drwxr-xr-x root/root usr/ drwxr-xr-x root/root usr/lib/ drwxr-xr-x root/root usr/lib/R/ drwxr-xr-x root/root usr/lib/R/library/ drwxr-xr-x root/root usr/lib/R/library/Rhtslib/ -rw-r--r-- root/root usr/lib/R/library/Rhtslib/DESCRIPTION -rw-r--r-- root/root usr/lib/R/library/Rhtslib/INDEX drwxr-xr-x root/root usr/lib/R/library/Rhtslib/Meta/ -rw-r--r-- root/root usr/lib/R/library/Rhtslib/Meta/Rd.rds -rw-r--r-- root/root usr/lib/R/library/Rhtslib/Meta/features.rds -rw-r--r-- root/root usr/lib/R/library/Rhtslib/Meta/hsearch.rds -rw-r--r-- root/root usr/lib/R/library/Rhtslib/Meta/links.rds -rw-r--r-- root/root usr/lib/R/library/Rhtslib/Meta/nsInfo.rds -rw-r--r-- root/root usr/lib/R/library/Rhtslib/Meta/package.rds -rw-r--r-- root/root usr/lib/R/library/Rhtslib/Meta/vignette.rds -rw-r--r-- root/root usr/lib/R/library/Rhtslib/NAMESPACE -rw-r--r-- root/root usr/lib/R/library/Rhtslib/NEWS drwxr-xr-x root/root usr/lib/R/library/Rhtslib/R/ -rw-r--r-- root/root usr/lib/R/library/Rhtslib/R/Rhtslib -rw-r--r-- root/root usr/lib/R/library/Rhtslib/R/Rhtslib.rdb -rw-r--r-- root/root usr/lib/R/library/Rhtslib/R/Rhtslib.rdx drwxr-xr-x root/root usr/lib/R/library/Rhtslib/doc/ -rw-r--r-- root/root usr/lib/R/library/Rhtslib/doc/Rhtslib.R -rw-r--r-- root/root usr/lib/R/library/Rhtslib/doc/Rhtslib.Rmd -rw-r--r-- root/root usr/lib/R/library/Rhtslib/doc/Rhtslib.html -rw-r--r-- root/root usr/lib/R/library/Rhtslib/doc/index.html drwxr-xr-x root/root usr/lib/R/library/Rhtslib/help/ -rw-r--r-- root/root usr/lib/R/library/Rhtslib/help/AnIndex -rw-r--r-- root/root usr/lib/R/library/Rhtslib/help/Rhtslib.rdb -rw-r--r-- root/root usr/lib/R/library/Rhtslib/help/Rhtslib.rdx -rw-r--r-- root/root usr/lib/R/library/Rhtslib/help/aliases.rds -rw-r--r-- root/root usr/lib/R/library/Rhtslib/help/paths.rds drwxr-xr-x root/root usr/lib/R/library/Rhtslib/html/ -rw-r--r-- root/root usr/lib/R/library/Rhtslib/html/00Index.html -rw-r--r-- root/root usr/lib/R/library/Rhtslib/html/R.css drwxr-xr-x root/root usr/lib/R/library/Rhtslib/include/ -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/README -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/bam.c -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/bam.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/bam_cat.c -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/bam_plbuf.c -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/bam_plbuf.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/bam_sort.c -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/bam_sort.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/bedidx.c -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/bedidx.h drwxr-xr-x root/root usr/lib/R/library/Rhtslib/include/htslib/ -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/bgzf.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/cram.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/faidx.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/hfile.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/hts.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/hts_defs.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/hts_endian.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/hts_expr.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/hts_log.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/hts_os.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/kbitset.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/kfunc.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/khash.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/khash_str2int.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/klist.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/knetfile.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/kroundup.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/kseq.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/ksort.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/kstring.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/regidx.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/sam.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/synced_bcf_reader.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/tbx.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/thread_pool.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/vcf.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/vcf_sweep.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/htslib/vcfutils.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/sam_opts.c -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/sam_opts.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/sam_utils.c -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/sam_utils.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/samtools-1.7-compat.h -rw-r--r-- root/root usr/lib/R/library/Rhtslib/include/samtools.h drwxr-xr-x root/root usr/lib/R/library/Rhtslib/libs/ -rwxr-xr-x root/root usr/lib/R/library/Rhtslib/libs/Rhtslib.so drwxr-xr-x root/root usr/lib/R/library/Rhtslib/testdata/ -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/auxf#values.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/auxf#values_java.cram -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/auxf.fa -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/auxf.fa.fai -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/c1#bounds.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/c1#clip.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/c1#noseq.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/c1#pad1.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/c1#pad2.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/c1#pad3.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/c1#unknown.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/c1.fa -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/c1.fa.fai -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/c2#pad.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/c2.fa -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/c2.fa.fai -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/ce#1.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/ce#1000.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/ce#2.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/ce#5.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/ce#5b.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/ce#5b_java.cram -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/ce#large_seq.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/ce#supp.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/ce#tag_depadded.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/ce#tag_padded.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/ce#unmap.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/ce#unmap1.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/ce#unmap2.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/ce.fa -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/ce.fa.fai -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/colons.bam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/fieldarith.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/formatcols.vcf -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/formatmissing-out.vcf -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/formatmissing.vcf -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/index.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/index.vcf -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/index2.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/index_dos.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/md#1.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/md.fa -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/md.fa.fai -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/modhdr.expected.vcf -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/no_hdr_sq_1.bam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/no_hdr_sq_1.expected.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/noroundtrip-out.vcf -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/noroundtrip.vcf -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/range.bam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/range.cram -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/realn01.fa -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/realn01.fa.fai -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/realn01.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/realn01_exp-a.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/realn01_exp-e.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/realn01_exp.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/realn02-r.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/realn02.fa -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/realn02.fa.fai -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/realn02.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/realn02_exp-a.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/realn02_exp-e.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/realn02_exp.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/realn03.fa -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/realn03.fa.fai -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/realn03.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/realn03_exp.sam drwxr-xr-x root/root usr/lib/R/library/Rhtslib/testdata/tabix/ -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/tabix/bed_file.bed -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/tabix/gff_file.gff -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/tabix/large_chr.vcf -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/tabix/vcf_file.bcf -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/tabix/vcf_file.vcf -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/test-vcf-hdr-in.vcf -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/vcf_meta_meta.vcf -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/xx#MD.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/xx#MD2.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/xx#blank.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/xx#large_aux.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/xx#large_aux2.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/xx#large_aux_java.cram -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/xx#minimal.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/xx#pair.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/xx#repeated.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/xx#rg.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/xx#tlen.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/xx#tlen2.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/xx#triplet.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/xx#unsorted.sam -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/xx.fa -rw-r--r-- root/root usr/lib/R/library/Rhtslib/testdata/xx.fa.fai drwxr-xr-x root/root usr/lib/R/library/Rhtslib/usrlib/ -rw-r--r-- root/root usr/lib/R/library/Rhtslib/usrlib/libhts.a -rwxr-xr-x root/root usr/lib/R/library/Rhtslib/usrlib/libhts.so lrwxrwxrwx root/root usr/lib/R/library/Rhtslib/usrlib/libhts.so.2 -> libhts.so