data/samtools-1.11/AUTHORS: ASCII text data/samtools-1.11/ChangeLog.old: Git commit 2 data/samtools-1.11/INSTALL: ASCII text data/samtools-1.11/LICENSE: ASCII text data/samtools-1.11/Makefile: makefile script, ASCII text data/samtools-1.11/NEWS: Variant Call Format (VCF) version 4.1' as well as the samtools, UTF-8 Unicode text data/samtools-1.11/README: ASCII text data/samtools-1.11/amplicon_stats.c: C source, ASCII text data/samtools-1.11/bam.c: C source, ASCII text data/samtools-1.11/bam.h: C source, ASCII text data/samtools-1.11/bam2bcf.c: C source, ASCII text data/samtools-1.11/bam2bcf.h: C source, ASCII text data/samtools-1.11/bam2bcf_indel.c: C source, ASCII text data/samtools-1.11/bam2depth.c: C source, ASCII text data/samtools-1.11/bam_addrprg.c: C source, ASCII text data/samtools-1.11/bam_ampliconclip.c: C source, ASCII text data/samtools-1.11/bam_ampliconclip.h: C source, ASCII text data/samtools-1.11/bam_aux.c: C source, ASCII text data/samtools-1.11/bam_cat.c: C source, ASCII text data/samtools-1.11/bam_color.c: C source, ASCII text data/samtools-1.11/bam_endian.h: C source, ASCII text data/samtools-1.11/bam_fastq.c: C source, ASCII text data/samtools-1.11/bam_flags.c: C source, ASCII text data/samtools-1.11/bam_index.c: C source, ASCII text data/samtools-1.11/bam_lpileup.c: C source, ASCII text data/samtools-1.11/bam_lpileup.h: C source, ASCII text data/samtools-1.11/bam_markdup.c: C source, ASCII text data/samtools-1.11/bam_mate.c: C source, ASCII text data/samtools-1.11/bam_md.c: C source, ASCII text data/samtools-1.11/bam_plbuf.c: C source, ASCII text data/samtools-1.11/bam_plbuf.h: C source, ASCII text data/samtools-1.11/bam_plcmd.c: C source, ASCII text data/samtools-1.11/bam_quickcheck.c: C source, ASCII text data/samtools-1.11/bam_reheader.c: C source, ASCII text data/samtools-1.11/bam_rmdup.c: C source, ASCII text data/samtools-1.11/bam_rmdupse.c: C source, ASCII text data/samtools-1.11/bam_sort.c: C source, ASCII text data/samtools-1.11/bam_split.c: C source, ASCII text data/samtools-1.11/bam_stat.c: C source, ASCII text data/samtools-1.11/bam_tview.c: C source, UTF-8 Unicode text data/samtools-1.11/bam_tview.h: C source, UTF-8 Unicode text data/samtools-1.11/bam_tview_curses.c: C source, UTF-8 Unicode text data/samtools-1.11/bam_tview_html.c: C source, UTF-8 Unicode text data/samtools-1.11/bamshuf.c: C source, ASCII text data/samtools-1.11/bamtk.c: C source, ASCII text data/samtools-1.11/bedcov.c: C source, ASCII text data/samtools-1.11/bedidx.c: C source, ASCII text data/samtools-1.11/bedidx.h: C source, ASCII text data/samtools-1.11/config.mk.in: makefile script, ASCII text data/samtools-1.11/configure.ac: M4 macro processor script, ASCII text data/samtools-1.11/coverage.c: C source, UTF-8 Unicode text data/samtools-1.11/cut_target.c: C source, ASCII text data/samtools-1.11/dict.c: C source, ASCII text data/samtools-1.11/doc/samtools-addreplacerg.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-ampliconclip.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-ampliconstats.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-bedcov.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-calmd.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-cat.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-collate.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-coverage.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-depad.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-depth.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-dict.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-faidx.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-fasta.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-fastq.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-fixmate.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-flags.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-flagstat.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-fqidx.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-idxstats.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-index.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-markdup.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-merge.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-mpileup.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-phase.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-quickcheck.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-reheader.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-rmdup.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-sort.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-split.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-stats.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-targetcut.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-tview.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools-view.1: troff or preprocessor input, ASCII text data/samtools-1.11/doc/samtools.1: troff or preprocessor input, ASCII text data/samtools-1.11/examples/00README.txt: ASCII text data/samtools-1.11/examples/ex1.fa: ASCII text data/samtools-1.11/examples/ex1.sam.gz: gzip compressed data, last modified: Wed Apr 8 14:16:26 2009, from Unix, original size modulo 2^32 559422 data/samtools-1.11/examples/toy.fa: ASCII text data/samtools-1.11/examples/toy.sam: Sequence Alignment/Map (SAM), ASCII text data/samtools-1.11/faidx.c: C source, ASCII text data/samtools-1.11/install-sh: POSIX shell script, ASCII text executable data/samtools-1.11/lz4/LICENSE: ASCII text data/samtools-1.11/lz4/lz4.c: C source, ASCII text data/samtools-1.11/lz4/lz4.h: C source, ASCII text data/samtools-1.11/m4/ax_with_htslib.m4: M4 macro processor script, ASCII text data/samtools-1.11/m4/hts_prog_cc_warnings.m4: M4 macro processor script, ASCII text data/samtools-1.11/m4/hts_with_curses.m4: ASCII text data/samtools-1.11/misc/HmmGlocal.java: Java source, ASCII text data/samtools-1.11/misc/ace2sam.c: C source, ASCII text data/samtools-1.11/misc/blast2sam.pl: Perl script text executable data/samtools-1.11/misc/bowtie2sam.pl: Perl script text executable data/samtools-1.11/misc/export2sam.pl: Perl script text executable data/samtools-1.11/misc/interpolate_sam.pl: Perl script text executable data/samtools-1.11/misc/maq2sam.c: C source, ASCII text data/samtools-1.11/misc/md5fa.c: C source, ASCII text data/samtools-1.11/misc/md5sum-lite.c: C source, ASCII text data/samtools-1.11/misc/novo2sam.pl: Perl script text executable data/samtools-1.11/misc/plot-ampliconstats: Perl script text executable data/samtools-1.11/misc/plot-bamstats: Perl script text executable data/samtools-1.11/misc/psl2sam.pl: Perl script text executable data/samtools-1.11/misc/r2plot.lua: Lua script, ASCII text executable data/samtools-1.11/misc/sam2vcf.pl: Perl script text executable data/samtools-1.11/misc/samtools.pl: Perl script text executable data/samtools-1.11/misc/samtools_tab_completion: ASCII text data/samtools-1.11/misc/seq_cache_populate.pl: Perl script text executable data/samtools-1.11/misc/soap2sam.pl: Perl script text executable data/samtools-1.11/misc/vcfutils.lua: Lua script, ASCII text executable data/samtools-1.11/misc/wgsim.1: troff or preprocessor input, ASCII text data/samtools-1.11/misc/wgsim.c: C source, ASCII text data/samtools-1.11/misc/wgsim_eval.pl: Perl script text executable data/samtools-1.11/misc/zoom2sam.pl: Perl script text executable data/samtools-1.11/padding.c: C source, ASCII text data/samtools-1.11/phase.c: C source, ASCII text data/samtools-1.11/sam.c: C source, ASCII text data/samtools-1.11/sam.h: C source, ASCII text data/samtools-1.11/sam_opts.c: C source, ASCII text data/samtools-1.11/sam_opts.h: C source, ASCII text data/samtools-1.11/sam_utils.c: C source, ASCII text data/samtools-1.11/sam_view.c: C source, ASCII text data/samtools-1.11/sample.c: C source, ASCII text data/samtools-1.11/sample.h: C source, ASCII text data/samtools-1.11/samtools.h: C source, ASCII text data/samtools-1.11/stats.c: C source, ASCII text data/samtools-1.11/stats_isize.c: C source, ASCII text data/samtools-1.11/stats_isize.h: C source, ASCII text data/samtools-1.11/test/addrprg/1_fixup.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/addrprg/1_fixup.sam.expected: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/addrprg/1_fixup.sam.expected.err: empty data/samtools-1.11/test/addrprg/2_fixup_orphan.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/addrprg/2_fixup_orphan.sam.expected: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/addrprg/2_fixup_orphan.sam.expected.err: empty data/samtools-1.11/test/addrprg/3_fixup.sam.expected: empty data/samtools-1.11/test/addrprg/3_fixup.sam.expected.err: ASCII text data/samtools-1.11/test/addrprg/4_fixup_norg.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/addrprg/4_fixup_norg.sam.expected: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/addrprg/4_fixup_norg.sam.expected.err: empty data/samtools-1.11/test/ampliconclip/1_delete_tag.expected.sam: Sequence Alignment/Map (SAM), with header version 1.5 data/samtools-1.11/test/ampliconclip/1_fail.expected.sam: Sequence Alignment/Map (SAM), with header version 1.5 data/samtools-1.11/test/ampliconclip/1_filter.expected.sam: Sequence Alignment/Map (SAM), with header version 1.5 data/samtools-1.11/test/ampliconclip/1_hard_clipped.expected.sam: Sequence Alignment/Map (SAM), with header version 1.5 data/samtools-1.11/test/ampliconclip/1_original_tag.expected.sam: Sequence Alignment/Map (SAM), with header version 1.5 data/samtools-1.11/test/ampliconclip/1_soft_clipped.expected.sam: Sequence Alignment/Map (SAM), with header version 1.5 data/samtools-1.11/test/ampliconclip/1_soft_clipped_strand.expected.sam: Sequence Alignment/Map (SAM), with header version 1.5 data/samtools-1.11/test/ampliconclip/1_test_data.sam: Sequence Alignment/Map (SAM), with header version 1.5 data/samtools-1.11/test/ampliconclip/2_both_clipped.expected.sam: Sequence Alignment/Map (SAM), with header version 1.5 data/samtools-1.11/test/ampliconclip/2_both_test_data.sam: Sequence Alignment/Map (SAM), with header version 1.5 data/samtools-1.11/test/ampliconclip/ac_test.bed: ASCII text data/samtools-1.11/test/ampliconstats/stats.expected.txt: ASCII text data/samtools-1.11/test/bam2fq/1.1.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/1.2.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/1.stdout.expected: empty data/samtools-1.11/test/bam2fq/10.1.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/10.2.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/10.s.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/11.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/12.1.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/12.2.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/12.i.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/12.s.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/13.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/2.1.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/2.2.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/2.s.fq.expected: empty data/samtools-1.11/test/bam2fq/2.stdout.expected: empty data/samtools-1.11/test/bam2fq/3.1.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/3.2.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/3.s.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/3.stdout.expected: empty data/samtools-1.11/test/bam2fq/4.1.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/4.2.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/4.s.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/4.stdout.expected: empty data/samtools-1.11/test/bam2fq/5.1.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/5.2.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/5.s.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/6.1.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/6.2.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/6.s.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/7.1.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/7.2.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/7.s.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/8.1.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/8.2.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/8.i.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/8.s.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/9.1.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/9.2.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/bc.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/bc10.fq.expected: ASCII text data/samtools-1.11/test/bam2fq/bc_split.fq.expected: ASCII text data/samtools-1.11/test/bedcov/bedcov.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 2849 data/samtools-1.11/test/bedcov/bedcov.bam.bai: SAMtools BAI (BAM indexing format), with 195 reference sequences data/samtools-1.11/test/bedcov/bedcov.bed: ASCII text data/samtools-1.11/test/bedcov/bedcov.expected: ASCII text data/samtools-1.11/test/bedcov/bedcov_gG.bed: ASCII text data/samtools-1.11/test/bedcov/bedcov_gG.expected: ASCII text data/samtools-1.11/test/bedcov/bedcov_j.expected: ASCII text data/samtools-1.11/test/collate/1_fast_collate.sam.expected: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/collate/2_fast_collate_with_tmp_used.sam.expected: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/collate/collate.expected.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/collate/fast_collate.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/dat/bam2fq.001.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/dat/bam2fq.002.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/dat/bam2fq.003.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/dat/bam2fq.004.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/dat/bam2fq.005.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/dat/bam2fq.010.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/dat/bam2fq.013.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/dat/bam2fq.703.sam: Sequence Alignment/Map (SAM), with header version 1.5 data/samtools-1.11/test/dat/cat.hdr: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/dat/cram_md5/08c04d512d4797d9ba2a156c1daba468: ASCII text data/samtools-1.11/test/dat/cram_md5/7c35feac7036c1cdef3bee0cc4b21437: ASCII text data/samtools-1.11/test/dat/cram_md5/89b96de7acc5918c2858ef92710be7d4: ASCII text data/samtools-1.11/test/dat/cram_md5/8a3d8deb9edd4ce3346b6061fcee6d0b: ASCII text data/samtools-1.11/test/dat/depad.001.fa: ASCII text data/samtools-1.11/test/dat/depad.001.fa.fai: ASCII text data/samtools-1.11/test/dat/depad.001p.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/dat/depad.001u.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/dat/dict.alias.fa: ASCII text data/samtools-1.11/test/dat/dict.alias.out: ASCII text data/samtools-1.11/test/dat/dict.fa: data data/samtools-1.11/test/dat/dict.out: Sequence Alignment/Map (SAM), with header version 1.0 data/samtools-1.11/test/dat/empty.expected: empty data/samtools-1.11/test/dat/large_chrom.out: Sequence Alignment/Map (SAM), ASCII text data/samtools-1.11/test/dat/large_chrom.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/dat/large_chrom_bai_index.err: ASCII text data/samtools-1.11/test/dat/mpileup.1.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/samtools-1.11/test/dat/mpileup.2.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/samtools-1.11/test/dat/mpileup.3.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/samtools-1.11/test/dat/mpileup.err.1: ASCII text data/samtools-1.11/test/dat/mpileup.out.1: ASCII text data/samtools-1.11/test/dat/mpileup.out.2: Variant Call Format (VCF) version 4.2, ASCII text data/samtools-1.11/test/dat/mpileup.out.3: ASCII text data/samtools-1.11/test/dat/mpileup.out.4: Variant Call Format (VCF) version 4.2, ASCII text, with very long lines data/samtools-1.11/test/dat/mpileup.out.5: ASCII text data/samtools-1.11/test/dat/mpileup.ref.fa: ASCII text data/samtools-1.11/test/dat/mpileup.ref.fa.fai: ASCII text data/samtools-1.11/test/dat/test_input_1_a.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 216 data/samtools-1.11/test/dat/test_input_1_a.bam.bai.expected: SAMtools BAI (BAM indexing format), with 4 reference sequences data/samtools-1.11/test/dat/test_input_1_a.cram: CRAM version 3.0 (identified as test_input_1_a.cram) data/samtools-1.11/test/dat/test_input_1_a.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/dat/test_input_1_a_regex.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/dat/test_input_1_ab.X.expected: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/dat/test_input_1_b.X.expected: Sequence Alignment/Map (SAM), ASCII text data/samtools-1.11/test/dat/test_input_1_b.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 222 data/samtools-1.11/test/dat/test_input_1_b.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/dat/test_input_1_b_regex.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/dat/test_input_1_c.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 213 data/samtools-1.11/test/dat/test_input_1_c.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/dat/test_input_1_d.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/dat/view.001.01.bed: ASCII text data/samtools-1.11/test/dat/view.001.02.bed: ASCII text data/samtools-1.11/test/dat/view.001.fa: ASCII text data/samtools-1.11/test/dat/view.001.fa.fai: ASCII text data/samtools-1.11/test/dat/view.001.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/dat/view.002.01.bed: ASCII text data/samtools-1.11/test/dat/view.002.02.bed: ASCII text data/samtools-1.11/test/dat/view.002.fa: ASCII text data/samtools-1.11/test/dat/view.002.fa.fai: ASCII text data/samtools-1.11/test/dat/view.002.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/dat/view.003.expected.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/dat/view.003.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/dat/view.004.expected.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/fixmate/1_coord_sort.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/fixmate/1_coord_sort.sam.expected: empty data/samtools-1.11/test/fixmate/1_coord_sort.sam.expected.err: ASCII text data/samtools-1.11/test/fixmate/2_isize_overflow.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/fixmate/2_isize_overflow.sam.expected: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/fixmate/3_reverse_read_pp_lt.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/fixmate/3_reverse_read_pp_lt.sam.expected: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/fixmate/4_reverse_read_pp_equal.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/fixmate/4_reverse_read_pp_equal.sam.expected: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/fixmate/5_ct.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/fixmate/5_ct.sam.expected: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/fixmate/6_ct_replace.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/fixmate/6_ct_replace.sam.expected: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/fixmate/7_two_read_mapped.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/fixmate/7_two_read_mapped.sam.expected: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/fixmate/8_isize_overflow_64bit.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/fixmate/8_isize_overflow_64bit.sam.expected: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/idxstats/test_input_1_a.bam.expected: ASCII text data/samtools-1.11/test/idxstats/test_input_1_a.bam.expected.err: empty data/samtools-1.11/test/large_pos/depth.expected.out: ASCII text data/samtools-1.11/test/large_pos/depth_bed.expected.out: ASCII text data/samtools-1.11/test/large_pos/longref.sam: Sequence Alignment/Map (SAM), with header version 1.6 data/samtools-1.11/test/large_pos/longref2.sam: Sequence Alignment/Map (SAM), with header version 1.6 data/samtools-1.11/test/large_pos/longref3.expected.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/large_pos/longref3.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/large_pos/longref_idx.expected.sam: Sequence Alignment/Map (SAM), with header version 1.6 data/samtools-1.11/test/large_pos/longref_name.sam: Sequence Alignment/Map (SAM), with header version 1.6 data/samtools-1.11/test/large_pos/merge.expected.sam: Sequence Alignment/Map (SAM), with header version 1.6 data/samtools-1.11/test/large_pos/test.bed: ASCII text data/samtools-1.11/test/large_pos/tview.expected.out: ASCII text data/samtools-1.11/test/maintainer/check_copyright.pl: Perl script text executable data/samtools-1.11/test/maintainer/check_spaces.pl: Perl script text executable data/samtools-1.11/test/markdup/1_name_sort.expected.sam: empty data/samtools-1.11/test/markdup/1_name_sort.expected.sam.err: ASCII text data/samtools-1.11/test/markdup/1_name_sort.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/markdup/2_bad_order.expected.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/markdup/2_bad_order.expected.sam.err: ASCII text data/samtools-1.11/test/markdup/2_bad_order.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/markdup/3_missing_mc.expected.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/markdup/3_missing_mc.expected.sam.err: ASCII text data/samtools-1.11/test/markdup/3_missing_mc.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/markdup/4_missing_ms.expected.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/markdup/4_missing_ms.expected.sam.err: ASCII text data/samtools-1.11/test/markdup/4_missing_ms.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/markdup/5_markdup.expected.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/markdup/5_markdup.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/markdup/6_remove_dups.expected.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/markdup/6_remove_dups.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/markdup/7_mark_supp_dup.expected.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/markdup/7_mark_supp_dup.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/markdup/8_optical_dup.expected.sam: Sequence Alignment/Map (SAM), with header version 1.5 data/samtools-1.11/test/markdup/8_optical_dup.sam: Sequence Alignment/Map (SAM), with header version 1.5 data/samtools-1.11/test/markdup/9_optical_dup_qcfail.expected.sam: Sequence Alignment/Map (SAM), with header version 1.5 data/samtools-1.11/test/markdup/9_optical_dup_qcfail.sam: Sequence Alignment/Map (SAM), with header version 1.5 data/samtools-1.11/test/merge/2.merge.expected.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/merge/3.merge.expected.err: ASCII text data/samtools-1.11/test/merge/3.merge.expected.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/merge/4.merge.expected.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/merge/5.merge.expected.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/merge/6.merge.expected.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/merge/7.merge.expected.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/merge/merge.bed: ASCII text data/samtools-1.11/test/merge/merge.bed.1.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/merge/merge.bed.2.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/merge/merge.bed.expected.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/merge/tag.pg.merge.expected.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/merge/tag.pg.n.merge.expected.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/merge/test_3.fofn: ASCII text data/samtools-1.11/test/merge/test_bam_translate.c: C source, ASCII text data/samtools-1.11/test/merge/test_header.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/merge/test_no_pg_rg_co.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/merge/test_rtrans_build.c: C source, ASCII text data/samtools-1.11/test/merge/test_trans_tbl_init.c: C source, ASCII text data/samtools-1.11/test/mpileup/1read.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 235 data/samtools-1.11/test/mpileup/1read.sam: ASCII text data/samtools-1.11/test/mpileup/anomalous.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/samtools-1.11/test/mpileup/c1#clip.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 62 data/samtools-1.11/test/mpileup/c1#pad1.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 62 data/samtools-1.11/test/mpileup/c1#pad2.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 62 data/samtools-1.11/test/mpileup/c1#pad3.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 91 data/samtools-1.11/test/mpileup/c1.fa: ASCII text data/samtools-1.11/test/mpileup/c1.fa.fai: ASCII text data/samtools-1.11/test/mpileup/ce#5b.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 288 data/samtools-1.11/test/mpileup/ce#5b.bam.bai: SAMtools BAI (BAM indexing format), with 5 reference sequences data/samtools-1.11/test/mpileup/ce#5b.cram: CRAM version 2.0 (identified as -) data/samtools-1.11/test/mpileup/ce#5b.cram.crai: gzip compressed data, from Unix, original size modulo 2^32 110 data/samtools-1.11/test/mpileup/ce#5b.sam: Sequence Alignment/Map (SAM), ASCII text, with very long lines data/samtools-1.11/test/mpileup/ce#large_seq.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 80 data/samtools-1.11/test/mpileup/ce#unmap.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 33 data/samtools-1.11/test/mpileup/ce#unmap1.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 272 data/samtools-1.11/test/mpileup/ce#unmap2.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 272 data/samtools-1.11/test/mpileup/ce.fa: ASCII text data/samtools-1.11/test/mpileup/ce.fa.fai: ASCII text data/samtools-1.11/test/mpileup/deep.sam: ASCII text data/samtools-1.11/test/mpileup/depth.reg: ASCII text data/samtools-1.11/test/mpileup/depth_del.sam: ASCII text data/samtools-1.11/test/mpileup/expected/1.out.f3-6.gz: gzip compressed data, was "1.out.f3-6", last modified: Wed Jul 29 10:08:55 2015, max compression, from Unix, original size modulo 2^32 8152540 data/samtools-1.11/test/mpileup/expected/10.out: ASCII text data/samtools-1.11/test/mpileup/expected/11.out: ASCII text data/samtools-1.11/test/mpileup/expected/12.out: ASCII text data/samtools-1.11/test/mpileup/expected/13.out: ASCII text data/samtools-1.11/test/mpileup/expected/14.out: ASCII text data/samtools-1.11/test/mpileup/expected/15.out: ASCII text data/samtools-1.11/test/mpileup/expected/16.out: ASCII text data/samtools-1.11/test/mpileup/expected/17.out: ASCII text data/samtools-1.11/test/mpileup/expected/18.out: ASCII text data/samtools-1.11/test/mpileup/expected/19.out: ASCII text data/samtools-1.11/test/mpileup/expected/2.out: empty data/samtools-1.11/test/mpileup/expected/20.out: ASCII text data/samtools-1.11/test/mpileup/expected/21.out: ASCII text data/samtools-1.11/test/mpileup/expected/22.out: ASCII text data/samtools-1.11/test/mpileup/expected/23.out: ASCII text data/samtools-1.11/test/mpileup/expected/24.out: ASCII text data/samtools-1.11/test/mpileup/expected/25.out: ASCII text data/samtools-1.11/test/mpileup/expected/26.out: ASCII text data/samtools-1.11/test/mpileup/expected/27.out: ASCII text data/samtools-1.11/test/mpileup/expected/28.out: ASCII text data/samtools-1.11/test/mpileup/expected/29.out: empty data/samtools-1.11/test/mpileup/expected/3.out: empty data/samtools-1.11/test/mpileup/expected/30.out: ASCII text data/samtools-1.11/test/mpileup/expected/31.out: ASCII text data/samtools-1.11/test/mpileup/expected/32.out: ASCII text data/samtools-1.11/test/mpileup/expected/33.out: ASCII text data/samtools-1.11/test/mpileup/expected/34.out: ASCII text data/samtools-1.11/test/mpileup/expected/35.out: ASCII text data/samtools-1.11/test/mpileup/expected/37.out: ASCII text data/samtools-1.11/test/mpileup/expected/38.out: ASCII text data/samtools-1.11/test/mpileup/expected/39.out: ASCII text data/samtools-1.11/test/mpileup/expected/4.out: ASCII text data/samtools-1.11/test/mpileup/expected/40.out: ASCII text data/samtools-1.11/test/mpileup/expected/41.out: ASCII text data/samtools-1.11/test/mpileup/expected/42.out: empty data/samtools-1.11/test/mpileup/expected/43.out: ASCII text data/samtools-1.11/test/mpileup/expected/44.out: ASCII text data/samtools-1.11/test/mpileup/expected/45.out: ASCII text data/samtools-1.11/test/mpileup/expected/46.out: ASCII text data/samtools-1.11/test/mpileup/expected/47.out: ASCII text data/samtools-1.11/test/mpileup/expected/48.out: ASCII text data/samtools-1.11/test/mpileup/expected/49.out: ASCII text data/samtools-1.11/test/mpileup/expected/5.out: ASCII text data/samtools-1.11/test/mpileup/expected/50.out: ASCII text data/samtools-1.11/test/mpileup/expected/51.out: ASCII text data/samtools-1.11/test/mpileup/expected/52.out: Variant Call Format (VCF) version 4.2, ASCII text data/samtools-1.11/test/mpileup/expected/53.out: ASCII text data/samtools-1.11/test/mpileup/expected/54.out: ASCII text data/samtools-1.11/test/mpileup/expected/55.out: ASCII text data/samtools-1.11/test/mpileup/expected/56.out: ASCII text data/samtools-1.11/test/mpileup/expected/57.out: ASCII text data/samtools-1.11/test/mpileup/expected/58.out: ASCII text data/samtools-1.11/test/mpileup/expected/59.out: ASCII text data/samtools-1.11/test/mpileup/expected/6.out: ASCII text data/samtools-1.11/test/mpileup/expected/60.out: empty data/samtools-1.11/test/mpileup/expected/61.out: ASCII text data/samtools-1.11/test/mpileup/expected/62.out: empty data/samtools-1.11/test/mpileup/expected/63.out: ASCII text data/samtools-1.11/test/mpileup/expected/64.out: empty data/samtools-1.11/test/mpileup/expected/65.out: ASCII text data/samtools-1.11/test/mpileup/expected/66.out: empty data/samtools-1.11/test/mpileup/expected/67.out: ASCII text data/samtools-1.11/test/mpileup/expected/68.out: empty data/samtools-1.11/test/mpileup/expected/69.out: empty data/samtools-1.11/test/mpileup/expected/7.out: ASCII text data/samtools-1.11/test/mpileup/expected/70.out: ASCII text data/samtools-1.11/test/mpileup/expected/71.out: ASCII text data/samtools-1.11/test/mpileup/expected/72.out: empty data/samtools-1.11/test/mpileup/expected/73.out: ASCII text data/samtools-1.11/test/mpileup/expected/74.out: empty data/samtools-1.11/test/mpileup/expected/75.out: ASCII text data/samtools-1.11/test/mpileup/expected/76.out: ASCII text data/samtools-1.11/test/mpileup/expected/77.out: CSV text data/samtools-1.11/test/mpileup/expected/78.out: ASCII text data/samtools-1.11/test/mpileup/expected/79.out: ASCII text data/samtools-1.11/test/mpileup/expected/8.out: ASCII text data/samtools-1.11/test/mpileup/expected/9.out: ASCII text data/samtools-1.11/test/mpileup/expected/a0.out: ASCII text data/samtools-1.11/test/mpileup/expected/a1.out: ASCII text data/samtools-1.11/test/mpileup/expected/a10.out: ASCII text data/samtools-1.11/test/mpileup/expected/a11.out: ASCII text data/samtools-1.11/test/mpileup/expected/a13.out: ASCII text data/samtools-1.11/test/mpileup/expected/a14.out: ASCII text data/samtools-1.11/test/mpileup/expected/a15.out: ASCII text data/samtools-1.11/test/mpileup/expected/a16.out: ASCII text data/samtools-1.11/test/mpileup/expected/a17.out: ASCII text data/samtools-1.11/test/mpileup/expected/a2.out: ASCII text data/samtools-1.11/test/mpileup/expected/a3.out: ASCII text data/samtools-1.11/test/mpileup/expected/a4.out: ASCII text data/samtools-1.11/test/mpileup/expected/a5.out: ASCII text data/samtools-1.11/test/mpileup/expected/a6.out: ASCII text data/samtools-1.11/test/mpileup/expected/a8.out: ASCII text data/samtools-1.11/test/mpileup/expected/a9.out: ASCII text data/samtools-1.11/test/mpileup/expected/d1_1.out: ASCII text data/samtools-1.11/test/mpileup/expected/d1_12.out: ASCII text data/samtools-1.11/test/mpileup/expected/d1_2.out: ASCII text data/samtools-1.11/test/mpileup/expected/d2_12r.out: ASCII text data/samtools-1.11/test/mpileup/expected/d3_12.out: ASCII text data/samtools-1.11/test/mpileup/expected/d3_12r1a.out: ASCII text data/samtools-1.11/test/mpileup/expected/d3_12r2a.out: ASCII text data/samtools-1.11/test/mpileup/expected/d3_3.out: ASCII text data/samtools-1.11/test/mpileup/expected/d4_12.out: ASCII text data/samtools-1.11/test/mpileup/expected/d4_12b.out: ASCII text data/samtools-1.11/test/mpileup/expected/d4_12r.out: ASCII text data/samtools-1.11/test/mpileup/expected/d5_all1.out: ASCII text data/samtools-1.11/test/mpileup/expected/d5_all2.out: ASCII text data/samtools-1.11/test/mpileup/expected/d5_all3.out: ASCII text data/samtools-1.11/test/mpileup/expected/d5_all4.out: ASCII text data/samtools-1.11/test/mpileup/expected/d5_b3.out: ASCII text data/samtools-1.11/test/mpileup/expected/d5_b3a.out: ASCII text data/samtools-1.11/test/mpileup/expected/d5_b3aa.out: ASCII text data/samtools-1.11/test/mpileup/expected/d5_blank.out: empty data/samtools-1.11/test/mpileup/expected/d5_xx1.out: ASCII text data/samtools-1.11/test/mpileup/expected/d5_xx2.out: ASCII text data/samtools-1.11/test/mpileup/expected/d5_xx3.out: ASCII text data/samtools-1.11/test/mpileup/expected/d5_xy1.out: ASCII text data/samtools-1.11/test/mpileup/expected/d6_nodel.out: ASCII text data/samtools-1.11/test/mpileup/expected/d6_wdel.out: ASCII text data/samtools-1.11/test/mpileup/expected/d7_nodup.out: ASCII text data/samtools-1.11/test/mpileup/expected/m5_all1.out: ASCII text data/samtools-1.11/test/mpileup/expected/m5_all2.out: ASCII text data/samtools-1.11/test/mpileup/expected/m5_all3.out: ASCII text data/samtools-1.11/test/mpileup/expected/m5_b3.out: ASCII text data/samtools-1.11/test/mpileup/expected/m5_b3a.out: ASCII text data/samtools-1.11/test/mpileup/expected/m5_b3aa.out: ASCII text data/samtools-1.11/test/mpileup/expected/m5_blank.out: empty data/samtools-1.11/test/mpileup/expected/m5_xx1.out: ASCII text data/samtools-1.11/test/mpileup/expected/m5_xx2.out: ASCII text data/samtools-1.11/test/mpileup/expected/m5_xx3.out: ASCII text data/samtools-1.11/test/mpileup/expected/m5_xy1.out: ASCII text data/samtools-1.11/test/mpileup/expected/mp_D.out: ASCII text data/samtools-1.11/test/mpileup/expected/mp_DI.out: ASCII text data/samtools-1.11/test/mpileup/expected/mp_I.out: ASCII text data/samtools-1.11/test/mpileup/expected/mp_ID.out: ASCII text data/samtools-1.11/test/mpileup/expected/mp_ID_rev.out: ASCII text data/samtools-1.11/test/mpileup/expected/mp_N.out: ASCII text data/samtools-1.11/test/mpileup/expected/mp_N2.out: ASCII text data/samtools-1.11/test/mpileup/expected/mp_P.out: ASCII text data/samtools-1.11/test/mpileup/indels.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/samtools-1.11/test/mpileup/md5/02099b2aad2cfe707759353724fb40ae: ASCII text, with no line terminators data/samtools-1.11/test/mpileup/md5/0d4dfc45807d6a11439e858605cb364d: ASCII text, with no line terminators data/samtools-1.11/test/mpileup/md5/351f64d4f4f9ddd45b35336ad97aa6de: ASCII text, with very long lines, with no line terminators data/samtools-1.11/test/mpileup/md5/6ec590eb82c361a61e6baabce20109bc: ASCII text, with no line terminators data/samtools-1.11/test/mpileup/md5/6f60cdf4c739651ae72d53e2e94825c1: ASCII text, with no line terminators data/samtools-1.11/test/mpileup/md5/73d180d5cb3860a2713927b6812eab0e: ASCII text, with no line terminators data/samtools-1.11/test/mpileup/mp.fa: ASCII text data/samtools-1.11/test/mpileup/mp.fa.fai: ASCII text data/samtools-1.11/test/mpileup/mp_D.sam: ASCII text data/samtools-1.11/test/mpileup/mp_DI.sam: ASCII text data/samtools-1.11/test/mpileup/mp_I.sam: ASCII text data/samtools-1.11/test/mpileup/mp_ID.sam: ASCII text data/samtools-1.11/test/mpileup/mp_ID_rev.sam: ASCII text data/samtools-1.11/test/mpileup/mp_N.sam: ASCII text data/samtools-1.11/test/mpileup/mp_N2.sam: ASCII text data/samtools-1.11/test/mpileup/mp_P.sam: ASCII text data/samtools-1.11/test/mpileup/mpileup-E.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 93 data/samtools-1.11/test/mpileup/mpileup.1.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 5165 data/samtools-1.11/test/mpileup/mpileup.1.bam.bai: SAMtools BAI (BAM indexing format), with 86 reference sequences data/samtools-1.11/test/mpileup/mpileup.2.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 4678 data/samtools-1.11/test/mpileup/mpileup.3.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 4679 data/samtools-1.11/test/mpileup/mpileup.ref.fa: ASCII text data/samtools-1.11/test/mpileup/mpileup.ref.fa.fai: ASCII text data/samtools-1.11/test/mpileup/mpileup.reg: ASCII text data/samtools-1.11/test/mpileup/overlap.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 96 data/samtools-1.11/test/mpileup/overlap50.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/samtools-1.11/test/mpileup/overlapIllumina.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 295 data/samtools-1.11/test/mpileup/regions: ASCII text data/samtools-1.11/test/mpileup/regression.sh: POSIX shell script, ASCII text executable data/samtools-1.11/test/mpileup/xx#depth1.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/mpileup/xx#depth2.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/mpileup/xx#depth3.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/mpileup/xx#depth4.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/mpileup/xx#minimal.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 71 data/samtools-1.11/test/mpileup/xx#triplet.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 71 data/samtools-1.11/test/mpileup/xx.bed: ASCII text data/samtools-1.11/test/mpileup/xx.bed2: ASCII text data/samtools-1.11/test/mpileup/xx.bed3: ASCII text data/samtools-1.11/test/mpileup/xx.fa: ASCII text data/samtools-1.11/test/mpileup/xx.fa.fai: ASCII text data/samtools-1.11/test/quickcheck/1.quickcheck.badeof.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 376 data/samtools-1.11/test/quickcheck/10.quickcheck.notargets.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 71 data/samtools-1.11/test/quickcheck/2.quickcheck.badheader.bam: gzip compressed data, extra field, original size modulo 2^32 0 data/samtools-1.11/test/quickcheck/3.quickcheck.ok.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 376 data/samtools-1.11/test/quickcheck/4.quickcheck.ok.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 375 data/samtools-1.11/test/quickcheck/5.quickcheck.scramble30.truncated.cram: CRAM version 3.0 (identified as -) data/samtools-1.11/test/quickcheck/6.quickcheck.cram21.ok.cram: CRAM version 2.1 (identified as _cram21.cram) data/samtools-1.11/test/quickcheck/7.quickcheck.cram30.ok.cram: CRAM version 3.0 (identified as _cram30.cram) data/samtools-1.11/test/quickcheck/8.quickcheck.cram21.truncated.cram: CRAM version 2.1 (identified as _cram21.cram) data/samtools-1.11/test/quickcheck/9.quickcheck.cram30.truncated.cram: CRAM version 3.0 (identified as _cram30.cram) data/samtools-1.11/test/quickcheck/all.expected: ASCII text data/samtools-1.11/test/reheader/1_view1.sam.expected: Sequence Alignment/Map (SAM), ASCII text, with very long lines data/samtools-1.11/test/reheader/1_view1.sam.expected.err: empty data/samtools-1.11/test/reheader/2_view1.sam.expected: Sequence Alignment/Map (SAM), ASCII text, with very long lines data/samtools-1.11/test/reheader/2_view1.sam.expected.err: empty data/samtools-1.11/test/reheader/3_view1.sam.expected: Sequence Alignment/Map (SAM), ASCII text, with very long lines data/samtools-1.11/test/reheader/3_view1.sam.expected.err: empty data/samtools-1.11/test/reheader/4_view1.sam.expected: Sequence Alignment/Map (SAM), ASCII text, with very long lines data/samtools-1.11/test/reheader/5_view1.sam.expected: Sequence Alignment/Map (SAM), ASCII text, with very long lines data/samtools-1.11/test/reheader/hdr.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/sort/name.sort.expected.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/sort/pos.sort.expected.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/sort/tag.as.sort.expected.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/sort/tag.fi.sort.expected.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/sort/tag.rg.n.sort.expected.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/sort/tag.rg.sort.expected.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/split/split.expected.grp1.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/split/split.expected.grp2.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/split/split.expected.unk.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/split/split.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/split/test_count_rg.c: C source, ASCII text data/samtools-1.11/test/split/test_expand_format_string.c: C source, ASCII text data/samtools-1.11/test/split/test_filter_header_rg.c: C source, ASCII text data/samtools-1.11/test/split/test_parse_args.c: C source, ASCII text data/samtools-1.11/test/stat/1.stats.expected: ASCII text, with very long lines data/samtools-1.11/test/stat/1.stats.large.expected: ASCII text, with very long lines data/samtools-1.11/test/stat/10.stats.expected: ASCII text, with very long lines data/samtools-1.11/test/stat/10_map_cigar.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/stat/10_map_cigar.sam_s1_a_1.expected.bamstat: ASCII text, with very long lines data/samtools-1.11/test/stat/10_map_cigar.sam_s1_b_1.expected.bamstat: ASCII text, with very long lines data/samtools-1.11/test/stat/11.stats.expected: ASCII text data/samtools-1.11/test/stat/11.stats.g4.expected: ASCII text data/samtools-1.11/test/stat/11.stats.targets: ASCII text data/samtools-1.11/test/stat/11_target.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 974 data/samtools-1.11/test/stat/11_target.bam.bai: SAMtools BAI (BAM indexing format), with 4 reference sequences data/samtools-1.11/test/stat/11_target.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/stat/12.2reads.nooverlap.expected: ASCII text data/samtools-1.11/test/stat/12.2reads.overlap.expected: ASCII text data/samtools-1.11/test/stat/12.3reads.nooverlap.expected: ASCII text data/samtools-1.11/test/stat/12.3reads.overlap.expected: ASCII text data/samtools-1.11/test/stat/12_2reads.bed: ASCII text data/samtools-1.11/test/stat/12_3reads.bed: ASCII text data/samtools-1.11/test/stat/12_overlaps.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 278 data/samtools-1.11/test/stat/13.barcodes.bc.ok.expected: ASCII text data/samtools-1.11/test/stat/13.barcodes.ox.ok.expected: ASCII text data/samtools-1.11/test/stat/13_barcodes_fail_bc_length.sam: Sequence Alignment/Map (SAM), with header version 1.5 data/samtools-1.11/test/stat/13_barcodes_fail_hyphen.sam: Sequence Alignment/Map (SAM), with header version 1.5 data/samtools-1.11/test/stat/13_barcodes_fail_qt_length.sam: Sequence Alignment/Map (SAM), with header version 1.5 data/samtools-1.11/test/stat/13_barcodes_ok.sam: Sequence Alignment/Map (SAM), with header version 1.5 data/samtools-1.11/test/stat/13_barcodes_ok_ox_bz.sam: Sequence Alignment/Map (SAM), with header version 1.5 data/samtools-1.11/test/stat/1_map_cigar.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/stat/1_map_cigar.sam_s1_a_1.expected.bamstat: ASCII text, with very long lines data/samtools-1.11/test/stat/1_map_cigar_large.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/stat/2.stats.expected: ASCII text, with very long lines data/samtools-1.11/test/stat/2.stats.large.expected: ASCII text, with very long lines data/samtools-1.11/test/stat/2_equal_cigar_full_seq.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/stat/2_equal_cigar_full_seq_large.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/stat/3.stats.expected: ASCII text, with very long lines data/samtools-1.11/test/stat/3.stats.large.expected: ASCII text, with very long lines data/samtools-1.11/test/stat/3_map_cigar_equal_seq.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/stat/3_map_cigar_equal_seq_large.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/stat/4.stats.expected: ASCII text, with very long lines data/samtools-1.11/test/stat/4.stats.large.expected: ASCII text, with very long lines data/samtools-1.11/test/stat/4_X_cigar_full_seq.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/stat/4_X_cigar_full_seq_large.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/stat/5.stats.expected: ASCII text, with very long lines data/samtools-1.11/test/stat/5.stats.large.expected: ASCII text, with very long lines data/samtools-1.11/test/stat/5_insert_cigar.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/stat/5_insert_cigar_large.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/stat/6.stats.expected: ASCII text, with very long lines data/samtools-1.11/test/stat/7.stats.expected: ASCII text, with very long lines data/samtools-1.11/test/stat/7.stats.large.expected: ASCII text, with very long lines data/samtools-1.11/test/stat/7_supp.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/stat/7_supp_large.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/stat/8.stats.expected: ASCII text, with very long lines data/samtools-1.11/test/stat/8.stats.large.expected: ASCII text, with very long lines data/samtools-1.11/test/stat/8_secondary.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/stat/8_secondary_large.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/samtools-1.11/test/stat/9.stats.expected: ASCII text, with very long lines data/samtools-1.11/test/stat/test.fa: ASCII text data/samtools-1.11/test/stat/test.fa.fai: ASCII text data/samtools-1.11/test/test.c: C source, ASCII text data/samtools-1.11/test/test.h: C source, ASCII text data/samtools-1.11/test/test.pl: Perl script text executable data/samtools-1.11/test/tview/test_get_rg_sample.c: C source, ASCII text data/samtools-1.11/test/vcf-miniview.c: C source, ASCII text data/samtools-1.11/tmp_file.c: C source, ASCII text data/samtools-1.11/tmp_file.h: C source, ASCII text data/samtools-1.11/version.sh: POSIX shell script, ASCII text executable data/samtools-1.11/debian/NEWS: ASCII text data/samtools-1.11/debian/README.Debian: UTF-8 Unicode text data/samtools-1.11/debian/ax_with_curses.m4: ASCII text data/samtools-1.11/debian/ax_with_htslib.m4: M4 macro processor script, ASCII text data/samtools-1.11/debian/changelog: UTF-8 Unicode text data/samtools-1.11/debian/control: ASCII text data/samtools-1.11/debian/copyright: UTF-8 Unicode text data/samtools-1.11/debian/gbp.conf: ASCII text data/samtools-1.11/debian/mans/ace2sam.1: troff or preprocessor input, ASCII text data/samtools-1.11/debian/mans/samtools.pl.1: troff or preprocessor input, ASCII text data/samtools-1.11/debian/mans/wgsim.1: troff or preprocessor input, ASCII text data/samtools-1.11/debian/rules: a /usr/bin/make -f script, ASCII text executable data/samtools-1.11/debian/salsa-ci.yml: ASCII text data/samtools-1.11/debian/samtools-Dockerfile: ASCII text data/samtools-1.11/debian/samtools-docker.yml: ASCII text data/samtools-1.11/debian/samtools-faidx.cwl: a /usr/bin/cwl-runner script, ASCII text executable data/samtools-1.11/debian/samtools-index.cwl: a /usr/bin/cwl-runner script, ASCII text executable data/samtools-1.11/debian/samtools-metadata.yaml: ASCII text data/samtools-1.11/debian/samtools-rmdup.cwl: a /usr/bin/cwl-runner script, ASCII text executable data/samtools-1.11/debian/samtools-sort.cwl: a /usr/bin/cwl-runner script, ASCII text executable data/samtools-1.11/debian/samtools-test.install: ASCII text data/samtools-1.11/debian/samtools-view.cwl: a /usr/bin/cwl-runner script, ASCII text executable data/samtools-1.11/debian/samtools.bash-completion: ASCII text data/samtools-1.11/debian/samtools.docs: ASCII text data/samtools-1.11/debian/samtools.examples: ASCII text data/samtools-1.11/debian/samtools.install: ASCII text data/samtools-1.11/debian/samtools.lintian-overrides: ASCII text data/samtools-1.11/debian/source/format: ASCII text data/samtools-1.11/debian/source/options: ASCII text data/samtools-1.11/debian/tests/control: ASCII text data/samtools-1.11/debian/tests/samtools-test: POSIX shell script, ASCII text executable data/samtools-1.11/debian/upstream/metadata: ASCII text data/samtools-1.11/debian/watch: ASCII text data/samtools-1.11/.pc/.version: ASCII text data/samtools-1.11/.pc/.quilt_patches: ASCII text data/samtools-1.11/.pc/.quilt_series: ASCII text data/samtools-1.11/.pc/applied-patches: empty