https://github.com/cmdcolin)) - [#3163](https://github.com/GMOD/jbrowse-components/pull/3163) Note for user to wait before re-launching app on desktop update ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3180](https://github.com/GMOD/jbrowse-components/pull/3180) Improve adding assemblies internally, and use the assembly displayName in more places in the UI ([@garrettjstevens](https://github.com/garrettjstevens)) - [#3183](https://github.com/GMOD/jbrowse-components/pull/3183) Make pluginManager param to getFetcher optional ([@garrettjstevens](https://github.com/garrettjstevens)) - [#3183](https://github.com/GMOD/jbrowse-components/pull/3183) Make pluginManager param to getFetcher optional ([@garrettjstevens](https://github.com/garrettjstevens)) #### :bug: Bug Fix - `core` - [#3168](https://github.com/GMOD/jbrowse-components/pull/3168) Fix search behavior when there are multiple matches in LGV header and when feature description matched in import form ([@cmdcolin](https://github.com/cmdcolin)) - [#3182](https://github.com/GMOD/jbrowse-components/pull/3182) Fix "dead state tree node" error by creating snapshots of parent region for block calculations ([@cmdcolin](https://github.com/cmdcolin)) - [#3182](https://github.com/GMOD/jbrowse-components/pull/3182) Fix "dead state tree node" error by creating snapshots of parent region for block calculations ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#3170](https://github.com/GMOD/jbrowse-components/pull/3170) Fix drawing inverted CIGAR segments on dotplot ([@cmdcolin](https://github.com/cmdcolin)) - [#3170](https://github.com/GMOD/jbrowse-components/pull/3170) Fix drawing inverted CIGAR segments on dotplot ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#3138](https://github.com/GMOD/jbrowse-components/pull/3138) Documentation overhaul ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - [#3138](https://github.com/GMOD/jbrowse-components/pull/3138) Documentation overhaul ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) #### :house: Internal - Other - [#3179](https://github.com/GMOD/jbrowse-components/pull/3179) Add extendSession extension point to web and desktop ([@garrettjstevens](https://github.com/garrettjstevens)) - [#3179](https://github.com/GMOD/jbrowse-components/pull/3179) Add extendSession extension point to web and desktop ([@garrettjstevens](https://github.com/garrettjstevens)) - [#3165](https://github.com/GMOD/jbrowse-components/pull/3165) Use more defaults in rollup plugins ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - [#3183](https://github.com/GMOD/jbrowse-components/pull/3183) Make pluginManager param to getFetcher optional ([@garrettjstevens](https://github.com/garrettjstevens)) - [#3164](https://github.com/GMOD/jbrowse-components/pull/3164) Typescript the QuickLRU module in @jbrowse/core ([@cmdcolin](https://github.com/cmdcolin)) - [#3183](https://github.com/GMOD/jbrowse-components/pull/3183) Make pluginManager param to getFetcher optional ([@garrettjstevens](https://github.com/garrettjstevens)) - [#3164](https://github.com/GMOD/jbrowse-components/pull/3164) Typescript the QuickLRU module in @jbrowse/core ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 - Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens))
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-jobs-management | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-protein | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-text-indexing | | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

## 2.1.1 (2022-08-25)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-jobs-management | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-protein | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-text-indexing | | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - Other - [#3152](https://github.com/GMOD/jbrowse-components/pull/3152) Render CSQ and ANN fields in VCF feature details as data grids ([@cmdcolin](https://github.com/cmdcolin)) - [#3137](https://github.com/GMOD/jbrowse-components/pull/3137) Make ideogram menu item similar to others ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - [#3159](https://github.com/GMOD/jbrowse-components/pull/3159) Sequence search track ([@cmdcolin](https://github.com/cmdcolin)) - [#3132](https://github.com/GMOD/jbrowse-components/pull/3132) Extend theme with module augmentation ([@garrettjstevens](https://github.com/garrettjstevens)) #### :bug: Bug Fix - Other - [#3157](https://github.com/GMOD/jbrowse-components/pull/3157) Support the "name" field on multi-wiggle adapter subadapters instead of source ([@cmdcolin](https://github.com/cmdcolin)) - [#3154](https://github.com/GMOD/jbrowse-components/pull/3154) Use the union of all the subadapter refNames for the MultiWiggleAdapter getRefNames ([@cmdcolin](https://github.com/cmdcolin)) - [#3156](https://github.com/GMOD/jbrowse-components/pull/3156) Fix for mouseover/mouse click on wiggle/multi-wiggle causing errors in embedded mode ([@cmdcolin](https://github.com/cmdcolin)) - [#3151](https://github.com/GMOD/jbrowse-components/pull/3151) Fix ability to click and drag overview scale bar dragging right to left ([@cmdcolin](https://github.com/cmdcolin)) - [#3133](https://github.com/GMOD/jbrowse-components/pull/3133) Update the ref name box when assembly is changed in LGV import form ([@garrettjstevens](https://github.com/garrettjstevens)) - [#3131](https://github.com/GMOD/jbrowse-components/pull/3131) Use "code" instead of "key" for undo/redo keyboard event, fixes shift+ctrl+z redo ([@garrettjstevens](https://github.com/garrettjstevens)) - [#3119](https://github.com/GMOD/jbrowse-components/pull/3119) Use es2015 setting for commonjs builds of packages to fix @jbrowse/img ([@cmdcolin](https://github.com/cmdcolin)) - [#3142](https://github.com/GMOD/jbrowse-components/pull/3142) Fix unicode arrow icon not rendering with some fonts in configuration editor ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - [#3120](https://github.com/GMOD/jbrowse-components/pull/3120) Fix menu items for changing display type from track menu ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) ## 2.1.0 (2022-07-28)
Packages in this release

| Package | Download | | ------------------------------------ | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-hic | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-menus | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - `core` - [#3111](https://github.com/GMOD/jbrowse-components/pull/3111) Create undo manager in jbrowse-web and jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) - [#3115](https://github.com/GMOD/jbrowse-components/pull/3115) Add warning when dotplot renders outside of it's boundaries, and create click-and-drag panning of dotplot view ([@cmdcolin](https://github.com/cmdcolin)) - [#3102](https://github.com/GMOD/jbrowse-components/pull/3102) Allow creating alternative "add track workflows" from within the "Add track" widget ([@cmdcolin](https://github.com/cmdcolin)) - [#3043](https://github.com/GMOD/jbrowse-components/pull/3043) Create MultiWiggle track type, adapter, and renderers ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#3113](https://github.com/GMOD/jbrowse-components/pull/3113) Improve SVG performance by avoiding re-render when feature is clicked ([@cmdcolin](https://github.com/cmdcolin)) - [#3110](https://github.com/GMOD/jbrowse-components/pull/3110) Remove TSDX from plugin development tools ([@garrettjstevens](https://github.com/garrettjstevens)) - [#3106](https://github.com/GMOD/jbrowse-components/pull/3106) Add "emphasis" mode for no fill/scatterplot mode in XYPlot type renderings ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#3109](https://github.com/GMOD/jbrowse-components/pull/3109) Better support for developing plugins from within yarn 2+ workspaces (include \_\_virtual folder in build) ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - [#3095](https://github.com/GMOD/jbrowse-components/pull/3095) Add MUI exports to re-exports list ([@garrettjstevens](https://github.com/garrettjstevens)) - [#3092](https://github.com/GMOD/jbrowse-components/pull/3092) Fix use of embedded components with vite 3.0 using tsc to compile @jbrowse/core ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#3116](https://github.com/GMOD/jbrowse-components/pull/3116) Add docs for multi-wiggle tracks ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) ## 2.0.1 (2022-07-13)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-jobs-management | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-protein | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-text-indexing | | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - `core` - [#3089](https://github.com/GMOD/jbrowse-components/pull/3089) Clarify error message when adapter has no features ([@garrettjstevens](https://github.com/garrettjstevens)) - [#3084](https://github.com/GMOD/jbrowse-components/pull/3084) Show a descriptive error if an adapter doesn't provide a sequence ([@garrettjstevens](https://github.com/garrettjstevens)) - [#3071](https://github.com/GMOD/jbrowse-components/pull/3071) Add ability to mouseover/click on synteny feature polygons in the linear synteny view ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#3081](https://github.com/GMOD/jbrowse-components/pull/3081) Add ability to toggle gridlines on the LGV ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#3088](https://github.com/GMOD/jbrowse-components/pull/3088) Fix labels being cut-off in SVG features by rendering feature labels on main thread ([@cmdcolin](https://github.com/cmdcolin)) - [#3085](https://github.com/GMOD/jbrowse-components/pull/3085) Fix zoom to behavior being inaccurate with many displayed regions visible ([@cmdcolin](https://github.com/cmdcolin)) - [#3082](https://github.com/GMOD/jbrowse-components/pull/3082) Fix negative strand CIGAR renderings on linear synteny view ([@cmdcolin](https://github.com/cmdcolin)) - [#3077](https://github.com/GMOD/jbrowse-components/pull/3077) Fix crash opening multiple synteny track selectors launched from dotplot view ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3086](https://github.com/GMOD/jbrowse-components/pull/3086) Fix pxToBp and bpToPx calculations when there are many displayed regions ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) ## 2.0.0 (2022-07-07)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/text-indexing | | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-jobs-management | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-protein | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-text-indexing | | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - Other - [#3001](https://github.com/GMOD/jbrowse-components/pull/3001) Draw SNPs in modifications/methylation views ([@cmdcolin](https://github.com/cmdcolin)) - [#3068](https://github.com/GMOD/jbrowse-components/pull/3068) Allow HTML in feature tooltips, remove react-simple-code-editor ([@cmdcolin](https://github.com/cmdcolin)) - [#3065](https://github.com/GMOD/jbrowse-components/pull/3065) Allow changing between xyplot,line,density for linear wiggle tracks and other small fixes ([@cmdcolin](https://github.com/cmdcolin)) - `text-indexing` - [#3058](https://github.com/GMOD/jbrowse-components/pull/3058) Improve bundle size and code splitting on embedded builds (v2) ([@cmdcolin](https://github.com/cmdcolin)) - `__mocks__`, `core`, `text-indexing` - [#2949](https://github.com/GMOD/jbrowse-components/pull/2949) Upgrade to MUI v5, @jbrowse/mobx-state-tree v5, mobx-react v6, mobx-react v7 ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#3072](https://github.com/GMOD/jbrowse-components/pull/3072) Fix the display of inversions for MCScan alignments ([@cmdcolin](https://github.com/cmdcolin)) - [#3057](https://github.com/GMOD/jbrowse-components/pull/3057) Fix export SVG crash on some BigWig tracks ([@cmdcolin](https://github.com/cmdcolin)) - [#3052](https://github.com/GMOD/jbrowse-components/pull/3052) Fix negative value quantitative display in svg exports ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3064](https://github.com/GMOD/jbrowse-components/pull/3064) Fix opening link in new tab by default in feature details ([@cmdcolin](https://github.com/cmdcolin)) - [#3053](https://github.com/GMOD/jbrowse-components/pull/3053) Avoid displaying [object Object] on deeply nested data in base feature details ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - [#3067](https://github.com/GMOD/jbrowse-components/pull/3067) Typescriptify some integration tests ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) ## 1.7.11 (2022-06-22)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/text-indexing | | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-jobs-management | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-protein | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-text-indexing | | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | jbrowse-predefined-sessions | | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - `core` - [#3044](https://github.com/GMOD/jbrowse-components/pull/3044) Remove node-canvas from @jbrowse/core dependencies ([@cmdcolin](https://github.com/cmdcolin)) - [#3041](https://github.com/GMOD/jbrowse-components/pull/3041) Fix ability to search and load data files using lower case refName aliases ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#3042](https://github.com/GMOD/jbrowse-components/pull/3042) Add fetch with proxy support to jbrowse CLI ([@cmdcolin](https://github.com/cmdcolin)) - [#3038](https://github.com/GMOD/jbrowse-components/pull/3038) Display coordinates in overview scalebar when no cytoband available ([@cmdcolin](https://github.com/cmdcolin)) - [#3015](https://github.com/GMOD/jbrowse-components/pull/3015) Add plaintext bed support with BedAdapter ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - [#3049](https://github.com/GMOD/jbrowse-components/pull/3049) Fix ability to use callbacks for the linear arc renderer ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#2831](https://github.com/GMOD/jbrowse-components/pull/2831) Update commands for sorting GFF3 for tabix ([@cmdcolin](https://github.com/cmdcolin)) - [#3018](https://github.com/GMOD/jbrowse-components/pull/3018) Add desktop specific plugin example ([@cmdcolin](https://github.com/cmdcolin)) - [#3022](https://github.com/GMOD/jbrowse-components/pull/3022) Add example using embedded components with next.js ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - [#3035](https://github.com/GMOD/jbrowse-components/pull/3035) Add typescripting to hierarchical track selector ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) ## 1.7.10 (2022-06-13)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | jbrowse-predefined-sessions | | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - Other - [#3025](https://github.com/GMOD/jbrowse-components/pull/3025) Add dotplot session spec ([@cmdcolin](https://github.com/cmdcolin)) - [#2975](https://github.com/GMOD/jbrowse-components/pull/2975) Add simplified URL format for loading synteny views ([@cmdcolin](https://github.com/cmdcolin)) - [#3023](https://github.com/GMOD/jbrowse-components/pull/3023) Add error handling in case of invalid OAuth2 configuration used. ([@andrzejgrzelak](https://github.com/andrzejgrzelak)) - [#3020](https://github.com/GMOD/jbrowse-components/pull/3020) Allow choosing trackId when using text-index with --file with --fileId ([@cmdcolin](https://github.com/cmdcolin)) - [#3016](https://github.com/GMOD/jbrowse-components/pull/3016) Allow whitespace separated refname,start,end type locstring ([@cmdcolin](https://github.com/cmdcolin)) - [#3006](https://github.com/GMOD/jbrowse-components/pull/3006) Add string array configuration slot UI improvements ([@cmdcolin](https://github.com/cmdcolin)) - [#2998](https://github.com/GMOD/jbrowse-components/pull/2998) Avoid rendering offscreen contents in pileup renderer ([@cmdcolin](https://github.com/cmdcolin)) - [#3000](https://github.com/GMOD/jbrowse-components/pull/3000) Add reference base and correct percentage calculations to tooltip on SNPCoverage display ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#2981](https://github.com/GMOD/jbrowse-components/pull/2981) Add simplified URL format for loading spreadsheet and SV inspector ([@cmdcolin](https://github.com/cmdcolin)) - [#2990](https://github.com/GMOD/jbrowse-components/pull/2990) Use shortened megabases (M) display when zoomed out, and option to hide the "open track selector" button ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - [#3003](https://github.com/GMOD/jbrowse-components/pull/3003) Add ability to run field formatters on the feature details panel ([@cmdcolin](https://github.com/cmdcolin)) - [#3017](https://github.com/GMOD/jbrowse-components/pull/3017) Add button to copy track config in About track dialog ([@cmdcolin](https://github.com/cmdcolin)) - [#2999](https://github.com/GMOD/jbrowse-components/pull/2999) Generate clickable links to track data in about track dialog ([@cmdcolin](https://github.com/cmdcolin)) - `__mocks__`, `core` - [#3005](https://github.com/GMOD/jbrowse-components/pull/3005) Use cascading menu helper library for track menu to avoid menu going offscreen ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#3021](https://github.com/GMOD/jbrowse-components/pull/3021) Fix mouseover display of read name to alignments track ([@cmdcolin](https://github.com/cmdcolin)) - [#3012](https://github.com/GMOD/jbrowse-components/pull/3012) Small fix to rankSearchResults logic ([@cmdcolin](https://github.com/cmdcolin)) - [#3009](https://github.com/GMOD/jbrowse-components/pull/3009) Add jsdom to jbrowse-img to fix --noRasterize option ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#3007](https://github.com/GMOD/jbrowse-components/pull/3007) Fix read vs ref dotplot view ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 - Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - [@andrzejgrzelak](https://github.com/andrzejgrzelak) ## 1.7.9 (2022-06-02)
Packages in this release

| Package | Download | | ------------------------------------ | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - `core` - [#2991](https://github.com/GMOD/jbrowse-components/pull/2991) Use canvas2svg for SVG export, fixes non-rasterized usage of bezier, arcs, and more ([@cmdcolin](https://github.com/cmdcolin)) - [#2483](https://github.com/GMOD/jbrowse-components/pull/2483) Add setting to color by query score per alignment for dotplot, support HTML in config slot descriptions ([@cmdcolin](https://github.com/cmdcolin)) - [#2983](https://github.com/GMOD/jbrowse-components/pull/2983) Set target=\_blank by default in user HTML links ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#2994](https://github.com/GMOD/jbrowse-components/pull/2994) Allow choosing filename for svg export ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - [#2989](https://github.com/GMOD/jbrowse-components/pull/2989) Fix bezierCurveTo ponyfill on firefox ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#2977](https://github.com/GMOD/jbrowse-components/pull/2977) Respect --indexFile option when adding VCF and BED tracks ([@heavywatal](https://github.com/heavywatal)) - [#2974](https://github.com/GMOD/jbrowse-components/pull/2974) Fix track indexing being ignored after first add track widget usage ([@teresam856](https://github.com/teresam856)) #### :house: Internal - [#2980](https://github.com/GMOD/jbrowse-components/pull/2980) Remove errors related to test coverage in CI ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 4 - Adam Wright ([@adamjohnwright](https://github.com/adamjohnwright)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Teresa Martinez ([@teresam856](https://github.com/teresam856)) - Watal M. Iwasaki ([@heavywatal](https://github.com/heavywatal)) ## 1.7.8 (2022-05-20)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - [#2970](https://github.com/GMOD/jbrowse-components/pull/2970) Draw indels in modifications/methylation mode ([@cmdcolin](https://github.com/cmdcolin)) - [#2961](https://github.com/GMOD/jbrowse-components/pull/2961) Add more visible pileup mismatches when zoomed out ([@cmdcolin](https://github.com/cmdcolin)) - [#2960](https://github.com/GMOD/jbrowse-components/pull/2960) Avoid performing a text index search if input looks like a locstring ([@cmdcolin](https://github.com/cmdcolin)) - [#2954](https://github.com/GMOD/jbrowse-components/pull/2954) Support in-memory GFF3 and GTF in JBrowse 1 connection ([@garrettjstevens](https://github.com/garrettjstevens)) - [#2947](https://github.com/GMOD/jbrowse-components/pull/2947) Optimization for SNPCoverageAdapter and CRAM parsing ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - [#2969](https://github.com/GMOD/jbrowse-components/pull/2969) Fix link on yeast synteny demo and fix CIGAR rendering on dotplot ([@cmdcolin](https://github.com/cmdcolin)) - [#2964](https://github.com/GMOD/jbrowse-components/pull/2964) Fix crash displaying modifications called on softclipped regions of reads ([@cmdcolin](https://github.com/cmdcolin)) - [#2965](https://github.com/GMOD/jbrowse-components/pull/2965) Fix filter functionality on pileup tracks ([@cmdcolin](https://github.com/cmdcolin)) - [#2953](https://github.com/GMOD/jbrowse-components/pull/2953) Fix "Open" button on LGV ImportForm ([@cmdcolin](https://github.com/cmdcolin)) - [#2952](https://github.com/GMOD/jbrowse-components/pull/2952) Fix read vs ref not finding primary alignment on certain CRAM files ([@cmdcolin](https://github.com/cmdcolin)) - [#2951](https://github.com/GMOD/jbrowse-components/pull/2951) Fix viewing soft/hardclip indicator in some regions ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#2946](https://github.com/GMOD/jbrowse-components/pull/2946) Small doc updates ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - [#2955](https://github.com/GMOD/jbrowse-components/pull/2955) Re-enable eslint autofix for prettier rules ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) ## 1.7.7 (2022-05-04)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :bug: Bug Fix - [#2941](https://github.com/GMOD/jbrowse-components/pull/2941) Fix linear read vs ref hanging in v1.7.5 ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - [#2944](https://github.com/GMOD/jbrowse-components/pull/2944) Avoid stalling on undefined assemblyName during ref name renaming ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) ## 1.7.6 (2022-04-26)
Packages in this release

| Package | Download | | ---------------- | -------- | | @jbrowse/desktop | |

#### :bug: Bug Fix - [#2939](https://github.com/GMOD/jbrowse-components/pull/2939) Fix loading CRAM, TwoBit, and other modules that use @gmod/binary-parser on jbrowse desktop ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) ## 1.7.5 (2022-04-26)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/text-indexing | | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-jobs-management | | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-text-indexing | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - `core` - [#2885](https://github.com/GMOD/jbrowse-components/pull/2885) Reduce serialization overhead on alignments tracks and access feature details asynchronously ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#2935](https://github.com/GMOD/jbrowse-components/pull/2935) Use the name "Read Sequence" for the read vs ref view ([@cmdcolin](https://github.com/cmdcolin)) - [#2916](https://github.com/GMOD/jbrowse-components/pull/2916) Add vite setup to our embedded component demos ([@cmdcolin](https://github.com/cmdcolin)) - [#2927](https://github.com/GMOD/jbrowse-components/pull/2927) Optimize gtf by only parsing lazily per-refName ([@cmdcolin](https://github.com/cmdcolin)) - [#2928](https://github.com/GMOD/jbrowse-components/pull/2928) Add vanillajs/script tag loading embedded components demos ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `text-indexing` - [#2684](https://github.com/GMOD/jbrowse-components/pull/2684) Text-indexing in desktop ([@teresam856](https://github.com/teresam856)) #### :bug: Bug Fix - [#2863](https://github.com/GMOD/jbrowse-components/pull/2863) Render gene with CDS subfeatures properly ([@cmdcolin](https://github.com/cmdcolin)) - [#2934](https://github.com/GMOD/jbrowse-components/pull/2934) Bump @gmod/trix to fix prefix size calculation and searching first word in index ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - Teresa Martinez ([@teresam856](https://github.com/teresam856)) ## 1.7.4 (2022-04-19)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-protein | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :bug: Bug Fix - Other - [#2925](https://github.com/GMOD/jbrowse-components/pull/2925) Fix embedded vanillaJS/script tag usage of embedded components ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#2923](https://github.com/GMOD/jbrowse-components/pull/2923) Add babel/runtime to dependencies ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens))
Packages in this release

| Package | Download | | ----------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

Packages in this release

| Package | Download | | --------------------------------- | --------------------------------------------------------------- | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |

## 1.7.1 (2022-04-15)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-protein | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :bug: Bug Fix - `core` - [#2917](https://github.com/GMOD/jbrowse-components/pull/2917) Create tsconfig.build.json to add types to plugins/embedded components ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#2914](https://github.com/GMOD/jbrowse-components/pull/2914) Manually polyfill fetch in @jbrowse/img ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#2903](https://github.com/GMOD/jbrowse-components/pull/2903) Add download link for jbrowse web on downloads page ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) ## 1.7.0 (2022-04-14)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-protein | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | jbrowse-predefined-sessions | | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - Other - [#2909](https://github.com/GMOD/jbrowse-components/pull/2909) Add --prefixSize flag to @jbrowse/cli text-index ([@cmdcolin](https://github.com/cmdcolin)) - [#2887](https://github.com/GMOD/jbrowse-components/pull/2887) Optimize filtering on alignments tracks ([@cmdcolin](https://github.com/cmdcolin)) - [#2879](https://github.com/GMOD/jbrowse-components/pull/2879) Multi-level synteny rubberband ([@cmdcolin](https://github.com/cmdcolin)) - [#2874](https://github.com/GMOD/jbrowse-components/pull/2874) Optimizations for rendering long syntenic alignments e.g. CHM13 vs GRCh38 ([@cmdcolin](https://github.com/cmdcolin)) - [#2872](https://github.com/GMOD/jbrowse-components/pull/2872) Better connection between paired-end alignments in breakpoint split view and optimizations ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#2902](https://github.com/GMOD/jbrowse-components/pull/2902) Standardize heights of widgets in LGV import form ([@cmdcolin](https://github.com/cmdcolin)) - [#2781](https://github.com/GMOD/jbrowse-components/pull/2781) Add floating labels to SVG features ([@cmdcolin](https://github.com/cmdcolin)) - [#2875](https://github.com/GMOD/jbrowse-components/pull/2875) Make assembly selector remember your last selected assembly ([@cmdcolin](https://github.com/cmdcolin)) - [#2860](https://github.com/GMOD/jbrowse-components/pull/2860) Avoid performing many peekTransferables to optimize RPC serialization ([@rbuels](https://github.com/rbuels)) #### :bug: Bug Fix - Other - [#2908](https://github.com/GMOD/jbrowse-components/pull/2908) Fix AboutDialog under vite for embedded components ([@cmdcolin](https://github.com/cmdcolin)) - [#2900](https://github.com/GMOD/jbrowse-components/pull/2900) Fix the 'Open assembly' menu item in jbrowse desktop ([@cmdcolin](https://github.com/cmdcolin)) - [#2882](https://github.com/GMOD/jbrowse-components/pull/2882) Add padding at the bottom of the configuration editor to help color editing popup being cutoff ([@cmdcolin](https://github.com/cmdcolin)) - [#2877](https://github.com/GMOD/jbrowse-components/pull/2877) Fix strand on arrows in horizontally flipped mode ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#2891](https://github.com/GMOD/jbrowse-components/pull/2891) Use a user-supplied fetchESM callback to import ESM plugins to fix 'Critical dependency...' errors from embedded components ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#2894](https://github.com/GMOD/jbrowse-components/pull/2894) Add create-react-app v5 embedded component demos ([@cmdcolin](https://github.com/cmdcolin)) - [#2830](https://github.com/GMOD/jbrowse-components/pull/2830) Documentation comparing main app with embedded components ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) #### :house: Internal - `core` - [#2904](https://github.com/GMOD/jbrowse-components/pull/2904) Use a user-supplied fetchCJS callback to import CJS plugins ([@cmdcolin](https://github.com/cmdcolin)) - [#2891](https://github.com/GMOD/jbrowse-components/pull/2891) Use a user-supplied fetchESM callback to import ESM plugins to fix 'Critical dependency...' errors from embedded components ([@cmdcolin](https://github.com/cmdcolin)) - [#2857](https://github.com/GMOD/jbrowse-components/pull/2857) Refactor and improve types of OffscreenCanvas shim and ponyfill ([@rbuels](https://github.com/rbuels)) - `__mocks__`, `core` - [#2905](https://github.com/GMOD/jbrowse-components/pull/2905) Use react-use-measure instead of react-use-dimensions ([@cmdcolin](https://github.com/cmdcolin)) - [#2646](https://github.com/GMOD/jbrowse-components/pull/2646) Upgrade repository to use webpack 5/CRA 5 ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 - Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Robert Buels ([@rbuels](https://github.com/rbuels))
Packages in this release

| Package | Download | | ----------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

Packages in this release

| Package | Download | | ----------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

## 1.6.8 (2022-03-25)
Packages in this release

| Package | Download | | ------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - Other - [#2847](https://github.com/GMOD/jbrowse-components/pull/2847) Add option to color all the letters on all the reads to the pileup renderer ([@cmdcolin](https://github.com/cmdcolin)) - [#2849](https://github.com/GMOD/jbrowse-components/pull/2849) Avoid drawing intron subfeatures for gene glyphs ([@cmdcolin](https://github.com/cmdcolin)) - [#2835](https://github.com/GMOD/jbrowse-components/pull/2835) Hide add track and connection menu items when using embedded component ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - [#2836](https://github.com/GMOD/jbrowse-components/pull/2836) Display low-quality modifications in SNPCoverage renderer for MM tag ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#2809](https://github.com/GMOD/jbrowse-components/pull/2809) Optimizations for alignments tracks and BAM parsing ([@cmdcolin](https://github.com/cmdcolin)) - [#2828](https://github.com/GMOD/jbrowse-components/pull/2828) Change calculation for number of webworkers for web/desktop ([@cmdcolin](https://github.com/cmdcolin)) - [#2829](https://github.com/GMOD/jbrowse-components/pull/2829) Allow user to specify number of workers ([@garrettjstevens](https://github.com/garrettjstevens)) - [#2775](https://github.com/GMOD/jbrowse-components/pull/2775) New SVG gene glyph with directional arrows ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#2852](https://github.com/GMOD/jbrowse-components/pull/2852) Fix misaligned features under breakpoint split view ([@cmdcolin](https://github.com/cmdcolin)) - [#2844](https://github.com/GMOD/jbrowse-components/pull/2844) Fix layout of small features without labels for SvgFeatureRenderer ([@cmdcolin](https://github.com/cmdcolin)) - [#2839](https://github.com/GMOD/jbrowse-components/pull/2839) Fix the drawing of SNP height when the SNPCoverage track is using log scale ([@cmdcolin](https://github.com/cmdcolin)) - [#2825](https://github.com/GMOD/jbrowse-components/pull/2825) Fix tracklabels positioning not updating in UI after user selection ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#2841](https://github.com/GMOD/jbrowse-components/pull/2841) Fix alignments tracks loading excessive data on chromosomes where no features exist ([@cmdcolin](https://github.com/cmdcolin)) - [#2829](https://github.com/GMOD/jbrowse-components/pull/2829) Allow user to specify number of workers ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 3 - Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) ## 1.6.7 (2022-03-16)
Packages in this release

| Package | Download | | ------------------------------------ | ----------------------------------------------------------------- | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - [#2820](https://github.com/GMOD/jbrowse-components/pull/2820) Add optimization for BAM and unzip operations ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - [#2821](https://github.com/GMOD/jbrowse-components/pull/2821) Fixup scroll on wiggle tracks with trackLabels->offset ([@cmdcolin](https://github.com/cmdcolin)) - [#2819](https://github.com/GMOD/jbrowse-components/pull/2819) Fix bug in desktop where first track gets stuck loading ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) ## 1.6.6 (2022-03-15)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/development-tools | https://www.npmjs.com/package/@jbrowse/development-tools | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-protein | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | jbrowse-predefined-sessions | | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - `core` - [#2796](https://github.com/GMOD/jbrowse-components/pull/2796) Add collapsible accordion sections in configuration editor ([@cmdcolin](https://github.com/cmdcolin)) - [#2791](https://github.com/GMOD/jbrowse-components/pull/2791) Add new coloring options for dotplot and ability to "rectangularize" dotplot view ([@cmdcolin](https://github.com/cmdcolin)) - [#2741](https://github.com/GMOD/jbrowse-components/pull/2741) Allow ability to enter a space-separated locstring to open a list of regions ([@cmdcolin](https://github.com/cmdcolin)) - [#2725](https://github.com/GMOD/jbrowse-components/pull/2725) Refactor InternetAccounts, add standard getFetcher ([@garrettjstevens](https://github.com/garrettjstevens)) - [#2787](https://github.com/GMOD/jbrowse-components/pull/2787) Display the total bp viewed in the header of the dotplot view ([@cmdcolin](https://github.com/cmdcolin)) - [#2767](https://github.com/GMOD/jbrowse-components/pull/2767) Wiggle and SNPCoverage look and feel improvements ([@cmdcolin](https://github.com/cmdcolin)) - [#2746](https://github.com/GMOD/jbrowse-components/pull/2746) Add .delta and .chain format adapters, fix ref name aliasing in synteny/dotplot views, and optimize very long CIGAR string in synteny view ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#2799](https://github.com/GMOD/jbrowse-components/pull/2799) Exit process after rendering to speed up jb2export ([@cmdcolin](https://github.com/cmdcolin)) - [#2793](https://github.com/GMOD/jbrowse-components/pull/2793) Add abortcontroller polyfill to jbrowse-img to allow it to run under node 14 ([@cmdcolin](https://github.com/cmdcolin)) - [#2761](https://github.com/GMOD/jbrowse-components/pull/2761) Add a --clean argument to `jbrowse upgrade` to clean up old files ([@cmdcolin](https://github.com/cmdcolin)) - [#2760](https://github.com/GMOD/jbrowse-components/pull/2760) Make a configurable refNameColumn in RefNameAliasAdapter ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - [#2798](https://github.com/GMOD/jbrowse-components/pull/2798) Fix bug where web worker would sometimes be called before it was ready ([@garrettjstevens](https://github.com/garrettjstevens)) - Other - [#2797](https://github.com/GMOD/jbrowse-components/pull/2797) Fix crash plotting methylation in sparse regions ([@cmdcolin](https://github.com/cmdcolin)) - [#2782](https://github.com/GMOD/jbrowse-components/pull/2782) Fix display of cytobands when horizontally flipped ([@cmdcolin](https://github.com/cmdcolin)) - [#2678](https://github.com/GMOD/jbrowse-components/pull/2678) Preserve double border line when using trackLabel offset and use smaller gap between snpcoverage and reads ([@cmdcolin](https://github.com/cmdcolin)) - [#2774](https://github.com/GMOD/jbrowse-components/pull/2774) Fix overwriting broken symlink with --force in add-track CLI ([@cmdcolin](https://github.com/cmdcolin)) - [#2773](https://github.com/GMOD/jbrowse-components/pull/2773) Fix using global stats autoscale on wiggle tracks ([@cmdcolin](https://github.com/cmdcolin)) - [#2766](https://github.com/GMOD/jbrowse-components/pull/2766) Add a check for empty content blocks to fix rare empty stats estimation ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#2804](https://github.com/GMOD/jbrowse-components/pull/2804) Add note about additional pre-requisites to README ([@cmdcolin](https://github.com/cmdcolin)) - [#2762](https://github.com/GMOD/jbrowse-components/pull/2762) Add bookmark widget docs to user guide ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - [#2813](https://github.com/GMOD/jbrowse-components/pull/2813) Create codeVerifierPKCE only when needed ([@garrettjstevens](https://github.com/garrettjstevens)) - [#2808](https://github.com/GMOD/jbrowse-components/pull/2808) Polyfill window.crypto.getRandomValues in tests ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) ## 1.6.5 (2022-02-18)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-hic | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - [#2736](https://github.com/GMOD/jbrowse-components/pull/2736) Add better display of error state in dotplot view and load gzipped PAF files ([@cmdcolin](https://github.com/cmdcolin)) - [#2705](https://github.com/GMOD/jbrowse-components/pull/2705) Increase admin-server payload limit ([@garrettjstevens](https://github.com/garrettjstevens)) #### :bug: Bug Fix - Other - [#2758](https://github.com/GMOD/jbrowse-components/pull/2758) Use VariantTrack for plaintext VCF type ([@cmdcolin](https://github.com/cmdcolin)) - [#2738](https://github.com/GMOD/jbrowse-components/pull/2738) Add better catch for XS and TS tag detection from CRAM ([@cmdcolin](https://github.com/cmdcolin)) - [#2733](https://github.com/GMOD/jbrowse-components/pull/2733) Use sparse array for alignments coverage to fix bug viewing large sparse regions ([@cmdcolin](https://github.com/cmdcolin)) - [#2734](https://github.com/GMOD/jbrowse-components/pull/2734) Use node fetch instead of follow-redirects in cli ([@cmdcolin](https://github.com/cmdcolin)) - [#2726](https://github.com/GMOD/jbrowse-components/pull/2726) Handle .bgz file extension for text-index ([@cmdcolin](https://github.com/cmdcolin)) - [#2727](https://github.com/GMOD/jbrowse-components/pull/2727) Add engines 16 to @jbrowse/img ([@cmdcolin](https://github.com/cmdcolin)) - [#2723](https://github.com/GMOD/jbrowse-components/pull/2723) Make jbrowse desktop more robust to errors when reading recent sessions file ([@cmdcolin](https://github.com/cmdcolin)) - [#2715](https://github.com/GMOD/jbrowse-components/pull/2715) Change --target to --root for jbrowse CLI admin-server ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#2757](https://github.com/GMOD/jbrowse-components/pull/2757) Fix type confusion with stats estimation causing BAM files to fail byte size calculation ([@cmdcolin](https://github.com/cmdcolin)) - [#2750](https://github.com/GMOD/jbrowse-components/pull/2750) Add bezierCurveTo to offscreen canvas ponyfill to fix sashimi arcs rendering in alignments track in webkit and firefox ([@cmdcolin](https://github.com/cmdcolin)) - [#2719](https://github.com/GMOD/jbrowse-components/pull/2719) Avoid uninitialized state during stats estimation ([@cmdcolin](https://github.com/cmdcolin)) - [#2707](https://github.com/GMOD/jbrowse-components/pull/2707) Fix ability to use authenticated assembly files ([@garrettjstevens](https://github.com/garrettjstevens)) - [#2695](https://github.com/GMOD/jbrowse-components/pull/2695) Fix disabled state on the linear genome view track labels dropdown menu ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#2716](https://github.com/GMOD/jbrowse-components/pull/2716) Update to node12 requirement for @jbrowse/cli ([@cmdcolin](https://github.com/cmdcolin)) - [#2605](https://github.com/GMOD/jbrowse-components/pull/2605) Developer guide reorganization and create new API document ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - [#2664](https://github.com/GMOD/jbrowse-components/pull/2664) Use babel config from core in root ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 3 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - Sebastian Benjamin ([@hextraza](https://github.com/hextraza))
Packages in this release

| Package | Download | | ----------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

Packages in this release

| Package | Download | | ------------ | ------------------------------------------ | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli |

Packages in this release

| Package | Download | | ----------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

Packages in this release

| Package | Download | | ----------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

## 1.6.0 (2022-01-28)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - `core` - [#2679](https://github.com/GMOD/jbrowse-components/pull/2679) Optimizations and usability improvements to synteny view ([@cmdcolin](https://github.com/cmdcolin)) - [#2677](https://github.com/GMOD/jbrowse-components/pull/2677) Save user settings from LGV ([@cmdcolin](https://github.com/cmdcolin)) - [#2571](https://github.com/GMOD/jbrowse-components/pull/2571) Add stats estimation to JB2 ([@cmdcolin](https://github.com/cmdcolin)) - [#2666](https://github.com/GMOD/jbrowse-components/pull/2666) Add option to display curved lines and to square the dotplot and synteny views ([@cmdcolin](https://github.com/cmdcolin)) - [#2672](https://github.com/GMOD/jbrowse-components/pull/2672) Optimize dot plot rendering ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#2680](https://github.com/GMOD/jbrowse-components/pull/2680) Improve error handling on jbrowse desktop open sequence dialog ([@cmdcolin](https://github.com/cmdcolin)) - [#2670](https://github.com/GMOD/jbrowse-components/pull/2670) Add mashmap PAF support ([@cmdcolin](https://github.com/cmdcolin)) - [#2659](https://github.com/GMOD/jbrowse-components/pull/2659) Draw size of deletion on reads in alignments track ([@cmdcolin](https://github.com/cmdcolin)) - `__mocks__`, `core` - [#2165](https://github.com/GMOD/jbrowse-components/pull/2165) Add ability to create new sessions solely from a "session spec" in the URL ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - [#2688](https://github.com/GMOD/jbrowse-components/pull/2688) Fix adapterType dropdown in add track widget ([@cmdcolin](https://github.com/cmdcolin)) - [#2654](https://github.com/GMOD/jbrowse-components/pull/2654) Fix broken @jbrowse/img by adding babel config back to core ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#2686](https://github.com/GMOD/jbrowse-components/pull/2686) Use path.resolve to fix --load symlink in jbrowse CLI ([@cmdcolin](https://github.com/cmdcolin)) - [#2660](https://github.com/GMOD/jbrowse-components/pull/2660) Fix custom glyphs to apply to features without subfeatures ([@bbimber](https://github.com/bbimber)) - [#2652](https://github.com/GMOD/jbrowse-components/pull/2652) Fix "module" of embedded React views ([@garrettjstevens](https://github.com/garrettjstevens)) #### :memo: Documentation - [#2663](https://github.com/GMOD/jbrowse-components/pull/2663) Add documentation for URL params and session spec ([@cmdcolin](https://github.com/cmdcolin)) - [#2655](https://github.com/GMOD/jbrowse-components/pull/2655) Add link to PAG 2022 youtube tutorial on demos page and course archive ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - [#2649](https://github.com/GMOD/jbrowse-components/pull/2649) Add Cypress test of package that uses embedded components ([@garrettjstevens](https://github.com/garrettjstevens)) - [#2648](https://github.com/GMOD/jbrowse-components/pull/2648) Avoid console.warns in tests due to writing to MST nodes that are not alive ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#2657](https://github.com/GMOD/jbrowse-components/pull/2657) Fix hot reload using yarn resolution on react-error-overlay ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - [@bbimber](https://github.com/bbimber) ## 1.6.0 (2022-01-28)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - `core` - [#2679](https://github.com/GMOD/jbrowse-components/pull/2679) Optimizations and usability improvements to synteny view ([@cmdcolin](https://github.com/cmdcolin)) - [#2677](https://github.com/GMOD/jbrowse-components/pull/2677) Save user settings from LGV ([@cmdcolin](https://github.com/cmdcolin)) - [#2571](https://github.com/GMOD/jbrowse-components/pull/2571) Add stats estimation to JB2 ([@cmdcolin](https://github.com/cmdcolin)) - [#2666](https://github.com/GMOD/jbrowse-components/pull/2666) Add option to display curved lines and to square the dotplot and synteny views ([@cmdcolin](https://github.com/cmdcolin)) - [#2672](https://github.com/GMOD/jbrowse-components/pull/2672) Optimize dot plot rendering ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#2680](https://github.com/GMOD/jbrowse-components/pull/2680) Improve error handling on jbrowse desktop open sequence dialog ([@cmdcolin](https://github.com/cmdcolin)) - [#2670](https://github.com/GMOD/jbrowse-components/pull/2670) Add mashmap PAF support ([@cmdcolin](https://github.com/cmdcolin)) - [#2659](https://github.com/GMOD/jbrowse-components/pull/2659) Draw size of deletion on reads in alignments track ([@cmdcolin](https://github.com/cmdcolin)) - `__mocks__`, `core` - [#2165](https://github.com/GMOD/jbrowse-components/pull/2165) Add ability to create new sessions solely from a "session spec" in the URL ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - [#2688](https://github.com/GMOD/jbrowse-components/pull/2688) Fix adapterType dropdown in add track widget ([@cmdcolin](https://github.com/cmdcolin)) - [#2654](https://github.com/GMOD/jbrowse-components/pull/2654) Fix broken @jbrowse/img by adding babel config back to core ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#2686](https://github.com/GMOD/jbrowse-components/pull/2686) Use path.resolve to fix --load symlink in jbrowse CLI ([@cmdcolin](https://github.com/cmdcolin)) - [#2660](https://github.com/GMOD/jbrowse-components/pull/2660) Fix custom glyphs to apply to features without subfeatures ([@bbimber](https://github.com/bbimber)) - [#2652](https://github.com/GMOD/jbrowse-components/pull/2652) Fix "module" of embedded React views ([@garrettjstevens](https://github.com/garrettjstevens)) #### :memo: Documentation - [#2663](https://github.com/GMOD/jbrowse-components/pull/2663) Add documentation for URL params and session spec ([@cmdcolin](https://github.com/cmdcolin)) - [#2655](https://github.com/GMOD/jbrowse-components/pull/2655) Add link to PAG 2022 youtube tutorial on demos page and course archive ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - [#2649](https://github.com/GMOD/jbrowse-components/pull/2649) Add Cypress test of package that uses embedded components ([@garrettjstevens](https://github.com/garrettjstevens)) - [#2648](https://github.com/GMOD/jbrowse-components/pull/2648) Avoid console.warns in tests due to writing to MST nodes that are not alive ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#2657](https://github.com/GMOD/jbrowse-components/pull/2657) Fix hot reload using yarn resolution on react-error-overlay ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - [@bbimber](https://github.com/bbimber) ## 1.6.0 (2022-01-28)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - `core` - [#2679](https://github.com/GMOD/jbrowse-components/pull/2679) Optimizations and usability improvements to synteny view ([@cmdcolin](https://github.com/cmdcolin)) - [#2677](https://github.com/GMOD/jbrowse-components/pull/2677) Save user settings from LGV ([@cmdcolin](https://github.com/cmdcolin)) - [#2571](https://github.com/GMOD/jbrowse-components/pull/2571) Add stats estimation to JB2 ([@cmdcolin](https://github.com/cmdcolin)) - [#2666](https://github.com/GMOD/jbrowse-components/pull/2666) Add option to display curved lines and to square the dotplot and synteny views ([@cmdcolin](https://github.com/cmdcolin)) - [#2672](https://github.com/GMOD/jbrowse-components/pull/2672) Optimize dot plot rendering ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#2680](https://github.com/GMOD/jbrowse-components/pull/2680) Improve error handling on jbrowse desktop open sequence dialog ([@cmdcolin](https://github.com/cmdcolin)) - [#2670](https://github.com/GMOD/jbrowse-components/pull/2670) Add mashmap PAF support ([@cmdcolin](https://github.com/cmdcolin)) - [#2659](https://github.com/GMOD/jbrowse-components/pull/2659) Draw size of deletion on reads in alignments track ([@cmdcolin](https://github.com/cmdcolin)) - `__mocks__`, `core` - [#2165](https://github.com/GMOD/jbrowse-components/pull/2165) Add ability to create new sessions solely from a "session spec" in the URL ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - [#2688](https://github.com/GMOD/jbrowse-components/pull/2688) Fix adapterType dropdown in add track widget ([@cmdcolin](https://github.com/cmdcolin)) - [#2654](https://github.com/GMOD/jbrowse-components/pull/2654) Fix broken @jbrowse/img by adding babel config back to core ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#2686](https://github.com/GMOD/jbrowse-components/pull/2686) Use path.resolve to fix --load symlink in jbrowse CLI ([@cmdcolin](https://github.com/cmdcolin)) - [#2660](https://github.com/GMOD/jbrowse-components/pull/2660) Fix custom glyphs to apply to features without subfeatures ([@bbimber](https://github.com/bbimber)) - [#2652](https://github.com/GMOD/jbrowse-components/pull/2652) Fix "module" of embedded React views ([@garrettjstevens](https://github.com/garrettjstevens)) #### :memo: Documentation - [#2663](https://github.com/GMOD/jbrowse-components/pull/2663) Add documentation for URL params and session spec ([@cmdcolin](https://github.com/cmdcolin)) - [#2655](https://github.com/GMOD/jbrowse-components/pull/2655) Add link to PAG 2022 youtube tutorial on demos page and course archive ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - [#2649](https://github.com/GMOD/jbrowse-components/pull/2649) Add Cypress test of package that uses embedded components ([@garrettjstevens](https://github.com/garrettjstevens)) - [#2648](https://github.com/GMOD/jbrowse-components/pull/2648) Avoid console.warns in tests due to writing to MST nodes that are not alive ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#2657](https://github.com/GMOD/jbrowse-components/pull/2657) Fix hot reload using yarn resolution on react-error-overlay ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - [@bbimber](https://github.com/bbimber) ## 1.5.9 (2022-01-13)
Packages in this release

| Package | Download | | ----------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :bug: Bug Fix - [#2645](https://github.com/GMOD/jbrowse-components/pull/2645) Fix core by not using absolute runtime in babel ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 1 - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens))
Packages in this release

| Package | Download | | ----------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

## 1.5.7 (2022-01-13)
Packages in this release

| Package | Download | | ---------------------------- | -------- | | @jbrowse/plugin-dotplot-view | | | @jbrowse/desktop | | | @jbrowse/web | |

#### :rocket: Enhancement - [#2632](https://github.com/GMOD/jbrowse-components/pull/2632) Add vertical resize handle to dotplot view ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) ## 1.5.6 (2022-01-12)
Packages in this release

| Package | Download | | ----------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - `core` - [#2629](https://github.com/GMOD/jbrowse-components/pull/2629) Add ability to get parent feature in jexl syntax with either parent(feature) or get(feature,'parent') ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Teresa Martinez ([@teresam856](https://github.com/teresam856))
Packages in this release

| Package | Download | | ----------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

## 1.5.4 (2022-01-07)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/development-tools | https://www.npmjs.com/package/@jbrowse/development-tools | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - Other - [#2601](https://github.com/GMOD/jbrowse-components/pull/2601) Allow opening multiple sequences from the desktop start screen ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#2623](https://github.com/GMOD/jbrowse-components/pull/2623) Adjust label width on base feature detail to enforce better alignment ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) #### :bug: Bug Fix - Other - [#2612](https://github.com/GMOD/jbrowse-components/pull/2612) Fix ability to remove plugins ([@cmdcolin](https://github.com/cmdcolin)) - [#2622](https://github.com/GMOD/jbrowse-components/pull/2622) Fix GUI color editor rgba string format ([@garrettjstevens](https://github.com/garrettjstevens)) - [#2607](https://github.com/GMOD/jbrowse-components/pull/2607) Fix wiggle tooltip crash on non-numerical inputs ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#2626](https://github.com/GMOD/jbrowse-components/pull/2626) Fix bad layout resulting in features being unable to be clicked in embedded mode ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - [#2595](https://github.com/GMOD/jbrowse-components/pull/2595) Use some newly available TypeScript types ([@garrettjstevens](https://github.com/garrettjstevens)) - [#2576](https://github.com/GMOD/jbrowse-components/pull/2576) Use TypeScript parameter properties ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 3 - Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) ## 1.5.3 (2021-12-21)
Packages in this release

| Package | Download | | -------------------------- | -------------------------------------------------------- | | @jbrowse/development-tools | https://www.npmjs.com/package/@jbrowse/development-tools |

#### :bug: Bug Fix - `development-tools` - [#2600](https://github.com/GMOD/jbrowse-components/pull/2600) Fix broken published build of jbrowse/development-tools ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 1 - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) ## 1.5.2 (2021-12-20)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/development-tools | https://www.npmjs.com/package/@jbrowse/development-tools | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-menus | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - Other - [#2579](https://github.com/GMOD/jbrowse-components/pull/2579) Add help text and help dialog for the RefNameAutocomplete ([@cmdcolin](https://github.com/cmdcolin)) - [#2553](https://github.com/GMOD/jbrowse-components/pull/2553) Add sashimi-style arcs for RNA-seq type skips on SNPCoverage display ([@cmdcolin](https://github.com/cmdcolin)) - [#2552](https://github.com/GMOD/jbrowse-components/pull/2552) Change border on non-cytoband OverviewScaleBar visible region back to blue and cytoband OverviewScaleBar to a little lighter fill ([@cmdcolin](https://github.com/cmdcolin)) - [#2509](https://github.com/GMOD/jbrowse-components/pull/2509) Implement prop interface for providing arbitrary user-defined glyphs to SvgFeatureRenderer ([@hextraza](https://github.com/hextraza)) - [#2485](https://github.com/GMOD/jbrowse-components/pull/2485) Only use one button, "Go", in text search ambiguous results dialog ([@cmdcolin](https://github.com/cmdcolin)) - [#2501](https://github.com/GMOD/jbrowse-components/pull/2501) Add a tooltip to desktop session path so you can see the full path if it's cut off ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - [#2580](https://github.com/GMOD/jbrowse-components/pull/2580) Make core snackbar notifications module with auto-dismissing info/success level notifications ([@cmdcolin](https://github.com/cmdcolin)) - [#2534](https://github.com/GMOD/jbrowse-components/pull/2534) New display type for drawing arcs ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - [#2590](https://github.com/GMOD/jbrowse-components/pull/2590) Add more exports that can be used by plugins ([@garrettjstevens](https://github.com/garrettjstevens)) - [#2578](https://github.com/GMOD/jbrowse-components/pull/2578) Add layouts code to core re-exports ([@garrettjstevens](https://github.com/garrettjstevens)) - [#2523](https://github.com/GMOD/jbrowse-components/pull/2523) Performance optimizations for alignments tracks, particularly those with many short reads ([@cmdcolin](https://github.com/cmdcolin)) - [#2500](https://github.com/GMOD/jbrowse-components/pull/2500) Add RenderProps to core/pluggableElementTypes export ([@garrettjstevens](https://github.com/garrettjstevens)) - `core`, `development-tools` - [#2487](https://github.com/GMOD/jbrowse-components/pull/2487) Add support for additional types of plugin formats (commonjs, esm) to allow access to node modules on jbrowse desktop ([@garrettjstevens](https://github.com/garrettjstevens)) #### :bug: Bug Fix - Other - [#2594](https://github.com/GMOD/jbrowse-components/pull/2594) Fix infinite loop bug while searching certain strings and handle multi-word searches better ([@cmdcolin](https://github.com/cmdcolin)) - [#2589](https://github.com/GMOD/jbrowse-components/pull/2589) Fix occasional failures observed from running text-index command ([@cmdcolin](https://github.com/cmdcolin)) - [#2583](https://github.com/GMOD/jbrowse-components/pull/2583) Fix for alignments track base modifications display regarding skipped bases on Mm tag ([@cmdcolin](https://github.com/cmdcolin)) - [#2556](https://github.com/GMOD/jbrowse-components/pull/2556) Fix ability to access BigWig tracks on http basic auth for some cases ([@cmdcolin](https://github.com/cmdcolin)) - [#2577](https://github.com/GMOD/jbrowse-components/pull/2577) Fix ability to use --indexFile on VCF/GFF tabix and CRAM files and add plaintext VCF, GFF, GTF support to add-track CLI ([@cmdcolin](https://github.com/cmdcolin)) - [#2521](https://github.com/GMOD/jbrowse-components/pull/2521) Fix ability to search for tracks with parentheses in tracklist ([@cmdcolin](https://github.com/cmdcolin)) - [#2512](https://github.com/GMOD/jbrowse-components/pull/2512) Fix [object Window] issue in alignment read vs reference dialog ([@cmdcolin](https://github.com/cmdcolin)) - [#2499](https://github.com/GMOD/jbrowse-components/pull/2499) Add missing dependency to CLI ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - [#2585](https://github.com/GMOD/jbrowse-components/pull/2585) Fix ability to use "Color by methylation" on files that require refname renaming ([@cmdcolin](https://github.com/cmdcolin)) - [#2517](https://github.com/GMOD/jbrowse-components/pull/2517) Remove aborting on adapter loading process to fix some tracks getting stuck in infinite loading state ([@cmdcolin](https://github.com/cmdcolin)) - [#2564](https://github.com/GMOD/jbrowse-components/pull/2564) Start looking for parents with parent, not self in findParentThat ([@garrettjstevens](https://github.com/garrettjstevens)) - [#2563](https://github.com/GMOD/jbrowse-components/pull/2563) Restore ability to load plugins from relative URL ([@garrettjstevens](https://github.com/garrettjstevens)) - [#2533](https://github.com/GMOD/jbrowse-components/pull/2533) Fix drawer widget minimized button being unclickable when overlapping with a view ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#2522](https://github.com/GMOD/jbrowse-components/pull/2522) Add circular genome view storybook ([@cmdcolin](https://github.com/cmdcolin)) - [#2508](https://github.com/GMOD/jbrowse-components/pull/2508) Update docs for embedded components ([@teresam856](https://github.com/teresam856)) - [#2495](https://github.com/GMOD/jbrowse-components/pull/2495) Improve organization on docs landing page ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - [#2597](https://github.com/GMOD/jbrowse-components/pull/2597) Fix flaky tests related to auth and canvas image snapshots ([@cmdcolin](https://github.com/cmdcolin)) - [#2504](https://github.com/GMOD/jbrowse-components/pull/2504) Spreadsheet change jbrequire to es6 imports ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 6 - Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - Peter Xie ([@peterkxie](https://github.com/peterkxie)) - Sebastian Benjamin ([@hextraza](https://github.com/hextraza)) - Teresa Martinez ([@teresam856](https://github.com/teresam856)) ## 1.5.1 (2021-11-04)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | jbrowse-predefined-sessions | | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - `core` - [#2488](https://github.com/GMOD/jbrowse-components/pull/2488) Improve usability of the search result autocomplete when typing in via keyboard ([@cmdcolin](https://github.com/cmdcolin)) - [#2267](https://github.com/GMOD/jbrowse-components/pull/2267) Add cytoband to overview scale bar in LGV ([@cmdcolin](https://github.com/cmdcolin)) - [#2447](https://github.com/GMOD/jbrowse-components/pull/2447) Drawer widget tooltips and use position: fixed on fab ([@cmdcolin](https://github.com/cmdcolin)) - [#2299](https://github.com/GMOD/jbrowse-components/pull/2299) Add new pluggable element type and properties to adapter type for registering adapter association with 'add track' workflow ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Other - [#2484](https://github.com/GMOD/jbrowse-components/pull/2484) "Add custom plugin" dialog improvements ([@cmdcolin](https://github.com/cmdcolin)) - [#2389](https://github.com/GMOD/jbrowse-components/pull/2389) Create plaintext GtfAdapter in plugins/gtf ([@teresam856](https://github.com/teresam856)) - [#2443](https://github.com/GMOD/jbrowse-components/pull/2443) Support plaintext fasta on desktop by dynamically creating a FAI file on the fly ([@cmdcolin](https://github.com/cmdcolin)) - [#2479](https://github.com/GMOD/jbrowse-components/pull/2479) Allow gzipped Gff3Adapter input and use 512MB limit ([@cmdcolin](https://github.com/cmdcolin)) - [#2467](https://github.com/GMOD/jbrowse-components/pull/2467) Set default session dialog redesign ([@cmdcolin](https://github.com/cmdcolin)) - [#2461](https://github.com/GMOD/jbrowse-components/pull/2461) Add assembly manager back into tools menu on jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) - [#2442](https://github.com/GMOD/jbrowse-components/pull/2442) Add simple loading screen for LGV ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#2494](https://github.com/GMOD/jbrowse-components/pull/2494) Add polyfill for text-index compatibility with node 10 ([@cmdcolin](https://github.com/cmdcolin)) - [#2492](https://github.com/GMOD/jbrowse-components/pull/2492) Fix ability to open breakpoint split view from a BEDPE row in SV inspector ([@cmdcolin](https://github.com/cmdcolin)) - [#2480](https://github.com/GMOD/jbrowse-components/pull/2480) Fix refName renaming on VcfAdapter for files that don't have ##contig lines ([@cmdcolin](https://github.com/cmdcolin)) - [#2469](https://github.com/GMOD/jbrowse-components/pull/2469) Fix embedded crash when opening dialogs ([@garrettjstevens](https://github.com/garrettjstevens)) - [#2451](https://github.com/GMOD/jbrowse-components/pull/2451) Fix issue with intermittent text-index failures and improve speed ([@cmdcolin](https://github.com/cmdcolin)) - [#2439](https://github.com/GMOD/jbrowse-components/pull/2439) Fix adding plugins on desktop ([@cmdcolin](https://github.com/cmdcolin)) - [#2426](https://github.com/GMOD/jbrowse-components/pull/2426) Fix CLI create/upgrade failing to find the latest release ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#2457](https://github.com/GMOD/jbrowse-components/pull/2457) Fix linear synteny view import form failure ([@cmdcolin](https://github.com/cmdcolin)) - [#2444](https://github.com/GMOD/jbrowse-components/pull/2444) Fix crash when chromSizesLocation not specified when loading TwoBitAdapter in GUI ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#2446](https://github.com/GMOD/jbrowse-components/pull/2446) Improve some CLI --help messages ([@cmdcolin](https://github.com/cmdcolin)) - [#2437](https://github.com/GMOD/jbrowse-components/pull/2437) Add example of defining and using a plugin with the embedded component ([@cmdcolin](https://github.com/cmdcolin)) - [#2430](https://github.com/GMOD/jbrowse-components/pull/2430) Website optimize for less layout shift ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - [#2445](https://github.com/GMOD/jbrowse-components/pull/2445) Create core snapshot error message component ([@cmdcolin](https://github.com/cmdcolin)) - [#2288](https://github.com/GMOD/jbrowse-components/pull/2288) Add extra re-exports for default modules ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 4 - Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - Teresa Martinez ([@teresam856](https://github.com/teresam856)) ## 1.5.0 (2021-10-18)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-hic | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | jbrowse-predefined-sessions | | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - `core` - [#2413](https://github.com/GMOD/jbrowse-components/pull/2413) Bundle size savings ([@cmdcolin](https://github.com/cmdcolin)) - [#2390](https://github.com/GMOD/jbrowse-components/pull/2390) Support plain text (non-tabix'ed) GFF files with new Gff3Adapter ([@teresam856](https://github.com/teresam856)) - [#2384](https://github.com/GMOD/jbrowse-components/pull/2384) Allow docking the drawer on the left side of the screen ([@cmdcolin](https://github.com/cmdcolin)) - [#2387](https://github.com/GMOD/jbrowse-components/pull/2387) Add bulk delete of sessions on jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) - [#2279](https://github.com/GMOD/jbrowse-components/pull/2279) Add ability to access authenticated resources using pluggable internet accounts framework ([@peterkxie](https://github.com/peterkxie)) - Other - [#2388](https://github.com/GMOD/jbrowse-components/pull/2388) Create "quickstart list" on jbrowse-desktop which users can add to ([@cmdcolin](https://github.com/cmdcolin)) - [#2385](https://github.com/GMOD/jbrowse-components/pull/2385) Ensure all dependencies are properly specified in package.json files using eslint-plugin-import ([@cmdcolin](https://github.com/cmdcolin)) - [#2373](https://github.com/GMOD/jbrowse-components/pull/2373) Add auto update functionality for jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) - [#2369](https://github.com/GMOD/jbrowse-components/pull/2369) Add tooltip with track description to track selector ([@garrettjstevens](https://github.com/garrettjstevens)) - [#2258](https://github.com/GMOD/jbrowse-components/pull/2258) Update admin-server to accept value from ?config= so that multiple configs could be edited ([@cmdcolin](https://github.com/cmdcolin)) - [#2321](https://github.com/GMOD/jbrowse-components/pull/2321) Add show descriptions toggle box to most feature tracks ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#2355](https://github.com/GMOD/jbrowse-components/pull/2355) Allow prefix and exact matches jb1 text search ([@cmdcolin](https://github.com/cmdcolin)) - [#2348](https://github.com/GMOD/jbrowse-components/pull/2348) Fix ability to use JB1 backcompat text search adapter ([@teresam856](https://github.com/teresam856)) - [#2322](https://github.com/GMOD/jbrowse-components/pull/2322) Fix install plugin workflow and error handling on desktop, update to electron 15 ([@cmdcolin](https://github.com/cmdcolin)) - [#2329](https://github.com/GMOD/jbrowse-components/pull/2329) Fix bugs preventing embedded circular genome view from rendering in some circumstances ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - [#2352](https://github.com/GMOD/jbrowse-components/pull/2352) Better keyboard navigations on text search autocomplete component ([@cmdcolin](https://github.com/cmdcolin)) - [#2332](https://github.com/GMOD/jbrowse-components/pull/2332) Fix ability to use LocalFile on nodejs-based apps e.g. @jbrowse/img ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#2407](https://github.com/GMOD/jbrowse-components/pull/2407) Update website for jbrowse-desktop release ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - [#2328](https://github.com/GMOD/jbrowse-components/pull/2328) Use ../ for all doc links and use trailing slash to fix links ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - Other - [#2382](https://github.com/GMOD/jbrowse-components/pull/2382) Export RefNameAutocomplete and ViewModel from LinearGenomeView for downstream usage ([@hextraza](https://github.com/hextraza)) - [#2336](https://github.com/GMOD/jbrowse-components/pull/2336) Add jbrowse-img to monorepo ([@cmdcolin](https://github.com/cmdcolin)) - [#2324](https://github.com/GMOD/jbrowse-components/pull/2324) Remove unused wrapForRpc functionality ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#2379](https://github.com/GMOD/jbrowse-components/pull/2379) Bump typescript to 4.4.3 ([@cmdcolin](https://github.com/cmdcolin)) - [#2363](https://github.com/GMOD/jbrowse-components/pull/2363) Add some typescripting of some MST models and components ([@cmdcolin](https://github.com/cmdcolin)) - [#2351](https://github.com/GMOD/jbrowse-components/pull/2351) Use main "module" field instead of "browser" from dependency package json files electron builds ([@cmdcolin](https://github.com/cmdcolin)) - [#2323](https://github.com/GMOD/jbrowse-components/pull/2323) Remove session related menu items from jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 6 - Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - Peter Xie ([@peterkxie](https://github.com/peterkxie)) - Sebastian Benjamin ([@hextraza](https://github.com/hextraza)) - Teresa Martinez ([@teresam856](https://github.com/teresam856)) ## 1.4.4 (2021-09-14)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-trix | | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - Other - [#2287](https://github.com/GMOD/jbrowse-components/pull/2287) Use react-popper to reduce tooltip lag on pages with many elements ([@cmdcolin](https://github.com/cmdcolin)) - [#2294](https://github.com/GMOD/jbrowse-components/pull/2294) Don't rely on SVTYPE=BND for breakend split view options and thicker mouseover chords on circular views ([@cmdcolin](https://github.com/cmdcolin)) - [#2272](https://github.com/GMOD/jbrowse-components/pull/2272) Auto adjust box RefNameAutocomplete width based on refName length ([@cmdcolin](https://github.com/cmdcolin)) - [#2243](https://github.com/GMOD/jbrowse-components/pull/2243) Import bookmarks functionality for grid bookmark widget ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#2247](https://github.com/GMOD/jbrowse-components/pull/2247) New jbrowse-desktop start screen design ([@cmdcolin](https://github.com/cmdcolin)) - [#2254](https://github.com/GMOD/jbrowse-components/pull/2254) Better error reporting from web worker and chrom sizes adapter errors ([@cmdcolin](https://github.com/cmdcolin)) - [#1881](https://github.com/GMOD/jbrowse-components/pull/1881) Add new text searching functionality to core, with `jbrowse text-index` CLI command to generate trix index ([@teresam856](https://github.com/teresam856)) #### :bug: Bug Fix - `core` - [#2320](https://github.com/GMOD/jbrowse-components/pull/2320) Fix issue where add track widget doesn't infer adapters on second usage ([@cmdcolin](https://github.com/cmdcolin)) - [#2250](https://github.com/GMOD/jbrowse-components/pull/2250) Prevent the ToggleButton for the FileSelector toggling to local file when only URL should be available ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#2309](https://github.com/GMOD/jbrowse-components/pull/2309) Fix mouseover selection appearing across unrelated blocks ([@cmdcolin](https://github.com/cmdcolin)) - [#2283](https://github.com/GMOD/jbrowse-components/pull/2283) Fix ability for the variant detail panel to create breakpoint split view for elements ([@cmdcolin](https://github.com/cmdcolin)) - [#2268](https://github.com/GMOD/jbrowse-components/pull/2268) Fix autocomplete height on small displays ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#2300](https://github.com/GMOD/jbrowse-components/pull/2300) Release announcement draft v1.4.0 ([@teresam856](https://github.com/teresam856)) - [#2310](https://github.com/GMOD/jbrowse-components/pull/2310) Add cancer demos to the demos page on website ([@cmdcolin](https://github.com/cmdcolin)) - [#2253](https://github.com/GMOD/jbrowse-components/pull/2253) Add note about legacy-peer-deps to embedded component readme ([@cmdcolin](https://github.com/cmdcolin)) - [#2262](https://github.com/GMOD/jbrowse-components/pull/2262) Add more MDX documentation pages to @jbrowse/react-linear-genome-view storybooks ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - [#2263](https://github.com/GMOD/jbrowse-components/pull/2263) Force publish all packages on release ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Teresa Martinez ([@teresam856](https://github.com/teresam856)) - [@Akusem](https://github.com/Akusem) ## 1.4.3 Failed NPM upload, partial release ## 1.4.2 Failed NPM upload, partial release ## 1.4.1 Broken releases missing some packages ## 1.4.0 Broken releases missing some packages ## 1.3.5 (2021-08-23)
Packages in this release

| Package | Download | | ----------------------------------- | ----------------------------------------------------------------- | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |

## 1.3.4 (2021-08-23)
Packages in this release

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-hic | | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - Other - [#2163](https://github.com/GMOD/jbrowse-components/pull/2163) Add new embeddable React Circular Genome View ([@garrettjstevens](https://github.com/garrettjstevens)) - [#2229](https://github.com/GMOD/jbrowse-components/pull/2229) Use extendPluggableElement for context menu items ([@garrettjstevens](https://github.com/garrettjstevens)) - [#2233](https://github.com/GMOD/jbrowse-components/pull/2233) Add optional chromSizes config slot to TwoBitAdapter to speed up loading of TwoBit files with many refseqs ([@cmdcolin](https://github.com/cmdcolin)) - [#2199](https://github.com/GMOD/jbrowse-components/pull/2199) Make the BED parser not interpret general tab delimited data as BED12 ([@cmdcolin](https://github.com/cmdcolin)) - [#2241](https://github.com/GMOD/jbrowse-components/pull/2241) Restore previous window location when re-opening on desktop ([@garrettjstevens](https://github.com/garrettjstevens)) - [#2203](https://github.com/GMOD/jbrowse-components/pull/2203) Add a helpful message if there is a 404 on config.json error ([@cmdcolin](https://github.com/cmdcolin)) - [#2204](https://github.com/GMOD/jbrowse-components/pull/2204) Hide reads with unmapped flag by default in alignments tracks ([@cmdcolin](https://github.com/cmdcolin)) - [#2198](https://github.com/GMOD/jbrowse-components/pull/2198) Add better inversion visualization to read vs reference visualizations ([@cmdcolin](https://github.com/cmdcolin)) - [#2154](https://github.com/GMOD/jbrowse-components/pull/2154) Add UMD build of react-linear-genome-view for plain-js use ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - [#2236](https://github.com/GMOD/jbrowse-components/pull/2236) Detect assembly loading error and encapsulate error instead of failing at app level ([@cmdcolin](https://github.com/cmdcolin)) - [#2029](https://github.com/GMOD/jbrowse-components/pull/2029) Polish desktop builds ([@elliothershberg](https://github.com/elliothershberg)) - [#2140](https://github.com/GMOD/jbrowse-components/pull/2140) New core plugin that adds a "bookmarked regions" list widget, new extension points system ([@elliothershberg](https://github.com/elliothershberg)) #### :bug: Bug Fix - `core` - [#2245](https://github.com/GMOD/jbrowse-components/pull/2245) Fix missing regenerator runtime dependency in core ([@garrettjstevens](https://github.com/garrettjstevens)) - [#2202](https://github.com/GMOD/jbrowse-components/pull/2202) Fixed a crash when an incompatible adapter is selected for provided data in 'open track' ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - [#2197](https://github.com/GMOD/jbrowse-components/pull/2197) Fix handle leak for killed worker checker ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#2208](https://github.com/GMOD/jbrowse-components/pull/2208) Fix issue where collapsed categories were not remembered after toggling a track ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#2192](https://github.com/GMOD/jbrowse-components/pull/2192) Update Linear Genome View embedding docs ([@garrettjstevens](https://github.com/garrettjstevens)) #### :house: Internal - `core` - [#2057](https://github.com/GMOD/jbrowse-components/pull/2057) Use idMaker for dataAdapterCache key for faster FromConfigAdapter performance ([@cmdcolin](https://github.com/cmdcolin)) - [#2231](https://github.com/GMOD/jbrowse-components/pull/2231) Export offscreenCanvasUtils ([@cmdcolin](https://github.com/cmdcolin)) - [#2226](https://github.com/GMOD/jbrowse-components/pull/2226) Use superRenderProps and superTrackMenuItems for better simulated inheritance model ([@cmdcolin](https://github.com/cmdcolin)) - [#1874](https://github.com/GMOD/jbrowse-components/pull/1874) Add aborting to CoreGetFeatures rpcManager call ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#2232](https://github.com/GMOD/jbrowse-components/pull/2232) Remove filtering display type from core ([@cmdcolin](https://github.com/cmdcolin)) - [#2234](https://github.com/GMOD/jbrowse-components/pull/2234) Add rootModel setError on jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 4 - Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Elliot Hershberg ([@elliothershberg](https://github.com/elliothershberg)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) ## 1.3.3 (2021-08-02)
Packages in this release

| Package | Download | | --------------------------------------- | ---------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-filtering | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-hic | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - Other - [#2127](https://github.com/GMOD/jbrowse-components/pull/2127) Add example dataset for COLO829 ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#2141](https://github.com/GMOD/jbrowse-components/pull/2141) Update to @material-ui/core@4.12.2 ([@cmdcolin](https://github.com/cmdcolin)) - [#2126](https://github.com/GMOD/jbrowse-components/pull/2126) Allow opening plaintext .vcf files from the "Add track" workflow ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#2159](https://github.com/GMOD/jbrowse-components/pull/2159) Stop local storage quota-exceeded errors preventing the app from starting ([@cmdcolin](https://github.com/cmdcolin)) - [#2161](https://github.com/GMOD/jbrowse-components/pull/2161) Remove outline from clicking on SVG chord tracks ([@cmdcolin](https://github.com/cmdcolin)) - [#2157](https://github.com/GMOD/jbrowse-components/pull/2157) Fix rendering of negative strand alignment modifications/methylation ([@cmdcolin](https://github.com/cmdcolin)) - [#2131](https://github.com/GMOD/jbrowse-components/pull/2131) Fix mouseovers/click handlers after "force load" button pressed ([@cmdcolin](https://github.com/cmdcolin)) - [#2128](https://github.com/GMOD/jbrowse-components/pull/2128) Fix using the "Color by modifications" setting on files that need ref renaming ([@cmdcolin](https://github.com/cmdcolin)) - [#2115](https://github.com/GMOD/jbrowse-components/pull/2115) Fix bug where sometimes plugin could not be removed from UI ([@garrettjstevens](https://github.com/garrettjstevens)) - [#2119](https://github.com/GMOD/jbrowse-components/pull/2119) Fix loading indicator on the reference sequence selector getting stuck ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#2101](https://github.com/GMOD/jbrowse-components/pull/2101) Fix behavior of the end-of-list indicator in refNameAutocomplete to always display as a disabled item ([@teresam856](https://github.com/teresam856)) #### :house: Internal - Other - [#2152](https://github.com/GMOD/jbrowse-components/pull/2152) Remove storybook symlink workaround ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - [#2099](https://github.com/GMOD/jbrowse-components/pull/2099) Use rbush data structure for layout of feature tracks ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - Teresa Martinez ([@teresam856](https://github.com/teresam856)) ## 1.3.2 (2021-07-07)
Packages in this release

| Package | Download | | --------------------------------- | --------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/desktop | | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - Other - [#2100](https://github.com/GMOD/jbrowse-components/pull/2100) Improve descriptions on VCF SVs ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#2106](https://github.com/GMOD/jbrowse-components/pull/2106) Use more accurate estimator for feature label widths ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - [#2109](https://github.com/GMOD/jbrowse-components/pull/2109) Make sure to wait for assembly to load before downloading canonical refnames in SV inspector ([@cmdcolin](https://github.com/cmdcolin)) - [#2111](https://github.com/GMOD/jbrowse-components/pull/2111) Fix "Can't resolve '@jbrowse/plugin-legacy-jbrowse'" in `@jbrowse/react-linear-genome-view` ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 2 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) ## 1.3.1 (2021-07-06)
Packages in this release

| Package | Download | | --------------------------------------- | ---------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-filtering | | | @jbrowse/plugin-hic | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-menus | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - `core` - [#2094](https://github.com/GMOD/jbrowse-components/pull/2094) More usage of typography to improve consistent text styling ([@cmdcolin](https://github.com/cmdcolin)) - [#2068](https://github.com/GMOD/jbrowse-components/pull/2068) Add non-indexed and plaintext VCF Adapter to variants plugin ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - [#2067](https://github.com/GMOD/jbrowse-components/pull/2067) Better error message if a file location has an empty string ([@garrettjstevens](https://github.com/garrettjstevens)) - [#2064](https://github.com/GMOD/jbrowse-components/pull/2064) Export offscreenCanvasPonyfil from core/util ([@garrettjstevens](https://github.com/garrettjstevens)) - [#2060](https://github.com/GMOD/jbrowse-components/pull/2060) Improve performance with large numbers of reference sequences by using MST volatiles ([@cmdcolin](https://github.com/cmdcolin)) - [#2050](https://github.com/GMOD/jbrowse-components/pull/2050) Configurable app logo for web ([@elliothershberg](https://github.com/elliothershberg)) - Other - [#2104](https://github.com/GMOD/jbrowse-components/pull/2104) Use ScopedCssBaseline to help style the embedded component ([@cmdcolin](https://github.com/cmdcolin)) - [#2015](https://github.com/GMOD/jbrowse-components/pull/2015) Deprecate ThemeProvider in `@jbrowse/react-linear-genome-view` ([@garrettjstevens](https://github.com/garrettjstevens)) #### :bug: Bug Fix - Other - [#2097](https://github.com/GMOD/jbrowse-components/pull/2097) Improve speed for laying out features for embedded/mainthreadrpc scenarios ([@cmdcolin](https://github.com/cmdcolin)) - [#2096](https://github.com/GMOD/jbrowse-components/pull/2096) Fix issue with page reload after editing session title ([@cmdcolin](https://github.com/cmdcolin)) - [#2074](https://github.com/GMOD/jbrowse-components/pull/2074) Fix support for opening local files in spreadsheet/SV inspector ([@cmdcolin](https://github.com/cmdcolin)) - [#2061](https://github.com/GMOD/jbrowse-components/pull/2061) Fix issue with using --force error when no track was previously loaded ([@cmdcolin](https://github.com/cmdcolin)) - [#2024](https://github.com/GMOD/jbrowse-components/pull/2024) Flip drawing of negative strand PAF features in linear synteny and dotplot views ([@cmdcolin](https://github.com/cmdcolin)) - [#2023](https://github.com/GMOD/jbrowse-components/pull/2023) Fix infinite loop in adding some plugins on desktop ([@cmdcolin](https://github.com/cmdcolin)) - [#2019](https://github.com/GMOD/jbrowse-components/pull/2019) Fix session import to use blob map for opening local files ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#2071](https://github.com/GMOD/jbrowse-components/pull/2071) Add indicator to the end of ref name dropdown to suggest user to type the searchbox for more ([@teresam856](https://github.com/teresam856)) - [#2056](https://github.com/GMOD/jbrowse-components/pull/2056) Fix infinite recursion in FromConfigAdaptor by avoiding mutating the passed in data when using SimpleFeature ([@cmdcolin](https://github.com/cmdcolin)) - [#2018](https://github.com/GMOD/jbrowse-components/pull/2018) Fix 3'UTR in sequence detail panels when no UTRs are in gff ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - [#1967](https://github.com/GMOD/jbrowse-components/pull/1967) Omit configurationSchema snapshot when it matches the default ([@garrettjstevens](https://github.com/garrettjstevens)) - [#2078](https://github.com/GMOD/jbrowse-components/pull/2078) Restore eslint rule for no-unused-vars ([@cmdcolin](https://github.com/cmdcolin)) - [#2051](https://github.com/GMOD/jbrowse-components/pull/2051) Add missing named exports to shared core modules ([@garrettjstevens](https://github.com/garrettjstevens)) - [#2045](https://github.com/GMOD/jbrowse-components/pull/2045) Add basic architecture for text searching ([@teresam856](https://github.com/teresam856)) - Other - [#2070](https://github.com/GMOD/jbrowse-components/pull/2070) Remove service worker from jbrowse-web ([@cmdcolin](https://github.com/cmdcolin)) - [#1995](https://github.com/GMOD/jbrowse-components/pull/1995) Pass initialDisplay snapshot via separate param to showTrack ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 5 - Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Elliot Hershberg ([@elliothershberg](https://github.com/elliothershberg)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - Teresa Martinez ([@teresam856](https://github.com/teresam856)) ## 1.3.0 (2021-05-24)
Packages in this release

| Package | Download | | --------------------------------------- | ---------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/development-tools | https://www.npmjs.com/package/@jbrowse/development-tools | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-filtering | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-hic | | | @jbrowse/plugin-legacy-jbrowse | | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-protein | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - Other - [#2001](https://github.com/GMOD/jbrowse-components/pull/2001) Make tracks added using the add track widget a session track if not in adminMode ([@cmdcolin](https://github.com/cmdcolin)) - [#1980](https://github.com/GMOD/jbrowse-components/pull/1980) Add popup confirmation dialog for unknown session plugins, and use plugins.json as a whitelist ([@cmdcolin](https://github.com/cmdcolin)) - [#1977](https://github.com/GMOD/jbrowse-components/pull/1977) Upgrade @material-ui/data-grid ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#1982](https://github.com/GMOD/jbrowse-components/pull/1982) Allow manually specifying adapter type if filename does not match expected pattern ([@cmdcolin](https://github.com/cmdcolin)) - [#1975](https://github.com/GMOD/jbrowse-components/pull/1975) Allow local files on the users computer to be opened as tracks in jbrowse-web ([@cmdcolin](https://github.com/cmdcolin)) - [#1865](https://github.com/GMOD/jbrowse-components/pull/1865) Show modified bases using MM and MP/ML tags in BAM/CRAM ([@cmdcolin](https://github.com/cmdcolin)) - [#1984](https://github.com/GMOD/jbrowse-components/pull/1984) Better feature details when there are short arrays of json supplied as feature data ([@cmdcolin](https://github.com/cmdcolin)) - [#1931](https://github.com/GMOD/jbrowse-components/pull/1931) Create in app graphical plugin store ([@elliothershberg](https://github.com/elliothershberg)) #### :bug: Bug Fix - `core` - [#1985](https://github.com/GMOD/jbrowse-components/pull/1985) Avoid error calculating UTR on features that have no exon subfeatures ([@cmdcolin](https://github.com/cmdcolin)) - [#1954](https://github.com/GMOD/jbrowse-components/pull/1954) Add more environments to configSchema create calls to fix ability to use custom jexl commands with main thread rendering ([@cmdcolin](https://github.com/cmdcolin)) - [#1963](https://github.com/GMOD/jbrowse-components/pull/1963) Fix ability to use DialogComponent (used for svg export, pileup sort, etc) on embedded components ([@cmdcolin](https://github.com/cmdcolin)) - [#1945](https://github.com/GMOD/jbrowse-components/pull/1945) Fix hic not being able to render due to incorrect lazy loading ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#1956](https://github.com/GMOD/jbrowse-components/pull/1956) Fix connection behavior ([@garrettjstevens](https://github.com/garrettjstevens)) - [#1966](https://github.com/GMOD/jbrowse-components/pull/1966) Fix ability to use add-track force on symlink tracks ([@cmdcolin](https://github.com/cmdcolin)) - [#1951](https://github.com/GMOD/jbrowse-components/pull/1951) Fix breakpoint split view demo configuration on website ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#2002](https://github.com/GMOD/jbrowse-components/pull/2002) Add @jbrowse/img to homepage ([@cmdcolin](https://github.com/cmdcolin)) - [#2007](https://github.com/GMOD/jbrowse-components/pull/2007) Update docs for modifications/methylation coloring, plugin store, and the sequence panel in feature details ([@cmdcolin](https://github.com/cmdcolin)) - [#1976](https://github.com/GMOD/jbrowse-components/pull/1976) reorganize the demo page to emphasize the cancer sv demo more ([@rbuels](https://github.com/rbuels)) - [#1952](https://github.com/GMOD/jbrowse-components/pull/1952) Add demo for 1000 genomes extended trio dataset to website ([@cmdcolin](https://github.com/cmdcolin)) - [#1862](https://github.com/GMOD/jbrowse-components/pull/1862) Add example for using a build-time included plugin to storybook ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - Other - [#2003](https://github.com/GMOD/jbrowse-components/pull/2003) Make SNPCoverage independently generate the modifications tag-color mapping ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `development-tools` - [#1930](https://github.com/GMOD/jbrowse-components/pull/1930) Upgrade react scripts+react to latest versions ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 4 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Elliot Hershberg ([@elliothershberg](https://github.com/elliothershberg)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - Robert Buels ([@rbuels](https://github.com/rbuels)) ## 1.2.0 (2021-05-03)
Packages in this release

| Package | Download | | --------------------------------------- | ---------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-filtering | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-hic | | | @jbrowse/plugin-legacy-jbrowse | | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-protein | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - `core` - [#1125](https://github.com/GMOD/jbrowse-components/pull/1125) Export SVG ([@cmdcolin](https://github.com/cmdcolin)) - [#1867](https://github.com/GMOD/jbrowse-components/pull/1867) Virtualized tree for tracklist to support having thousands of tracks ([@cmdcolin](https://github.com/cmdcolin)) - [#1660](https://github.com/GMOD/jbrowse-components/pull/1660) Allow connections to have multiple assemblies ([@garrettjstevens](https://github.com/garrettjstevens)) - [#1864](https://github.com/GMOD/jbrowse-components/pull/1864) Add Material UI's DataGrid to re-exports ([@garrettjstevens](https://github.com/garrettjstevens)) - [#1875](https://github.com/GMOD/jbrowse-components/pull/1875) Make drawer widget titles stay visible when scrolling inside the widget ([@cmdcolin](https://github.com/cmdcolin)) - [#1877](https://github.com/GMOD/jbrowse-components/pull/1877) Add ability to copy the text produced by the feature details sequence panel to MS Word/Google Docs and preserve styling ([@cmdcolin](https://github.com/cmdcolin)) - [#1854](https://github.com/GMOD/jbrowse-components/pull/1854) Make "About track" dialog available from tracklist and for non-LGV tracks ([@cmdcolin](https://github.com/cmdcolin)) - [#1853](https://github.com/GMOD/jbrowse-components/pull/1853) Add mouseovers in feature details that show field descriptions for VCF fields ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#1892](https://github.com/GMOD/jbrowse-components/pull/1892) Create new JB2 plugin store ([@elliothershberg](https://github.com/elliothershberg)) - [#1901](https://github.com/GMOD/jbrowse-components/pull/1901) Make using --out for add-assembly create output directory if it does not exist and fix outputting to symlink ([@cmdcolin](https://github.com/cmdcolin)) - [#1850](https://github.com/GMOD/jbrowse-components/pull/1850) Add true breakend ALT strings to the feature details panel ([@cmdcolin](https://github.com/cmdcolin)) - [#1878](https://github.com/GMOD/jbrowse-components/pull/1878) Add --delete to set-default-session, fix --session ([@garrettjstevens](https://github.com/garrettjstevens)) - [#1861](https://github.com/GMOD/jbrowse-components/pull/1861) Change Alignments track "Fade mismatches by quality" setting to a separate config param and made it less strict ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - [#1924](https://github.com/GMOD/jbrowse-components/pull/1924) Fix import of BED and navToLocString from spreadsheet views ([@cmdcolin](https://github.com/cmdcolin)) - [#1918](https://github.com/GMOD/jbrowse-components/pull/1918) Fix issue with some falsy values being hidden in feature details ([@cmdcolin](https://github.com/cmdcolin)) - [#1911](https://github.com/GMOD/jbrowse-components/pull/1911) Fix breakpoint split view visualizations for files that need ref renaming (e.g. chr1 vs 1) ([@cmdcolin](https://github.com/cmdcolin)) - [#1904](https://github.com/GMOD/jbrowse-components/pull/1904) Fix issue with synteny polygons displaying slightly offset ([@cmdcolin](https://github.com/cmdcolin)) - [#1884](https://github.com/GMOD/jbrowse-components/pull/1884) Fix rIC ponyfill for use on Safari ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#1912](https://github.com/GMOD/jbrowse-components/pull/1912) Fix reloading of local sessions when using React.StrictMode ([@cmdcolin](https://github.com/cmdcolin)) - [#1900](https://github.com/GMOD/jbrowse-components/pull/1900) Make clicking away from autocomplete popup on track container work ([@cmdcolin](https://github.com/cmdcolin)) - [#1878](https://github.com/GMOD/jbrowse-components/pull/1878) Add --delete to set-default-session, fix --session ([@garrettjstevens](https://github.com/garrettjstevens)) - [#1871](https://github.com/GMOD/jbrowse-components/pull/1871) Fix crash on dotplot/linear synteny import form and when closing linear synteny track ([@cmdcolin](https://github.com/cmdcolin)) - [#1860](https://github.com/GMOD/jbrowse-components/pull/1860) Fix alignments read filter jexl syntax ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#1914](https://github.com/GMOD/jbrowse-components/pull/1914) Use MDX to add proper image captions in web and pdf documentation ([@cmdcolin](https://github.com/cmdcolin)) - [#1855](https://github.com/GMOD/jbrowse-components/pull/1855) Add download page in website header and new super-quick-start guide ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - [#1932](https://github.com/GMOD/jbrowse-components/pull/1932) Update analytics and share API URLs to refer to more stable locations ([@peterkxie](https://github.com/peterkxie)) - [#1888](https://github.com/GMOD/jbrowse-components/pull/1888) More lazy loading of react components to reduce bundle size ([@cmdcolin](https://github.com/cmdcolin)) - [#1790](https://github.com/GMOD/jbrowse-components/pull/1790) Allow MainThreadRpcDriver to skip serialization during RPC, improving main-thread rendering performance ([@garrettjstevens](https://github.com/garrettjstevens)) - Other - [#1926](https://github.com/GMOD/jbrowse-components/pull/1926) Update website to link to demos on cloudfront for better compression ([@cmdcolin](https://github.com/cmdcolin)) - [#1868](https://github.com/GMOD/jbrowse-components/pull/1868) Export XYPlotRenderer and configSchema ([@elliothershberg](https://github.com/elliothershberg)) - [#1863](https://github.com/GMOD/jbrowse-components/pull/1863) Update @gmod/indexedfasta ([@cmdcolin](https://github.com/cmdcolin)) - [#1795](https://github.com/GMOD/jbrowse-components/pull/1795) Make LinearAlignmentsDisplay fully configurable in the UI ([@garrettjstevens](https://github.com/garrettjstevens)) - [#1822](https://github.com/GMOD/jbrowse-components/pull/1822) Let React LGV navigate without setting displayedRegion first ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 4 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Elliot Hershberg ([@elliothershberg](https://github.com/elliothershberg)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - Peter Xie ([@peterkxie](https://github.com/peterkxie)) ## 1.1.0 (2021-03-29)
Packages in this release

| Package | Download | | --------------------------------------- | ---------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-filtering | | | @jbrowse/plugin-hic | | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-protein | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - `core` - [#1846](https://github.com/GMOD/jbrowse-components/pull/1846) Improve copy+paste in the data grids for feature details ([@cmdcolin](https://github.com/cmdcolin)) - [#1814](https://github.com/GMOD/jbrowse-components/pull/1814) Add ability to get promoter sequence and intron sequence for genes from the feature details panel ([@cmdcolin](https://github.com/cmdcolin)) - [#1816](https://github.com/GMOD/jbrowse-components/pull/1816) Remove some animation effects ([@cmdcolin](https://github.com/cmdcolin)) - [#1778](https://github.com/GMOD/jbrowse-components/pull/1778) Adds dropdown to show drawer widget stack ([@teresam856](https://github.com/teresam856)) - [#1685](https://github.com/GMOD/jbrowse-components/pull/1685) Change callbacks language from JavaScript to Jexl ([@peterkxie](https://github.com/peterkxie)) - Other - [#1831](https://github.com/GMOD/jbrowse-components/pull/1831) Add dialog for launching breakpoint split view from variant feature details ([@cmdcolin](https://github.com/cmdcolin)) - [#1803](https://github.com/GMOD/jbrowse-components/pull/1803) Transcript and gene glyphs can now display implied UTRs, active by default ([@cmdcolin](https://github.com/cmdcolin)) - [#1808](https://github.com/GMOD/jbrowse-components/pull/1808) Add another heuristic for returning gene features from BigBed ([@cmdcolin](https://github.com/cmdcolin)) - [#1774](https://github.com/GMOD/jbrowse-components/pull/1774) Add warning dialog in LGV before returning to import form to prevent accidentally losing the current view ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - [#1811](https://github.com/GMOD/jbrowse-components/pull/1811) Check for existence of window more robustly to allow in SSR or node applications ([@elliothershberg](https://github.com/elliothershberg)) - [#1793](https://github.com/GMOD/jbrowse-components/pull/1793) Fix dotplot rendering outside it's allowed bounds ([@cmdcolin](https://github.com/cmdcolin)) - [#1783](https://github.com/GMOD/jbrowse-components/pull/1783) Add hic aborting and fix remoteAbort signal propagation ([@cmdcolin](https://github.com/cmdcolin)) - [#1723](https://github.com/GMOD/jbrowse-components/pull/1723) A few bugfixes ([@garrettjstevens](https://github.com/garrettjstevens)) - Other - [#1815](https://github.com/GMOD/jbrowse-components/pull/1815) Clear tracks when using "Return to import form" ([@cmdcolin](https://github.com/cmdcolin)) - [#1819](https://github.com/GMOD/jbrowse-components/pull/1819) Standardized sentence casing on drawer widget titles ([@cmdcolin](https://github.com/cmdcolin)) - [#1796](https://github.com/GMOD/jbrowse-components/pull/1796) Bump generic-filehandle for fixing CORS errors from Chrome cache pollution ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#1824](https://github.com/GMOD/jbrowse-components/pull/1824) Add storybook docs page for nextjs usage ([@elliothershberg](https://github.com/elliothershberg)) - [#1770](https://github.com/GMOD/jbrowse-components/pull/1770) 1469 storybook deploy ([@elliothershberg](https://github.com/elliothershberg)) - [#1807](https://github.com/GMOD/jbrowse-components/pull/1807) Update developer guide to cover displays, and highlight working external plugins ([@cmdcolin](https://github.com/cmdcolin)) - [#1779](https://github.com/GMOD/jbrowse-components/pull/1779) Collaborative release announcement editing ([@rbuels](https://github.com/rbuels)) - [#1791](https://github.com/GMOD/jbrowse-components/pull/1791) Add a couple more demos for our live version with MDX ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - Other - [#1820](https://github.com/GMOD/jbrowse-components/pull/1820) Create v1.1.0.md, draft of release announcements ([@garrettjstevens](https://github.com/garrettjstevens)) - [#1823](https://github.com/GMOD/jbrowse-components/pull/1823) Add note about previewing changelog to CONTRIBUTING.md ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - [#1834](https://github.com/GMOD/jbrowse-components/pull/1834) Change jbrowse-components monorepo default branch from 'master' to 'main' ([@rbuels](https://github.com/rbuels)) #### Committers: 6 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Elliot Hershberg ([@elliothershberg](https://github.com/elliothershberg)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - Peter Xie ([@peterkxie](https://github.com/peterkxie)) - Robert Buels ([@rbuels](https://github.com/rbuels)) - Teresa Martinez ([@teresam856](https://github.com/teresam856)) ## 1.0.4 (2021-03-08)
Packages in this release

| Package | Download | | --------------------------------------- | ---------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-filtering | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-legacy-jbrowse | | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/protein-widget | | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - `core` - [#1758](https://github.com/GMOD/jbrowse-components/pull/1758) Add ability to get stitched together CDS, protein, and cDNA sequences in feature details ([@cmdcolin](https://github.com/cmdcolin)) - [#1721](https://github.com/GMOD/jbrowse-components/pull/1721) Manually adjust feature height and spacing on alignments track ([@cmdcolin](https://github.com/cmdcolin)) - [#1728](https://github.com/GMOD/jbrowse-components/pull/1728) Add list of loaded plugins to the "About widget" ([@rbuels](https://github.com/rbuels)) - [#1711](https://github.com/GMOD/jbrowse-components/pull/1711) Add plugin top-level configuration ([@teresam856](https://github.com/teresam856)) - [#1699](https://github.com/GMOD/jbrowse-components/pull/1699) Add sequence track for both read and reference genome in the "Linear read vs ref" comparison ([@cmdcolin](https://github.com/cmdcolin)) - [#1701](https://github.com/GMOD/jbrowse-components/pull/1701) Add clickable navigation links to supplementary alignments/paired ends locations and BND/TRA endpoints in detail widgets ([@cmdcolin](https://github.com/cmdcolin)) - [#1601](https://github.com/GMOD/jbrowse-components/pull/1601) Add ability to color by per-base quality in alignment tracks ([@cmdcolin](https://github.com/cmdcolin)) - [#1640](https://github.com/GMOD/jbrowse-components/pull/1640) Move stats calculation to BaseFeatureAdapter ([@cmdcolin](https://github.com/cmdcolin)) - [#1588](https://github.com/GMOD/jbrowse-components/pull/1588) Add "Get sequence" action to LGV rubber-band ([@teresam856](https://github.com/teresam856)) - Other - [#1743](https://github.com/GMOD/jbrowse-components/pull/1743) Add color picker and choice of summary score style for wiggle track ([@cmdcolin](https://github.com/cmdcolin)) - [#1763](https://github.com/GMOD/jbrowse-components/pull/1763) Add a "CSS reset" to jbrowse-react-linear-genome-view to prevent parent styles from outside the component leaking in ([@cmdcolin](https://github.com/cmdcolin)) - [#1756](https://github.com/GMOD/jbrowse-components/pull/1756) Split alignments track menu items into "Pileup" and "SNPCoverage" submenus ([@cmdcolin](https://github.com/cmdcolin)) - [#1742](https://github.com/GMOD/jbrowse-components/pull/1742) Add ability to display crosshatches on the wiggle line/xyplot renderer ([@cmdcolin](https://github.com/cmdcolin)) - [#1736](https://github.com/GMOD/jbrowse-components/pull/1736) Fix CLI add-track --load inPlace to put exact contents into the config, add better CLI example docs ([@cmdcolin](https://github.com/cmdcolin)) - [#1394](https://github.com/GMOD/jbrowse-components/pull/1394) Add new menu items for show/hide feature labels, set max height, and set compact display mode ([@cmdcolin](https://github.com/cmdcolin)) - [#1720](https://github.com/GMOD/jbrowse-components/pull/1720) Standardize phred qual scaling between BAM and CRAM and add option to make mismatches render in a lighter color when quality is low ([@cmdcolin](https://github.com/cmdcolin)) - [#1704](https://github.com/GMOD/jbrowse-components/pull/1704) Add "Show all regions in assembly" to import form and make import form show entire region when refName selected ([@cmdcolin](https://github.com/cmdcolin)) - [#1687](https://github.com/GMOD/jbrowse-components/pull/1687) Threshold for indicators on SNPCoverage + inverted bargraph of interbase counts for sub-threshold events ([@cmdcolin](https://github.com/cmdcolin)) - [#1695](https://github.com/GMOD/jbrowse-components/pull/1695) Improve zoomed-out display of quantitative displays tracks when bicolor pivot is active ([@cmdcolin](https://github.com/cmdcolin)) - [#1680](https://github.com/GMOD/jbrowse-components/pull/1680) Add on click functionality to quantitative track features ([@teresam856](https://github.com/teresam856)) - [#1630](https://github.com/GMOD/jbrowse-components/pull/1630) Get column names from BED tabix files and other utils for external jbrowse-plugin-gwas support ([@cmdcolin](https://github.com/cmdcolin)) - [#1709](https://github.com/GMOD/jbrowse-components/pull/1709) Improve sorting and filtering in variant detail widget ([@cmdcolin](https://github.com/cmdcolin)) - [#1688](https://github.com/GMOD/jbrowse-components/pull/1688) Bold insertion indicator for large insertions on pileup track ([@cmdcolin](https://github.com/cmdcolin)) - [#1669](https://github.com/GMOD/jbrowse-components/pull/1669) Allow plain json encoding of the session in the URL ([@cmdcolin](https://github.com/cmdcolin)) - [#1642](https://github.com/GMOD/jbrowse-components/pull/1642) Enable locstring navigation from LGV import form ([@teresam856](https://github.com/teresam856)) - [#1655](https://github.com/GMOD/jbrowse-components/pull/1655) Add GFF3Tabix and BEDTabix inference to JB1 connection ([@garrettjstevens](https://github.com/garrettjstevens)) - [#1643](https://github.com/GMOD/jbrowse-components/pull/1643) Add an offset that allows all wiggle y-scalebar labels to be visible ([@cmdcolin](https://github.com/cmdcolin)) - [#1632](https://github.com/GMOD/jbrowse-components/pull/1632) Displays warnings when receiving a session with custom callbacks ([@peterkxie](https://github.com/peterkxie)) - [#1615](https://github.com/GMOD/jbrowse-components/pull/1615) Increase pileup maxHeight ([@cmdcolin](https://github.com/cmdcolin)) - [#1624](https://github.com/GMOD/jbrowse-components/pull/1624) GCContent adapter ([@cmdcolin](https://github.com/cmdcolin)) - [#1614](https://github.com/GMOD/jbrowse-components/pull/1614) Add insertion and clip indicators to SNPCoverage views (part of Alignments tracks) ([@cmdcolin](https://github.com/cmdcolin)) - [#1610](https://github.com/GMOD/jbrowse-components/pull/1610) Display error message from dynamodb session sharing error ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - [#1777](https://github.com/GMOD/jbrowse-components/pull/1777) Quick fix for block error ([@cmdcolin](https://github.com/cmdcolin)) - [#1748](https://github.com/GMOD/jbrowse-components/pull/1748) External plugins load after confirming config warning ([@peterkxie](https://github.com/peterkxie)) - [#1750](https://github.com/GMOD/jbrowse-components/pull/1750) Fix pileup sorting when using string tag ([@cmdcolin](https://github.com/cmdcolin)) - [#1747](https://github.com/GMOD/jbrowse-components/pull/1747) Fix the position of the popup menu after rubberband select when there is a margin on the component e.g. in embedded ([@cmdcolin](https://github.com/cmdcolin)) - [#1736](https://github.com/GMOD/jbrowse-components/pull/1736) Fix CLI add-track --load inPlace to put exact contents into the config, add better CLI example docs ([@cmdcolin](https://github.com/cmdcolin)) - [#1731](https://github.com/GMOD/jbrowse-components/pull/1731) Fix alignment track ability to remember the height of the SNPCoverage subtrack on refresh ([@cmdcolin](https://github.com/cmdcolin)) - [#1719](https://github.com/GMOD/jbrowse-components/pull/1719) Fix for navigation past end of chromosome ([@cmdcolin](https://github.com/cmdcolin)) - [#1698](https://github.com/GMOD/jbrowse-components/pull/1698) Fix rendering read vs ref comparisons with CIGAR strings that use = sign matches ([@cmdcolin](https://github.com/cmdcolin)) - [#1697](https://github.com/GMOD/jbrowse-components/pull/1697) Fix softclipping configuration setting causing bases to be missed ([@cmdcolin](https://github.com/cmdcolin)) - [#1689](https://github.com/GMOD/jbrowse-components/pull/1689) Disable copy/delete menu items for reference sequence track ([@teresam856](https://github.com/teresam856)) - [#1682](https://github.com/GMOD/jbrowse-components/pull/1682) Fix parsing of BED and BEDPE files with comment header for spreadsheet view ([@cmdcolin](https://github.com/cmdcolin)) - [#1679](https://github.com/GMOD/jbrowse-components/pull/1679) Fix issue with using launching the add track widget on views that are not displaying any regions ([@teresam856](https://github.com/teresam856)) - [#1642](https://github.com/GMOD/jbrowse-components/pull/1642) Enable locstring navigation from LGV import form ([@teresam856](https://github.com/teresam856)) - [#1626](https://github.com/GMOD/jbrowse-components/pull/1626) Bug Fix: specify assembly in locstring ([@teresam856](https://github.com/teresam856)) - [#1619](https://github.com/GMOD/jbrowse-components/pull/1619) Fix overview scale polygon not appearing properly in some cases ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#1714](https://github.com/GMOD/jbrowse-components/pull/1714) Fix ability to add a PAF on initial dotplot view creation ([@cmdcolin](https://github.com/cmdcolin)) - [#1657](https://github.com/GMOD/jbrowse-components/pull/1657) Fix for track using assembly alias not displaying ([@garrettjstevens](https://github.com/garrettjstevens)) - [#1620](https://github.com/GMOD/jbrowse-components/pull/1620) Add error reporting on a worker failure ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#1725](https://github.com/GMOD/jbrowse-components/pull/1725) JBrowseR release ([@elliothershberg](https://github.com/elliothershberg)) - [#1677](https://github.com/GMOD/jbrowse-components/pull/1677) Config guide updates ([@elliothershberg](https://github.com/elliothershberg)) - [#1665](https://github.com/GMOD/jbrowse-components/pull/1665) Add Nextstrain COVID storybook ([@elliothershberg](https://github.com/elliothershberg)) - [#1670](https://github.com/GMOD/jbrowse-components/pull/1670) typo in developer guide docs ([@teresam856](https://github.com/teresam856)) - [#1592](https://github.com/GMOD/jbrowse-components/pull/1592) Website copy edits ([@rbuels](https://github.com/rbuels)) - [#1646](https://github.com/GMOD/jbrowse-components/pull/1646) Fix "See code" link in CLI docs ([@garrettjstevens](https://github.com/garrettjstevens)) - [#1618](https://github.com/GMOD/jbrowse-components/pull/1618) Add whole-genome view and color/sort alignments tutorials to user guide ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - Other - [#1666](https://github.com/GMOD/jbrowse-components/pull/1666) Move "mouseover" config from BaseLinearDisplay to LinearBasicDisplay display ([@garrettjstevens](https://github.com/garrettjstevens)) - [#1751](https://github.com/GMOD/jbrowse-components/pull/1751) Make the variant display derive from the feature display ([@cmdcolin](https://github.com/cmdcolin)) - [#1716](https://github.com/GMOD/jbrowse-components/pull/1716) Stringify labels before adding to rendering to avoid undefineds on label.length ([@cmdcolin](https://github.com/cmdcolin)) - [#1713](https://github.com/GMOD/jbrowse-components/pull/1713) Add console.error log in block setError ([@cmdcolin](https://github.com/cmdcolin)) - [#1663](https://github.com/GMOD/jbrowse-components/pull/1663) Make LGV "initialized" not depend on displayedRegions ([@garrettjstevens](https://github.com/garrettjstevens)) - [#1672](https://github.com/GMOD/jbrowse-components/pull/1672) Fix import forms crashing if there are no assemblies ([@cmdcolin](https://github.com/cmdcolin)) - [#1644](https://github.com/GMOD/jbrowse-components/pull/1644) Bump electron from 9.3.1 to 9.4.0 ([@dependabot[bot]](https://github.com/apps/dependabot)) - [#1641](https://github.com/GMOD/jbrowse-components/pull/1641) Remove codecov pr annotations ([@cmdcolin](https://github.com/cmdcolin)) - [#1609](https://github.com/GMOD/jbrowse-components/pull/1609) Add extra checks for release script ([@peterkxie](https://github.com/peterkxie)) - `core` - [#1762](https://github.com/GMOD/jbrowse-components/pull/1762) Add requestidlecallback ponyfill in @jbrowse/core/util ([@cmdcolin](https://github.com/cmdcolin)) - [#1629](https://github.com/GMOD/jbrowse-components/pull/1629) Add RegionsAdapter/SequenceAdapter, reorganize base adapters ([@garrettjstevens](https://github.com/garrettjstevens)) - [#1625](https://github.com/GMOD/jbrowse-components/pull/1625) Make renderArgs consistent and don't duplicate data ([@garrettjstevens](https://github.com/garrettjstevens)) - [#1414](https://github.com/GMOD/jbrowse-components/pull/1414) Typescriptify and MST'ify the add track workflow ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 7 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Elliot Hershberg ([@elliothershberg](https://github.com/elliothershberg)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - Liu ZH ([@sqwwwok](https://github.com/sqwwwok)) - Peter Xie ([@peterkxie](https://github.com/peterkxie)) - Robert Buels ([@rbuels](https://github.com/rbuels)) - Teresa Martinez ([@teresam856](https://github.com/teresam856)) ## 1.0.3 (2021-01-11)
Packages in this release

| Package | Download | | --------------------------------------- | ---------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/development-tools | https://www.npmjs.com/package/@jbrowse/development-tools | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-hic | | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-menus | | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/protein-widget | | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - Other - [#1560](https://github.com/GMOD/jbrowse-components/pull/1560) Provide a dialog to add extra genomic context for linear read vs. ref visualization ([@elliothershberg](https://github.com/elliothershberg)) - [#1604](https://github.com/GMOD/jbrowse-components/pull/1604) Add ability to filter for read name to the alignments filter dialog ([@cmdcolin](https://github.com/cmdcolin)) - [#1599](https://github.com/GMOD/jbrowse-components/pull/1599) Replace 'show all regions' with 'show all regions in assembly' ([@cmdcolin](https://github.com/cmdcolin)) - [#1595](https://github.com/GMOD/jbrowse-components/pull/1595) Admin server GUI enhancements ([@elliothershberg](https://github.com/elliothershberg)) - [#1584](https://github.com/GMOD/jbrowse-components/pull/1584) Restructure demo page and release cancer demo ([@elliothershberg](https://github.com/elliothershberg)) - [#1579](https://github.com/GMOD/jbrowse-components/pull/1579) Create --branch and --nightly flags for `jbrowse create` and `jbrowse upgrade` commands ([@cmdcolin](https://github.com/cmdcolin)) - [#1575](https://github.com/GMOD/jbrowse-components/pull/1575) Improve @jbrowse/mobx-state-tree type validation errors ([@cmdcolin](https://github.com/cmdcolin)) - [#1574](https://github.com/GMOD/jbrowse-components/pull/1574) Make softclip indicator black if no seq available ([@cmdcolin](https://github.com/cmdcolin)) - [#1554](https://github.com/GMOD/jbrowse-components/pull/1554) Coloring options with simple color for tag ([@peterkxie](https://github.com/peterkxie)) - [#1565](https://github.com/GMOD/jbrowse-components/pull/1565) Rename jbrowse cli add-track --type to --trackType ([@cmdcolin](https://github.com/cmdcolin)) - [#1558](https://github.com/GMOD/jbrowse-components/pull/1558) Add docs for sequence track, variant track, launching synteny from dotplot, and add UCSC plugin to demo ([@cmdcolin](https://github.com/cmdcolin)) - [#1533](https://github.com/GMOD/jbrowse-components/pull/1533) Display file headers in pre tag in about dialogs and bump @gmod/bam and @gmod/tabix package versions ([@cmdcolin](https://github.com/cmdcolin)) - [#1541](https://github.com/GMOD/jbrowse-components/pull/1541) Add more info about adding a PAF file to the synteny import form ([@cmdcolin](https://github.com/cmdcolin)) - [#1509](https://github.com/GMOD/jbrowse-components/pull/1509) Combine Search and Dropdown component on LGV ([@teresam856](https://github.com/teresam856)) - [#1530](https://github.com/GMOD/jbrowse-components/pull/1530) Add spreadsheet filter support for derived columns ([@elliothershberg](https://github.com/elliothershberg)) - [#1483](https://github.com/GMOD/jbrowse-components/pull/1483) Add session export to and import from file ([@garrettjstevens](https://github.com/garrettjstevens)) - [#1519](https://github.com/GMOD/jbrowse-components/pull/1519) Add autoSql to the bigBed "About this track" dialog ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#1531](https://github.com/GMOD/jbrowse-components/pull/1531) Add track menu options for autoscale, log scale, histogram fill, setting min/max score, and zoom level/resolution for wiggle/snpcoverage tracks ([@cmdcolin](https://github.com/cmdcolin)) - [#1473](https://github.com/GMOD/jbrowse-components/pull/1473) Color, filter, and sort options for the alignments ([@cmdcolin](https://github.com/cmdcolin)) - [#1576](https://github.com/GMOD/jbrowse-components/pull/1576) Add location string to tooltip for wiggle and SNPCoverage tracks ([@cmdcolin](https://github.com/cmdcolin)) - [#1529](https://github.com/GMOD/jbrowse-components/pull/1529) Display subfeatures in feature details widget ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `development-tools` - [#1578](https://github.com/GMOD/jbrowse-components/pull/1578) Update build system for external plugins ([@garrettjstevens](https://github.com/garrettjstevens)) #### :bug: Bug Fix - Other - [#1608](https://github.com/GMOD/jbrowse-components/pull/1608) Take into account offsetX of the rubberband on scalebar zooming ([@cmdcolin](https://github.com/cmdcolin)) - [#1597](https://github.com/GMOD/jbrowse-components/pull/1597) Fix crash when there are undefined references in the state tree e.g. when a track is deleted but still referred to by a session ([@peterkxie](https://github.com/peterkxie)) - [#1598](https://github.com/GMOD/jbrowse-components/pull/1598) Disable 'copy to clipboard' while share url being generated ([@peterkxie](https://github.com/peterkxie)) - [#1589](https://github.com/GMOD/jbrowse-components/pull/1589) Fix the display of trackhub registry results ([@cmdcolin](https://github.com/cmdcolin)) - [#1573](https://github.com/GMOD/jbrowse-components/pull/1573) Update hic-straw to fix error for hic files with many scaffolds ([@cmdcolin](https://github.com/cmdcolin)) - [#1563](https://github.com/GMOD/jbrowse-components/pull/1563) Remove softclip and hardclip from being counted as SNPs in the SNPCoverage ([@cmdcolin](https://github.com/cmdcolin)) - [#1559](https://github.com/GMOD/jbrowse-components/pull/1559) Avoid errors from breakpoint split view related to getBoundingClientRect on null track ([@cmdcolin](https://github.com/cmdcolin)) - [#1540](https://github.com/GMOD/jbrowse-components/pull/1540) Fix memory leak when side scrolling LGV blocks ([@cmdcolin](https://github.com/cmdcolin)) - [#1534](https://github.com/GMOD/jbrowse-components/pull/1534) Fix breakpoint split view showing too many connections for paired end ends ([@cmdcolin](https://github.com/cmdcolin)) - [#1524](https://github.com/GMOD/jbrowse-components/pull/1524) Move loading flag for spreadsheet import wizard to volatile to avoid it persisting across refresh ([@cmdcolin](https://github.com/cmdcolin)) - [#1521](https://github.com/GMOD/jbrowse-components/pull/1521) Add missing dep to react-linear-genome-view ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - [#1587](https://github.com/GMOD/jbrowse-components/pull/1587) Fix positioning of scalebar tooltips, overview scalebar plotting, and refName label positioning when displaying many regions ([@cmdcolin](https://github.com/cmdcolin)) - [#1547](https://github.com/GMOD/jbrowse-components/pull/1547) Fix analytics crashing when using plugins ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#1594](https://github.com/GMOD/jbrowse-components/pull/1594) Add GFF3 example to quickstart ([@cmdcolin](https://github.com/cmdcolin)) - [#1581](https://github.com/GMOD/jbrowse-components/pull/1581) Add some features that are missing from jbrowse 2 to the feature comparison table ([@cmdcolin](https://github.com/cmdcolin)) - [#1558](https://github.com/GMOD/jbrowse-components/pull/1558) Add docs for sequence track, variant track, launching synteny from dotplot, and add UCSC plugin to demo ([@cmdcolin](https://github.com/cmdcolin)) - [#1537](https://github.com/GMOD/jbrowse-components/pull/1537) Add CONTRIBUTING.md with tips for getting started with codebase ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - [#1606](https://github.com/GMOD/jbrowse-components/pull/1606) Upgrade @testing-library/react and improve test reliability ([@cmdcolin](https://github.com/cmdcolin)) - [#1555](https://github.com/GMOD/jbrowse-components/pull/1555) Remove the TextDecoder/TextEncoder polyfill ([@cmdcolin](https://github.com/cmdcolin)) - [#1522](https://github.com/GMOD/jbrowse-components/pull/1522) Update oclif and remove now unnecessary file copy ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 6 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Elliot Hershberg ([@elliothershberg](https://github.com/elliothershberg)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - Peter Xie ([@peterkxie](https://github.com/peterkxie)) - Teresa Martinez ([@teresam856](https://github.com/teresam856)) - [@Akusem](https://github.com/Akusem) ## v1.0.2 (2020-12-02)
Packages in this release

| Package | Download | | --------------------------------------- | ---------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/development-tools | https://www.npmjs.com/package/@jbrowse/development-tools | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-filtering | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-hic | | | @jbrowse/plugin-legacy-jbrowse | | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-protein | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/protein-widget | | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - `core` - [#1513](https://github.com/GMOD/jbrowse-components/pull/1513) Add a custom scrollbar that overrides the auto-hiding behavior of scrollbars on OSX ([@elliothershberg](https://github.com/elliothershberg)) #### :bug: Bug Fix - Other - [#1514](https://github.com/GMOD/jbrowse-components/pull/1514) react-linear-genome-view bug fixes ([@garrettjstevens](https://github.com/garrettjstevens)) - [#1517](https://github.com/GMOD/jbrowse-components/pull/1517) Fix the use of filtering display on desktop ([@cmdcolin](https://github.com/cmdcolin)) - [#1512](https://github.com/GMOD/jbrowse-components/pull/1512) Fix setting maxDisplayedBpPerPx for pileup display, helps prevent too large an area from being rendered ([@cmdcolin](https://github.com/cmdcolin)) - [#1442](https://github.com/GMOD/jbrowse-components/pull/1442) Change track selector togglebutton to normal button ([@cmdcolin](https://github.com/cmdcolin)) - [#1506](https://github.com/GMOD/jbrowse-components/pull/1506) Fix horizontally flipped translation frames position ([@cmdcolin](https://github.com/cmdcolin)) - [#1501](https://github.com/GMOD/jbrowse-components/pull/1501) Fix CLI to allow jbrowse create to download newer monorepo tag format ([@cmdcolin](https://github.com/cmdcolin)) - `core` - [#1505](https://github.com/GMOD/jbrowse-components/pull/1505) Fix loading of local files in jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Elliot Hershberg ([@elliothershberg](https://github.com/elliothershberg)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) ## v1.0.1 (2020-11-25)
Packages in this release

| Package | Download | | --------------------------------------- | ---------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/development-tools | https://www.npmjs.com/package/@jbrowse/development-tools | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-filtering | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-hic | | | @jbrowse/plugin-legacy-jbrowse | | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-protein | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/protein-widget | | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

#### :rocket: Enhancement - Other - [#1462](https://github.com/GMOD/jbrowse-components/pull/1462) Allow importing gzip and bgzip files in the spreadsheet and SV inspector ([@cmdcolin](https://github.com/cmdcolin)) - [#1460](https://github.com/GMOD/jbrowse-components/pull/1460) Add support for more bigBed subtypes and fallback for unsupported types ([@peterkxie](https://github.com/peterkxie)) - [#1455](https://github.com/GMOD/jbrowse-components/pull/1455) Add the ability to use connection across refreshes in jbrowse-web using session connections ([@peterkxie](https://github.com/peterkxie)) - [#1439](https://github.com/GMOD/jbrowse-components/pull/1439) 1381 improve assembly add form ([@elliothershberg](https://github.com/elliothershberg)) - [#1433](https://github.com/GMOD/jbrowse-components/pull/1433) Make add track warning a bit more lenient ([@garrettjstevens](https://github.com/garrettjstevens)) - [#1420](https://github.com/GMOD/jbrowse-components/pull/1420) Add the assembly manager feature to jbrowse-desktop ([@elliothershberg](https://github.com/elliothershberg)) - `core` - [#1458](https://github.com/GMOD/jbrowse-components/pull/1458) Add three frame translation to the sequence track ([@cmdcolin](https://github.com/cmdcolin)) - [#1453](https://github.com/GMOD/jbrowse-components/pull/1453) Change "Factory reset" to "Reset session" in jbrowse-web ([@teresam856](https://github.com/teresam856)) - [#1441](https://github.com/GMOD/jbrowse-components/pull/1441) New icon for the track selector ([@cmdcolin](https://github.com/cmdcolin)) - [#1438](https://github.com/GMOD/jbrowse-components/pull/1438) Improve assembly loading time by moving to main thread ([@cmdcolin](https://github.com/cmdcolin)) - [#1434](https://github.com/GMOD/jbrowse-components/pull/1434) Create separate config schema for ReferenceSequenceTrack ([@elliothershberg](https://github.com/elliothershberg)) #### :bug: Bug Fix - `core` - [#1491](https://github.com/GMOD/jbrowse-components/pull/1491) Fix ability to add a PAF synteny track with add-track ([@cmdcolin](https://github.com/cmdcolin)) - [#1470](https://github.com/GMOD/jbrowse-components/pull/1470) Avoid rendering the literal string 'null' in the feature details ([@cmdcolin](https://github.com/cmdcolin)) - Other - [#1489](https://github.com/GMOD/jbrowse-components/pull/1489) Fix long read vs ref CIGAR rendering for horizontally flipped synteny view ([@cmdcolin](https://github.com/cmdcolin)) - [#1460](https://github.com/GMOD/jbrowse-components/pull/1460) Add support for more bigBed subtypes and fallback for unsupported types ([@peterkxie](https://github.com/peterkxie)) - [#1472](https://github.com/GMOD/jbrowse-components/pull/1472) Wait on assemblies that are being tracked by the assemblyManager only ([@cmdcolin](https://github.com/cmdcolin)) - [#1466](https://github.com/GMOD/jbrowse-components/pull/1466) Avoid rendering the display and renderer settings in the about this track dialog ([@cmdcolin](https://github.com/cmdcolin)) - [#1461](https://github.com/GMOD/jbrowse-components/pull/1461) Fix usage of jbrowse-cli on node 10.9 related to fs.promises ([@cmdcolin](https://github.com/cmdcolin)) - [#1452](https://github.com/GMOD/jbrowse-components/pull/1452) Bug: search box disappears from LGV header on smaller widths ([@teresam856](https://github.com/teresam856)) - [#1432](https://github.com/GMOD/jbrowse-components/pull/1432) Make global variables window.JBrowseSession and window.JBrowseRootModel available in jbrowse-web ([@teresam856](https://github.com/teresam856)) - [#1431](https://github.com/GMOD/jbrowse-components/pull/1431) Fix connection tracks not showing up in track selector ([@garrettjstevens](https://github.com/garrettjstevens)) - [#1428](https://github.com/GMOD/jbrowse-components/pull/1428) Fix the listVersions behavior of the jbrowse-cli returning duplicate entries ([@cmdcolin](https://github.com/cmdcolin)) - [#1422](https://github.com/GMOD/jbrowse-components/pull/1422) Fix crash from empty ALT field in VCF ([@cmdcolin](https://github.com/cmdcolin)) - [#1413](https://github.com/GMOD/jbrowse-components/pull/1413) Fix ability to add CRAM tracks using the web based add-track GUI ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation - [#1435](https://github.com/GMOD/jbrowse-components/pull/1435) Updates to quickstart guides ([@garrettjstevens](https://github.com/garrettjstevens)) #### :house: Internal - Other - [#1437](https://github.com/GMOD/jbrowse-components/pull/1437) Use lerna-changelog for changelog generation ([@cmdcolin](https://github.com/cmdcolin)) - [#1465](https://github.com/GMOD/jbrowse-components/pull/1465) Establish minimum node version of 10.4 for using jbrowse-cli tools ([@cmdcolin](https://github.com/cmdcolin)) - [#1454](https://github.com/GMOD/jbrowse-components/pull/1454) Fix GH workflow build ([@elliothershberg](https://github.com/elliothershberg)) - [#1448](https://github.com/GMOD/jbrowse-components/pull/1448) Move building and testing from Travis to GitHub Workflow ([@garrettjstevens](https://github.com/garrettjstevens)) - [#1450](https://github.com/GMOD/jbrowse-components/pull/1450) Fix website build ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - [#1468](https://github.com/GMOD/jbrowse-components/pull/1468) Have assembly manager get plugin manager from factory function args ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 5 - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Elliot Hershberg ([@elliothershberg](https://github.com/elliothershberg)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - Teresa Martinez ([@teresam856](https://github.com/teresam856)) - [@peterkxie](https://github.com/peterkxie)