{
  "$schema": "http://json-schema.org/draft-07/schema",
  "$id": "https://raw.githubusercontent.com/varfish-org/varfish-server/main/importer/schemas/case-qc-v1.json",
  "type": "object",
  "title": "varfish-server case QC info",
  "description": "Per case quality control information for varfish",
  "patternProperties": {
    ".*": {
      "$id": "#/per_sample_values",
      "type": "object",
      "properties": {
        "bamstats": {
          "$id": "#/per_sample_values/bamstats",
          "type": "object",
          "required": [
            "raw total sequences",
            "filtered sequences",
            "sequences",
            "is sorted",
            "1st fragments",
            "last fragments",
            "reads mapped",
            "reads mapped and paired",
            "reads unmapped",
            "reads properly paired",
            "reads paired",
            "reads duplicated",
            "reads MQ0",
            "reads QC failed",
            "non-primary alignments",
            "total length",
            "total first fragment length",
            "total last fragment length",
            "bases mapped",
            "bases mapped (cigar)",
            "bases trimmed",
            "bases duplicated",
            "mismatches",
            "error rate",
            "average length",
            "average first fragment length",
            "average last fragment length",
            "maximum length",
            "maximum first fragment length",
            "maximum last fragment length",
            "average quality",
            "insert size average",
            "insert size standard deviation",
            "inward oriented pairs",
            "outward oriented pairs",
            "pairs with other orientation",
            "pairs on different chromosomes",
            "percentage of properly paired reads (%)"
          ],
          "properties": {
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              "$id": "#/properties/qual_thresholds/items/raw_total_sequences",
              "type": "integer",
              "title": "raw total sequences",
              "minimum": 0
            },
            "filtered sequences": {
              "$id": "#/properties/qual_thresholds/items/filtered_sequences",
              "type": "integer",
              "title": "filtered sequences",
              "minimum": 0
            },
            "sequences": {
              "$id": "#/properties/qual_thresholds/items/sequences",
              "type": "integer",
              "title": "sequences",
              "minimum": 0
            },
            "is sorted": {
              "$id": "#/properties/qual_thresholds/items/is_sorted",
              "type": "integer",
              "title": "is sorted",
              "minimum": 0
            },
            "1st fragments": {
              "$id": "#/properties/qual_thresholds/items/1st_fragments",
              "type": "integer",
              "title": "1st fragments",
              "minimum": 0
            },
            "last fragments": {
              "$id": "#/properties/qual_thresholds/items/last_fragments",
              "type": "integer",
              "title": "last fragments",
              "minimum": 0
            },
            "reads mapped": {
              "$id": "#/properties/qual_thresholds/items/reads_mapped",
              "type": "integer",
              "title": "reads mapped",
              "minimum": 0
            },
            "reads mapped and paired": {
              "$id": "#/properties/qual_thresholds/items/reads_mapped_and_paired",
              "type": "integer",
              "title": "reads mapped and paired",
              "minimum": 0
            },
            "reads unmapped": {
              "$id": "#/properties/qual_thresholds/items/reads_unmapped",
              "type": "integer",
              "title": "reads unmapped",
              "minimum": 0
            },
            "reads properly paired": {
              "$id": "#/properties/qual_thresholds/items/reads_properly_paired",
              "type": "integer",
              "title": "reads properly paired",
              "minimum": 0
            },
            "reads paired": {
              "$id": "#/properties/qual_thresholds/items/reads_paired",
              "type": "integer",
              "title": "reads paired",
              "minimum": 0
            },
            "reads duplicated": {
              "$id": "#/properties/qual_thresholds/items/reads_duplicated",
              "type": "integer",
              "title": "reads duplicated",
              "minimum": 0
            },
            "reads MQ0": {
              "$id": "#/properties/qual_thresholds/items/reads_MQ0",
              "type": "integer",
              "title": "reads MQ0",
              "minimum": 0
            },
            "reads QC failed": {
              "$id": "#/properties/qual_thresholds/items/reads_QC_failed",
              "type": "integer",
              "title": "reads QC failed",
              "minimum": 0
            },
            "non-primary alignments": {
              "$id": "#/properties/qual_thresholds/items/non-primary_alignments",
              "type": "integer",
              "title": "non-primary alignments",
              "minimum": 0
            },
            "total length": {
              "$id": "#/properties/qual_thresholds/items/total_length",
              "type": "integer",
              "title": "total length",
              "minimum": 0
            },
            "total first fragment length": {
              "$id": "#/properties/qual_thresholds/items/total_first_fragment_length",
              "type": "integer",
              "title": "total first fragment length",
              "minimum": 0
            },
            "total last fragment length": {
              "$id": "#/properties/qual_thresholds/items/total_last_fragment_length",
              "type": "integer",
              "title": "total last fragment length",
              "minimum": 0
            },
            "bases mapped": {
              "$id": "#/properties/qual_thresholds/items/bases_mapped",
              "type": "integer",
              "title": "bases mapped",
              "minimum": 0
            },
            "bases mapped (cigar)": {
              "$id": "#/properties/qual_thresholds/items/bases_mapped_(cigar)",
              "type": "integer",
              "title": "bases mapped (cigar)",
              "minimum": 0
            },
            "bases trimmed": {
              "$id": "#/properties/qual_thresholds/items/bases_trimmed",
              "type": "integer",
              "title": "bases trimmed",
              "minimum": 0
            },
            "bases duplicated": {
              "$id": "#/properties/qual_thresholds/items/bases_duplicated",
              "type": "integer",
              "title": "bases duplicated",
              "minimum": 0
            },
            "mismatches": {
              "$id": "#/properties/qual_thresholds/items/mismatches",
              "type": "integer",
              "title": "mismatches",
              "minimum": 0
            },
            "error rate": {
              "$id": "#/properties/qual_thresholds/items/error_rate",
              "type": "number",
              "title": "error rate",
              "description": "error rate as fractions of 1",
              "minimum": 0,
              "maximum": 1
            },
            "average length": {
              "$id": "#/properties/qual_thresholds/items/average_length",
              "type": "number",
              "title": "average length",
              "minimum": 0
            },
            "average first fragment length": {
              "$id": "#/properties/qual_thresholds/items/average_first_fragment_length",
              "type": "number",
              "title": "average first fragment length",
              "minimum": 0
            },
            "average last fragment length": {
              "$id": "#/properties/qual_thresholds/items/average_last_fragment_length",
              "type": "number",
              "title": "average last fragment length",
              "minimum": 0
            },
            "maximum length": {
              "$id": "#/properties/qual_thresholds/items/maximum_length",
              "type": "integer",
              "title": "maximum length",
              "minimum": 0
            },
            "maximum first fragment length": {
              "$id": "#/properties/qual_thresholds/items/maximum_first_fragment_length",
              "type": "integer",
              "title": "maximum first fragment length",
              "minimum": 0
            },
            "maximum last fragment length": {
              "$id": "#/properties/qual_thresholds/items/maximum_last_fragment_length",
              "type": "integer",
              "title": "maximum last fragment length",
              "minimum": 0
            },
            "average quality": {
              "$id": "#/properties/qual_thresholds/items/average_quality",
              "type": "number",
              "title": "average quality",
              "minimum": 0
            },
            "insert size average": {
              "$id": "#/properties/qual_thresholds/items/insert_size_average",
              "type": "number",
              "title": "insert size average",
              "minimum": 0
            },
            "insert size standard deviation": {
              "$id": "#/properties/qual_thresholds/items/insert_size_standard_deviation",
              "type": "number",
              "title": "insert size standard deviation",
              "minimum": 0
            },
            "inward oriented pairs": {
              "$id": "#/properties/qual_thresholds/items/inward_oriented_pairs",
              "type": "integer",
              "title": "inward oriented pairs",
              "minimum": 0
            },
            "outward oriented pairs": {
              "$id": "#/properties/qual_thresholds/items/outward_oriented_pairs",
              "type": "integer",
              "title": "outward oriented pairs",
              "minimum": 0
            },
            "pairs with other orientation": {
              "$id": "#/properties/qual_thresholds/items/pairs_with_other_orientation",
              "type": "integer",
              "title": "pairs with other orientation",
              "minimum": 0
            },
            "pairs on different chromosomes": {
              "$id": "#/properties/qual_thresholds/items/pairs_on_different_chromosomes",
              "type": "integer",
              "title": "pairs on different chromosomes",
              "minimum": 0
            },
            "percentage of properly paired reads (%)": {
              "$id": "#/properties/qual_thresholds/items/percentage_of_properly_paired_reads",
              "type": "number",
              "title": "percentage of properly paired reads (%)",
              "minimum": 0,
              "maximum": 100
            }
          }
        },
        "min_cov_target": {
          "$id": "#/per_sample_values/min_cov_target",
          "type": "object",
          "title": "Minimal coverage percentage, counted per target",
          "description": "Considering all targets, histogram of distribution regarding \"minimal coverage of...\", the smallest coverage on a target makes the whole target count at that value",
          "patternProperties": {
            "\\d+": {
              "$id": "#/per_sample_values/min_cov_target/entry",
              "type": "number",
              "title": "Minimal coverage value histogram entry",
              "minimum": 0,
              "maximum": 100,
              "examples": [
                100,
                99.9,
                0
              ]
            }
          },
          "additionalProperties": false
        },
        "min_cov_base": {
          "$id": "#/per_sample_values/min_cov_base",
          "type": "object",
          "title": "Minimal coverage percentage, counted per base",
          "description": "Considering all target bases, histogram of distribution regarding \"minimal coverage of...\"",
          "patternProperties": {
            "\\d+": {
              "$id": "#/per_sample_values/min_cov_base/entry",
              "type": "number",
              "title": "Minimal coverage value histogram entry",
              "minimum": 0,
              "maximum": 100,
              "examples": [
                100,
                99.9,
                0
              ]
            }
          },
          "additionalProperties": false
        },
        "summary": {
          "$id": "#/per_sample_values/summary",
          "type": "object",
          "title": "Coverage summary",
          "required": [
            "mean coverage",
            "target count",
            "total target size"
          ],
          "properties": {
            "mean coverage": {
              "$id": "#/per_sample_values/summary/mean_coverage",
              "type": "number",
              "title": "Mean on-target coverage",
              "minimum": 0,
              "examples": [
                0,
                100
              ]
            },
            "target count": {
              "$id": "#/per_sample_values/summary/target_count",
              "type": "integer",
              "title": "Total number of targets",
              "minimum": 0,
              "examples": [
                0,
                100
              ]
            },
            "total target size": {
              "$id": "#/per_sample_values/summary/total_target_size",
              "type": "integer",
              "title": "Total target size in bp",
              "minimum": 0,
              "examples": [
                0,
                100
              ]
            }
          },
          "additionalProperties": false
        },
        "idxstats": {
          "$id": "#/per_sample_values/idxstats",
          "type": "object",
          "patternProperties": {
            ".*": {
              "$id": "#/per_sample_values/idx_stats/per_chrom_values",
              "type": "object",
              "title": "Read count for each chromosome",
              "required": [
                "mapped",
                "unmapped"
              ],
              "properties": {
                "mapped": {
                  "$id": "#/per_sample_values/idx_stats/per_chrom_values/mapped",
                  "type": "integer",
                  "title": "Mapped read count",
                  "description": "Number of mapped read on chromosome",
                  "minimum": 0,
                  "examples": [
                    0,
                    100
                  ]
                },
                "unmapped": {
                  "$id": "#/per_sample_values/idx_stats/per_chrom_values/unmapped",
                  "type": "integer",
                  "title": "Unmapped read count",
                  "description": "Number of unmapped read on chromosome (usually the mate maps)",
                  "minimum": 0,
                  "examples": [
                    0,
                    100
                  ]
                }
              },
              "additionalProperties": false
            }
          }
        }
      }
    }
  }
}