samtools-1.12/
samtools-1.12/AUTHORS
samtools-1.12/ChangeLog.old
samtools-1.12/INSTALL
samtools-1.12/LICENSE
samtools-1.12/Makefile
samtools-1.12/NEWS
samtools-1.12/README
samtools-1.12/amplicon_stats.c
samtools-1.12/bam.c
samtools-1.12/bam.h
samtools-1.12/bam2bcf.c
samtools-1.12/bam2bcf.h
samtools-1.12/bam2bcf_indel.c
samtools-1.12/bam2depth.c
samtools-1.12/bam_addrprg.c
samtools-1.12/bam_ampliconclip.c
samtools-1.12/bam_ampliconclip.h
samtools-1.12/bam_aux.c
samtools-1.12/bam_cat.c
samtools-1.12/bam_color.c
samtools-1.12/bam_endian.h
samtools-1.12/bam_fastq.c
samtools-1.12/bam_flags.c
samtools-1.12/bam_index.c
samtools-1.12/bam_lpileup.c
samtools-1.12/bam_lpileup.h
samtools-1.12/bam_markdup.c
samtools-1.12/bam_mate.c
samtools-1.12/bam_md.c
samtools-1.12/bam_plbuf.c
samtools-1.12/bam_plbuf.h
samtools-1.12/bam_plcmd.c
samtools-1.12/bam_quickcheck.c
samtools-1.12/bam_reheader.c
samtools-1.12/bam_rmdup.c
samtools-1.12/bam_rmdupse.c
samtools-1.12/bam_sort.c
samtools-1.12/bam_split.c
samtools-1.12/bam_stat.c
samtools-1.12/bam_tview.c
samtools-1.12/bam_tview.h
samtools-1.12/bam_tview_curses.c
samtools-1.12/bam_tview_html.c
samtools-1.12/bamshuf.c
samtools-1.12/bamtk.c
samtools-1.12/bedcov.c
samtools-1.12/bedidx.c
samtools-1.12/bedidx.h
samtools-1.12/config.mk.in
samtools-1.12/configure.ac
samtools-1.12/coverage.c
samtools-1.12/cut_target.c
samtools-1.12/dict.c
samtools-1.12/doc/
samtools-1.12/doc/samtools-addreplacerg.1
samtools-1.12/doc/samtools-ampliconclip.1
samtools-1.12/doc/samtools-ampliconstats.1
samtools-1.12/doc/samtools-bedcov.1
samtools-1.12/doc/samtools-calmd.1
samtools-1.12/doc/samtools-cat.1
samtools-1.12/doc/samtools-collate.1
samtools-1.12/doc/samtools-coverage.1
samtools-1.12/doc/samtools-depad.1
samtools-1.12/doc/samtools-depth.1
samtools-1.12/doc/samtools-dict.1
samtools-1.12/doc/samtools-faidx.1
samtools-1.12/doc/samtools-fasta.1
samtools-1.12/doc/samtools-fastq.1
samtools-1.12/doc/samtools-fixmate.1
samtools-1.12/doc/samtools-flags.1
samtools-1.12/doc/samtools-flagstat.1
samtools-1.12/doc/samtools-fqidx.1
samtools-1.12/doc/samtools-idxstats.1
samtools-1.12/doc/samtools-index.1
samtools-1.12/doc/samtools-markdup.1
samtools-1.12/doc/samtools-merge.1
samtools-1.12/doc/samtools-mpileup.1
samtools-1.12/doc/samtools-phase.1
samtools-1.12/doc/samtools-quickcheck.1
samtools-1.12/doc/samtools-reheader.1
samtools-1.12/doc/samtools-rmdup.1
samtools-1.12/doc/samtools-sort.1
samtools-1.12/doc/samtools-split.1
samtools-1.12/doc/samtools-stats.1
samtools-1.12/doc/samtools-targetcut.1
samtools-1.12/doc/samtools-tview.1
samtools-1.12/doc/samtools-view.1
samtools-1.12/doc/samtools.1
samtools-1.12/examples/
samtools-1.12/examples/00README.txt
samtools-1.12/examples/ex1.fa
samtools-1.12/examples/ex1.sam.gz
samtools-1.12/examples/toy.fa
samtools-1.12/examples/toy.sam
samtools-1.12/faidx.c
samtools-1.12/install-sh
samtools-1.12/lz4/
samtools-1.12/lz4/LICENSE
samtools-1.12/lz4/lz4.c
samtools-1.12/lz4/lz4.h
samtools-1.12/m4/
samtools-1.12/m4/ax_with_htslib.m4
samtools-1.12/m4/hts_prog_cc_warnings.m4
samtools-1.12/m4/hts_with_curses.m4
samtools-1.12/misc/
samtools-1.12/misc/HmmGlocal.java
samtools-1.12/misc/ace2sam.c
samtools-1.12/misc/blast2sam.pl
samtools-1.12/misc/bowtie2sam.pl
samtools-1.12/misc/export2sam.pl
samtools-1.12/misc/fasta-sanitize.pl
samtools-1.12/misc/interpolate_sam.pl
samtools-1.12/misc/maq2sam.c
samtools-1.12/misc/md5fa.c
samtools-1.12/misc/md5sum-lite.c
samtools-1.12/misc/novo2sam.pl
samtools-1.12/misc/plot-ampliconstats
samtools-1.12/misc/plot-bamstats
samtools-1.12/misc/psl2sam.pl
samtools-1.12/misc/r2plot.lua
samtools-1.12/misc/sam2vcf.pl
samtools-1.12/misc/samtools.pl
samtools-1.12/misc/samtools_tab_completion
samtools-1.12/misc/seq_cache_populate.pl
samtools-1.12/misc/soap2sam.pl
samtools-1.12/misc/vcfutils.lua
samtools-1.12/misc/wgsim.1
samtools-1.12/misc/wgsim.c
samtools-1.12/misc/wgsim_eval.pl
samtools-1.12/misc/zoom2sam.pl
samtools-1.12/padding.c
samtools-1.12/phase.c
samtools-1.12/sam.c
samtools-1.12/sam.h
samtools-1.12/sam_opts.c
samtools-1.12/sam_opts.h
samtools-1.12/sam_utils.c
samtools-1.12/sam_view.c
samtools-1.12/sample.c
samtools-1.12/sample.h
samtools-1.12/samtools.h
samtools-1.12/stats.c
samtools-1.12/stats_isize.c
samtools-1.12/stats_isize.h
samtools-1.12/test/
samtools-1.12/test/addrprg/
samtools-1.12/test/addrprg/1_fixup.sam
samtools-1.12/test/addrprg/1_fixup.sam.expected
samtools-1.12/test/addrprg/1_fixup.sam.expected.err
samtools-1.12/test/addrprg/2_fixup_orphan.sam
samtools-1.12/test/addrprg/2_fixup_orphan.sam.expected
samtools-1.12/test/addrprg/2_fixup_orphan.sam.expected.err
samtools-1.12/test/addrprg/3_fixup.sam.expected
samtools-1.12/test/addrprg/3_fixup.sam.expected.err
samtools-1.12/test/addrprg/4_fixup_norg.sam
samtools-1.12/test/addrprg/4_fixup_norg.sam.expected
samtools-1.12/test/addrprg/4_fixup_norg.sam.expected.err
samtools-1.12/test/ampliconclip/
samtools-1.12/test/ampliconclip/1_delete_tag.expected.sam
samtools-1.12/test/ampliconclip/1_fail.expected.sam
samtools-1.12/test/ampliconclip/1_filter.expected.sam
samtools-1.12/test/ampliconclip/1_hard_clipped.expected.sam
samtools-1.12/test/ampliconclip/1_original_tag.expected.sam
samtools-1.12/test/ampliconclip/1_soft_clipped.expected.sam
samtools-1.12/test/ampliconclip/1_soft_clipped_strand.expected.sam
samtools-1.12/test/ampliconclip/1_test_data.sam
samtools-1.12/test/ampliconclip/2_both_clipped.expected.sam
samtools-1.12/test/ampliconclip/2_both_test_data.sam
samtools-1.12/test/ampliconclip/ac_test.bed
samtools-1.12/test/ampliconstats/
samtools-1.12/test/ampliconstats/stats.expected.txt
samtools-1.12/test/bam2fq/
samtools-1.12/test/bam2fq/1.1.fq.expected
samtools-1.12/test/bam2fq/1.2.fq.expected
samtools-1.12/test/bam2fq/1.stdout.expected
samtools-1.12/test/bam2fq/10.1.fq.expected
samtools-1.12/test/bam2fq/10.2.fq.expected
samtools-1.12/test/bam2fq/10.s.fq.expected
samtools-1.12/test/bam2fq/11.fq.expected
samtools-1.12/test/bam2fq/12.1.fq.expected
samtools-1.12/test/bam2fq/12.2.fq.expected
samtools-1.12/test/bam2fq/12.i.fq.expected
samtools-1.12/test/bam2fq/12.s.fq.expected
samtools-1.12/test/bam2fq/13.fq.expected
samtools-1.12/test/bam2fq/2.1.fq.expected
samtools-1.12/test/bam2fq/2.2.fq.expected
samtools-1.12/test/bam2fq/2.s.fq.expected
samtools-1.12/test/bam2fq/2.stdout.expected
samtools-1.12/test/bam2fq/3.1.fq.expected
samtools-1.12/test/bam2fq/3.2.fq.expected
samtools-1.12/test/bam2fq/3.s.fq.expected
samtools-1.12/test/bam2fq/3.stdout.expected
samtools-1.12/test/bam2fq/4.1.fq.expected
samtools-1.12/test/bam2fq/4.2.fq.expected
samtools-1.12/test/bam2fq/4.s.fq.expected
samtools-1.12/test/bam2fq/4.stdout.expected
samtools-1.12/test/bam2fq/5.1.fq.expected
samtools-1.12/test/bam2fq/5.2.fq.expected
samtools-1.12/test/bam2fq/5.s.fq.expected
samtools-1.12/test/bam2fq/6.1.fq.expected
samtools-1.12/test/bam2fq/6.2.fq.expected
samtools-1.12/test/bam2fq/6.s.fq.expected
samtools-1.12/test/bam2fq/7.1.fq.expected
samtools-1.12/test/bam2fq/7.2.fq.expected
samtools-1.12/test/bam2fq/7.s.fq.expected
samtools-1.12/test/bam2fq/8.1.fq.expected
samtools-1.12/test/bam2fq/8.2.fq.expected
samtools-1.12/test/bam2fq/8.i.fq.expected
samtools-1.12/test/bam2fq/8.s.fq.expected
samtools-1.12/test/bam2fq/9.1.fq.expected
samtools-1.12/test/bam2fq/9.2.fq.expected
samtools-1.12/test/bam2fq/bc.fq.expected
samtools-1.12/test/bam2fq/bc10.fq.expected
samtools-1.12/test/bam2fq/bc_split.fq.expected
samtools-1.12/test/bedcov/
samtools-1.12/test/bedcov/bedcov.bam
samtools-1.12/test/bedcov/bedcov.bam.bai
samtools-1.12/test/bedcov/bedcov.bed
samtools-1.12/test/bedcov/bedcov.expected
samtools-1.12/test/bedcov/bedcov_gG.bed
samtools-1.12/test/bedcov/bedcov_gG.expected
samtools-1.12/test/bedcov/bedcov_j.expected
samtools-1.12/test/collate/
samtools-1.12/test/collate/1_fast_collate.sam.expected
samtools-1.12/test/collate/2_fast_collate_with_tmp_used.sam.expected
samtools-1.12/test/collate/collate.expected.sam
samtools-1.12/test/collate/fast_collate.sam
samtools-1.12/test/dat/
samtools-1.12/test/dat/bam2fq.001.sam
samtools-1.12/test/dat/bam2fq.002.sam
samtools-1.12/test/dat/bam2fq.003.sam
samtools-1.12/test/dat/bam2fq.004.sam
samtools-1.12/test/dat/bam2fq.005.sam
samtools-1.12/test/dat/bam2fq.010.sam
samtools-1.12/test/dat/bam2fq.013.sam
samtools-1.12/test/dat/bam2fq.703.sam
samtools-1.12/test/dat/cat.hdr
samtools-1.12/test/dat/cram_md5/
samtools-1.12/test/dat/cram_md5/08c04d512d4797d9ba2a156c1daba468
samtools-1.12/test/dat/cram_md5/7c35feac7036c1cdef3bee0cc4b21437
samtools-1.12/test/dat/cram_md5/89b96de7acc5918c2858ef92710be7d4
samtools-1.12/test/dat/cram_md5/8a3d8deb9edd4ce3346b6061fcee6d0b
samtools-1.12/test/dat/depad.001.fa
samtools-1.12/test/dat/depad.001.fa.fai
samtools-1.12/test/dat/depad.001p.sam
samtools-1.12/test/dat/depad.001u.sam
samtools-1.12/test/dat/dict.alias.fa
samtools-1.12/test/dat/dict.alias.out
samtools-1.12/test/dat/dict.fa
samtools-1.12/test/dat/dict.out
samtools-1.12/test/dat/empty.expected
samtools-1.12/test/dat/large_chrom.out
samtools-1.12/test/dat/large_chrom.sam
samtools-1.12/test/dat/large_chrom_bai_index.err
samtools-1.12/test/dat/mpileup.1.sam
samtools-1.12/test/dat/mpileup.2.sam
samtools-1.12/test/dat/mpileup.3.sam
samtools-1.12/test/dat/mpileup.err.1
samtools-1.12/test/dat/mpileup.out.1
samtools-1.12/test/dat/mpileup.out.2
samtools-1.12/test/dat/mpileup.out.3
samtools-1.12/test/dat/mpileup.out.4
samtools-1.12/test/dat/mpileup.out.5
samtools-1.12/test/dat/mpileup.ref.fa
samtools-1.12/test/dat/mpileup.ref.fa.fai
samtools-1.12/test/dat/test_input_1_a.bam
samtools-1.12/test/dat/test_input_1_a.bam.bai.expected
samtools-1.12/test/dat/test_input_1_a.cram
samtools-1.12/test/dat/test_input_1_a.sam
samtools-1.12/test/dat/test_input_1_a_regex.sam
samtools-1.12/test/dat/test_input_1_ab.X.expected
samtools-1.12/test/dat/test_input_1_b.X.expected
samtools-1.12/test/dat/test_input_1_b.bam
samtools-1.12/test/dat/test_input_1_b.sam
samtools-1.12/test/dat/test_input_1_b_regex.sam
samtools-1.12/test/dat/test_input_1_c.bam
samtools-1.12/test/dat/test_input_1_c.sam
samtools-1.12/test/dat/test_input_1_d.sam
samtools-1.12/test/dat/view.001.01.bed
samtools-1.12/test/dat/view.001.02.bed
samtools-1.12/test/dat/view.001.fa
samtools-1.12/test/dat/view.001.fa.fai
samtools-1.12/test/dat/view.001.sam
samtools-1.12/test/dat/view.002.01.bed
samtools-1.12/test/dat/view.002.02.bed
samtools-1.12/test/dat/view.002.fa
samtools-1.12/test/dat/view.002.fa.fai
samtools-1.12/test/dat/view.002.sam
samtools-1.12/test/dat/view.003.expected.sam
samtools-1.12/test/dat/view.003.sam
samtools-1.12/test/dat/view.004.expected.sam
samtools-1.12/test/fixmate/
samtools-1.12/test/fixmate/1_coord_sort.sam
samtools-1.12/test/fixmate/1_coord_sort.sam.expected
samtools-1.12/test/fixmate/1_coord_sort.sam.expected.err
samtools-1.12/test/fixmate/2_isize_overflow.sam
samtools-1.12/test/fixmate/2_isize_overflow.sam.expected
samtools-1.12/test/fixmate/3_reverse_read_pp_lt.sam
samtools-1.12/test/fixmate/3_reverse_read_pp_lt.sam.expected
samtools-1.12/test/fixmate/4_reverse_read_pp_equal.sam
samtools-1.12/test/fixmate/4_reverse_read_pp_equal.sam.expected
samtools-1.12/test/fixmate/5_ct.sam
samtools-1.12/test/fixmate/5_ct.sam.expected
samtools-1.12/test/fixmate/6_ct_replace.sam
samtools-1.12/test/fixmate/6_ct_replace.sam.expected
samtools-1.12/test/fixmate/7_two_read_mapped.sam
samtools-1.12/test/fixmate/7_two_read_mapped.sam.expected
samtools-1.12/test/fixmate/8_isize_overflow_64bit.sam
samtools-1.12/test/fixmate/8_isize_overflow_64bit.sam.expected
samtools-1.12/test/idxstats/
samtools-1.12/test/idxstats/test_input_1_a.bam.expected
samtools-1.12/test/idxstats/test_input_1_a.bam.expected.err
samtools-1.12/test/large_pos/
samtools-1.12/test/large_pos/depth.expected.out
samtools-1.12/test/large_pos/depth_bed.expected.out
samtools-1.12/test/large_pos/longref.sam
samtools-1.12/test/large_pos/longref2.sam
samtools-1.12/test/large_pos/longref3.expected.sam
samtools-1.12/test/large_pos/longref3.sam
samtools-1.12/test/large_pos/longref_idx.expected.sam
samtools-1.12/test/large_pos/longref_name.sam
samtools-1.12/test/large_pos/merge.expected.sam
samtools-1.12/test/large_pos/test.bed
samtools-1.12/test/large_pos/tview.expected.out
samtools-1.12/test/maintainer/
samtools-1.12/test/maintainer/check_copyright.pl
samtools-1.12/test/maintainer/check_spaces.pl
samtools-1.12/test/markdup/
samtools-1.12/test/markdup/1_name_sort.expected.sam
samtools-1.12/test/markdup/1_name_sort.expected.sam.err
samtools-1.12/test/markdup/1_name_sort.sam
samtools-1.12/test/markdup/2_bad_order.expected.sam
samtools-1.12/test/markdup/2_bad_order.expected.sam.err
samtools-1.12/test/markdup/2_bad_order.sam
samtools-1.12/test/markdup/3_missing_mc.expected.sam
samtools-1.12/test/markdup/3_missing_mc.expected.sam.err
samtools-1.12/test/markdup/3_missing_mc.sam
samtools-1.12/test/markdup/4_missing_ms.expected.sam
samtools-1.12/test/markdup/4_missing_ms.expected.sam.err
samtools-1.12/test/markdup/4_missing_ms.sam
samtools-1.12/test/markdup/5_markdup.expected.sam
samtools-1.12/test/markdup/5_markdup.sam
samtools-1.12/test/markdup/6_remove_dups.expected.sam
samtools-1.12/test/markdup/6_remove_dups.sam
samtools-1.12/test/markdup/7_mark_supp_dup.expected.sam
samtools-1.12/test/markdup/7_mark_supp_dup.sam
samtools-1.12/test/markdup/8_optical_dup.expected.sam
samtools-1.12/test/markdup/8_optical_dup.sam
samtools-1.12/test/markdup/9_optical_dup_qcfail.expected.sam
samtools-1.12/test/markdup/9_optical_dup_qcfail.sam
samtools-1.12/test/merge/
samtools-1.12/test/merge/2.merge.expected.sam
samtools-1.12/test/merge/3.merge.expected.err
samtools-1.12/test/merge/3.merge.expected.sam
samtools-1.12/test/merge/4.merge.expected.sam
samtools-1.12/test/merge/5.merge.expected.sam
samtools-1.12/test/merge/6.merge.expected.sam
samtools-1.12/test/merge/7.merge.expected.sam
samtools-1.12/test/merge/merge.bed
samtools-1.12/test/merge/merge.bed.1.sam
samtools-1.12/test/merge/merge.bed.2.sam
samtools-1.12/test/merge/merge.bed.expected.sam
samtools-1.12/test/merge/tag.pg.merge.expected.sam
samtools-1.12/test/merge/tag.pg.n.merge.expected.sam
samtools-1.12/test/merge/test_3.fofn
samtools-1.12/test/merge/test_bam_translate.c
samtools-1.12/test/merge/test_header.sam
samtools-1.12/test/merge/test_no_pg_rg_co.sam
samtools-1.12/test/merge/test_rtrans_build.c
samtools-1.12/test/merge/test_trans_tbl_init.c
samtools-1.12/test/mpileup/
samtools-1.12/test/mpileup/1read.bam
samtools-1.12/test/mpileup/1read.sam
samtools-1.12/test/mpileup/anomalous.sam
samtools-1.12/test/mpileup/c1#clip.bam
samtools-1.12/test/mpileup/c1#pad1.bam
samtools-1.12/test/mpileup/c1#pad2.bam
samtools-1.12/test/mpileup/c1#pad3.bam
samtools-1.12/test/mpileup/c1.fa
samtools-1.12/test/mpileup/c1.fa.fai
samtools-1.12/test/mpileup/ce#5b.bam
samtools-1.12/test/mpileup/ce#5b.bam.bai
samtools-1.12/test/mpileup/ce#5b.cram
samtools-1.12/test/mpileup/ce#5b.cram.crai
samtools-1.12/test/mpileup/ce#5b.sam
samtools-1.12/test/mpileup/ce#large_seq.bam
samtools-1.12/test/mpileup/ce#unmap.bam
samtools-1.12/test/mpileup/ce#unmap1.bam
samtools-1.12/test/mpileup/ce#unmap2.bam
samtools-1.12/test/mpileup/ce.fa
samtools-1.12/test/mpileup/ce.fa.fai
samtools-1.12/test/mpileup/deep.sam
samtools-1.12/test/mpileup/depth.reg
samtools-1.12/test/mpileup/depth_del.sam
samtools-1.12/test/mpileup/expected/
samtools-1.12/test/mpileup/expected/1.out.f3-6.gz
samtools-1.12/test/mpileup/expected/10.out
samtools-1.12/test/mpileup/expected/11.out
samtools-1.12/test/mpileup/expected/12.out
samtools-1.12/test/mpileup/expected/13.out
samtools-1.12/test/mpileup/expected/14.out
samtools-1.12/test/mpileup/expected/15.out
samtools-1.12/test/mpileup/expected/16.out
samtools-1.12/test/mpileup/expected/17.out
samtools-1.12/test/mpileup/expected/18.out
samtools-1.12/test/mpileup/expected/19.out
samtools-1.12/test/mpileup/expected/2.out
samtools-1.12/test/mpileup/expected/20.out
samtools-1.12/test/mpileup/expected/21.out
samtools-1.12/test/mpileup/expected/22.out
samtools-1.12/test/mpileup/expected/23.out
samtools-1.12/test/mpileup/expected/24.out
samtools-1.12/test/mpileup/expected/25.out
samtools-1.12/test/mpileup/expected/26.out
samtools-1.12/test/mpileup/expected/27.out
samtools-1.12/test/mpileup/expected/28.out
samtools-1.12/test/mpileup/expected/29.out
samtools-1.12/test/mpileup/expected/3.out
samtools-1.12/test/mpileup/expected/30.out
samtools-1.12/test/mpileup/expected/31.out
samtools-1.12/test/mpileup/expected/32.out
samtools-1.12/test/mpileup/expected/33.out
samtools-1.12/test/mpileup/expected/34.out
samtools-1.12/test/mpileup/expected/35.out
samtools-1.12/test/mpileup/expected/37.out
samtools-1.12/test/mpileup/expected/38.out
samtools-1.12/test/mpileup/expected/39.out
samtools-1.12/test/mpileup/expected/4.out
samtools-1.12/test/mpileup/expected/40.out
samtools-1.12/test/mpileup/expected/41.out
samtools-1.12/test/mpileup/expected/42.out
samtools-1.12/test/mpileup/expected/43.out
samtools-1.12/test/mpileup/expected/44.out
samtools-1.12/test/mpileup/expected/45.out
samtools-1.12/test/mpileup/expected/46.out
samtools-1.12/test/mpileup/expected/47.out
samtools-1.12/test/mpileup/expected/48.out
samtools-1.12/test/mpileup/expected/49.out
samtools-1.12/test/mpileup/expected/5.out
samtools-1.12/test/mpileup/expected/50.out
samtools-1.12/test/mpileup/expected/51.out
samtools-1.12/test/mpileup/expected/52.out
samtools-1.12/test/mpileup/expected/53.out
samtools-1.12/test/mpileup/expected/54.out
samtools-1.12/test/mpileup/expected/55.out
samtools-1.12/test/mpileup/expected/56.out
samtools-1.12/test/mpileup/expected/57.out
samtools-1.12/test/mpileup/expected/58.out
samtools-1.12/test/mpileup/expected/59.out
samtools-1.12/test/mpileup/expected/6.out
samtools-1.12/test/mpileup/expected/60.out
samtools-1.12/test/mpileup/expected/61.out
samtools-1.12/test/mpileup/expected/62.out
samtools-1.12/test/mpileup/expected/63.out
samtools-1.12/test/mpileup/expected/64.out
samtools-1.12/test/mpileup/expected/65.out
samtools-1.12/test/mpileup/expected/66.out
samtools-1.12/test/mpileup/expected/67.out
samtools-1.12/test/mpileup/expected/68.out
samtools-1.12/test/mpileup/expected/69.out
samtools-1.12/test/mpileup/expected/7.out
samtools-1.12/test/mpileup/expected/70.out
samtools-1.12/test/mpileup/expected/71.out
samtools-1.12/test/mpileup/expected/72.out
samtools-1.12/test/mpileup/expected/73.out
samtools-1.12/test/mpileup/expected/74.out
samtools-1.12/test/mpileup/expected/75.out
samtools-1.12/test/mpileup/expected/76.out
samtools-1.12/test/mpileup/expected/77.out
samtools-1.12/test/mpileup/expected/78.out
samtools-1.12/test/mpileup/expected/79.out
samtools-1.12/test/mpileup/expected/8.out
samtools-1.12/test/mpileup/expected/9.out
samtools-1.12/test/mpileup/expected/a0.out
samtools-1.12/test/mpileup/expected/a1.out
samtools-1.12/test/mpileup/expected/a10.out
samtools-1.12/test/mpileup/expected/a11.out
samtools-1.12/test/mpileup/expected/a13.out
samtools-1.12/test/mpileup/expected/a14.out
samtools-1.12/test/mpileup/expected/a15.out
samtools-1.12/test/mpileup/expected/a16.out
samtools-1.12/test/mpileup/expected/a17.out
samtools-1.12/test/mpileup/expected/a2.out
samtools-1.12/test/mpileup/expected/a3.out
samtools-1.12/test/mpileup/expected/a4.out
samtools-1.12/test/mpileup/expected/a5.out
samtools-1.12/test/mpileup/expected/a6.out
samtools-1.12/test/mpileup/expected/a8.out
samtools-1.12/test/mpileup/expected/a9.out
samtools-1.12/test/mpileup/expected/d1_1.out
samtools-1.12/test/mpileup/expected/d1_12.out
samtools-1.12/test/mpileup/expected/d1_2.out
samtools-1.12/test/mpileup/expected/d2_12r.out
samtools-1.12/test/mpileup/expected/d3_12.out
samtools-1.12/test/mpileup/expected/d3_12r1a.out
samtools-1.12/test/mpileup/expected/d3_12r2a.out
samtools-1.12/test/mpileup/expected/d3_3.out
samtools-1.12/test/mpileup/expected/d4_12.out
samtools-1.12/test/mpileup/expected/d4_12b.out
samtools-1.12/test/mpileup/expected/d4_12r.out
samtools-1.12/test/mpileup/expected/d5_all1.out
samtools-1.12/test/mpileup/expected/d5_all2.out
samtools-1.12/test/mpileup/expected/d5_all3.out
samtools-1.12/test/mpileup/expected/d5_all4.out
samtools-1.12/test/mpileup/expected/d5_b3.out
samtools-1.12/test/mpileup/expected/d5_b3a.out
samtools-1.12/test/mpileup/expected/d5_b3aa.out
samtools-1.12/test/mpileup/expected/d5_blank.out
samtools-1.12/test/mpileup/expected/d5_xx1.out
samtools-1.12/test/mpileup/expected/d5_xx2.out
samtools-1.12/test/mpileup/expected/d5_xx3.out
samtools-1.12/test/mpileup/expected/d5_xy1.out
samtools-1.12/test/mpileup/expected/d6_nodel.out
samtools-1.12/test/mpileup/expected/d6_wdel.out
samtools-1.12/test/mpileup/expected/d7_nodup.out
samtools-1.12/test/mpileup/expected/m5_all1.out
samtools-1.12/test/mpileup/expected/m5_all2.out
samtools-1.12/test/mpileup/expected/m5_all3.out
samtools-1.12/test/mpileup/expected/m5_b3.out
samtools-1.12/test/mpileup/expected/m5_b3a.out
samtools-1.12/test/mpileup/expected/m5_b3aa.out
samtools-1.12/test/mpileup/expected/m5_blank.out
samtools-1.12/test/mpileup/expected/m5_xx1.out
samtools-1.12/test/mpileup/expected/m5_xx2.out
samtools-1.12/test/mpileup/expected/m5_xx3.out
samtools-1.12/test/mpileup/expected/m5_xy1.out
samtools-1.12/test/mpileup/expected/mp_D.out
samtools-1.12/test/mpileup/expected/mp_DI.out
samtools-1.12/test/mpileup/expected/mp_I.out
samtools-1.12/test/mpileup/expected/mp_ID.out
samtools-1.12/test/mpileup/expected/mp_ID_rev.out
samtools-1.12/test/mpileup/expected/mp_N.out
samtools-1.12/test/mpileup/expected/mp_N2.out
samtools-1.12/test/mpileup/expected/mp_P.out
samtools-1.12/test/mpileup/indels.sam
samtools-1.12/test/mpileup/md5/
samtools-1.12/test/mpileup/md5/02099b2aad2cfe707759353724fb40ae
samtools-1.12/test/mpileup/md5/0d4dfc45807d6a11439e858605cb364d
samtools-1.12/test/mpileup/md5/351f64d4f4f9ddd45b35336ad97aa6de
samtools-1.12/test/mpileup/md5/6ec590eb82c361a61e6baabce20109bc
samtools-1.12/test/mpileup/md5/6f60cdf4c739651ae72d53e2e94825c1
samtools-1.12/test/mpileup/md5/73d180d5cb3860a2713927b6812eab0e
samtools-1.12/test/mpileup/mp.fa
samtools-1.12/test/mpileup/mp.fa.fai
samtools-1.12/test/mpileup/mp_D.sam
samtools-1.12/test/mpileup/mp_DI.sam
samtools-1.12/test/mpileup/mp_I.sam
samtools-1.12/test/mpileup/mp_ID.sam
samtools-1.12/test/mpileup/mp_ID_rev.sam
samtools-1.12/test/mpileup/mp_N.sam
samtools-1.12/test/mpileup/mp_N2.sam
samtools-1.12/test/mpileup/mp_P.sam
samtools-1.12/test/mpileup/mpileup-E.bam
samtools-1.12/test/mpileup/mpileup.1.bam
samtools-1.12/test/mpileup/mpileup.1.bam.bai
samtools-1.12/test/mpileup/mpileup.2.bam
samtools-1.12/test/mpileup/mpileup.3.bam
samtools-1.12/test/mpileup/mpileup.ref.fa
samtools-1.12/test/mpileup/mpileup.ref.fa.fai
samtools-1.12/test/mpileup/mpileup.reg
samtools-1.12/test/mpileup/overlap.bam
samtools-1.12/test/mpileup/overlap50.sam
samtools-1.12/test/mpileup/overlapIllumina.bam
samtools-1.12/test/mpileup/regions
samtools-1.12/test/mpileup/regression.sh
samtools-1.12/test/mpileup/xx#depth1.sam
samtools-1.12/test/mpileup/xx#depth2.sam
samtools-1.12/test/mpileup/xx#depth3.sam
samtools-1.12/test/mpileup/xx#depth4.sam
samtools-1.12/test/mpileup/xx#minimal.bam
samtools-1.12/test/mpileup/xx#triplet.bam
samtools-1.12/test/mpileup/xx.bed
samtools-1.12/test/mpileup/xx.bed2
samtools-1.12/test/mpileup/xx.bed3
samtools-1.12/test/mpileup/xx.fa
samtools-1.12/test/mpileup/xx.fa.fai
samtools-1.12/test/quickcheck/
samtools-1.12/test/quickcheck/1.quickcheck.badeof.bam
samtools-1.12/test/quickcheck/10.quickcheck.notargets.bam
samtools-1.12/test/quickcheck/2.quickcheck.badheader.bam
samtools-1.12/test/quickcheck/3.quickcheck.ok.bam
samtools-1.12/test/quickcheck/4.quickcheck.ok.bam
samtools-1.12/test/quickcheck/5.quickcheck.scramble30.truncated.cram
samtools-1.12/test/quickcheck/6.quickcheck.cram21.ok.cram
samtools-1.12/test/quickcheck/7.quickcheck.cram30.ok.cram
samtools-1.12/test/quickcheck/8.quickcheck.cram21.truncated.cram
samtools-1.12/test/quickcheck/9.quickcheck.cram30.truncated.cram
samtools-1.12/test/quickcheck/all.expected
samtools-1.12/test/reheader/
samtools-1.12/test/reheader/1_view1.sam.expected
samtools-1.12/test/reheader/1_view1.sam.expected.err
samtools-1.12/test/reheader/2_view1.sam.expected
samtools-1.12/test/reheader/2_view1.sam.expected.err
samtools-1.12/test/reheader/3_view1.sam.expected
samtools-1.12/test/reheader/3_view1.sam.expected.err
samtools-1.12/test/reheader/4_view1.sam.expected
samtools-1.12/test/reheader/5_view1.sam.expected
samtools-1.12/test/reheader/hdr.sam
samtools-1.12/test/sort/
samtools-1.12/test/sort/name.sort.expected.sam
samtools-1.12/test/sort/pos.sort.expected.sam
samtools-1.12/test/sort/tag.as.sort.expected.sam
samtools-1.12/test/sort/tag.fi.sort.expected.sam
samtools-1.12/test/sort/tag.rg.n.sort.expected.sam
samtools-1.12/test/sort/tag.rg.sort.expected.sam
samtools-1.12/test/split/
samtools-1.12/test/split/split.expected.grp1.sam
samtools-1.12/test/split/split.expected.grp2.sam
samtools-1.12/test/split/split.expected.unk.sam
samtools-1.12/test/split/split.sam
samtools-1.12/test/split/test_count_rg.c
samtools-1.12/test/split/test_expand_format_string.c
samtools-1.12/test/split/test_filter_header_rg.c
samtools-1.12/test/split/test_parse_args.c
samtools-1.12/test/stat/
samtools-1.12/test/stat/1.stats.expected
samtools-1.12/test/stat/1.stats.large.expected
samtools-1.12/test/stat/10.stats.expected
samtools-1.12/test/stat/10_map_cigar.sam
samtools-1.12/test/stat/10_map_cigar.sam_s1_a_1.expected.bamstat
samtools-1.12/test/stat/10_map_cigar.sam_s1_b_1.expected.bamstat
samtools-1.12/test/stat/11.stats.expected
samtools-1.12/test/stat/11.stats.g4.expected
samtools-1.12/test/stat/11.stats.targets
samtools-1.12/test/stat/11_target.bam
samtools-1.12/test/stat/11_target.bam.bai
samtools-1.12/test/stat/11_target.sam
samtools-1.12/test/stat/12.2reads.nooverlap.expected
samtools-1.12/test/stat/12.2reads.overlap.expected
samtools-1.12/test/stat/12.3reads.nooverlap.expected
samtools-1.12/test/stat/12.3reads.overlap.expected
samtools-1.12/test/stat/12_2reads.bed
samtools-1.12/test/stat/12_3reads.bed
samtools-1.12/test/stat/12_overlaps.bam
samtools-1.12/test/stat/13.barcodes.bc.ok.expected
samtools-1.12/test/stat/13.barcodes.ox.ok.expected
samtools-1.12/test/stat/13_barcodes_fail_bc_length.sam
samtools-1.12/test/stat/13_barcodes_fail_hyphen.sam
samtools-1.12/test/stat/13_barcodes_fail_qt_length.sam
samtools-1.12/test/stat/13_barcodes_ok.sam
samtools-1.12/test/stat/13_barcodes_ok_ox_bz.sam
samtools-1.12/test/stat/1_map_cigar.sam
samtools-1.12/test/stat/1_map_cigar.sam_s1_a_1.expected.bamstat
samtools-1.12/test/stat/1_map_cigar_large.sam
samtools-1.12/test/stat/2.stats.expected
samtools-1.12/test/stat/2.stats.large.expected
samtools-1.12/test/stat/2_equal_cigar_full_seq.sam
samtools-1.12/test/stat/2_equal_cigar_full_seq_large.sam
samtools-1.12/test/stat/3.stats.expected
samtools-1.12/test/stat/3.stats.large.expected
samtools-1.12/test/stat/3_map_cigar_equal_seq.sam
samtools-1.12/test/stat/3_map_cigar_equal_seq_large.sam
samtools-1.12/test/stat/4.stats.expected
samtools-1.12/test/stat/4.stats.large.expected
samtools-1.12/test/stat/4_X_cigar_full_seq.sam
samtools-1.12/test/stat/4_X_cigar_full_seq_large.sam
samtools-1.12/test/stat/5.stats.expected
samtools-1.12/test/stat/5.stats.large.expected
samtools-1.12/test/stat/5_insert_cigar.sam
samtools-1.12/test/stat/5_insert_cigar_large.sam
samtools-1.12/test/stat/6.stats.expected
samtools-1.12/test/stat/7.stats.expected
samtools-1.12/test/stat/7.stats.large.expected
samtools-1.12/test/stat/7_supp.sam
samtools-1.12/test/stat/7_supp_large.sam
samtools-1.12/test/stat/8.stats.expected
samtools-1.12/test/stat/8.stats.large.expected
samtools-1.12/test/stat/8_secondary.sam
samtools-1.12/test/stat/8_secondary_large.sam
samtools-1.12/test/stat/9.stats.expected
samtools-1.12/test/stat/test.fa
samtools-1.12/test/stat/test.fa.fai
samtools-1.12/test/test.c
samtools-1.12/test/test.h
samtools-1.12/test/test.pl
samtools-1.12/test/tview/
samtools-1.12/test/tview/test_get_rg_sample.c
samtools-1.12/test/vcf-miniview.c
samtools-1.12/tmp_file.c
samtools-1.12/tmp_file.h
samtools-1.12/version.sh
samtools-1.12/config.h.in
samtools-1.12/configure
samtools-1.12/htslib-1.12/
samtools-1.12/htslib-1.12/INSTALL
samtools-1.12/htslib-1.12/LICENSE
samtools-1.12/htslib-1.12/Makefile
samtools-1.12/htslib-1.12/NEWS
samtools-1.12/htslib-1.12/README
samtools-1.12/htslib-1.12/README.large_positions.md
samtools-1.12/htslib-1.12/bcf_sr_sort.c
samtools-1.12/htslib-1.12/bcf_sr_sort.h
samtools-1.12/htslib-1.12/bgzf.c
samtools-1.12/htslib-1.12/bgzip.1
samtools-1.12/htslib-1.12/bgzip.c
samtools-1.12/htslib-1.12/config.mk.in
samtools-1.12/htslib-1.12/configure.ac
samtools-1.12/htslib-1.12/cram/
samtools-1.12/htslib-1.12/cram/cram.h
samtools-1.12/htslib-1.12/cram/cram_codecs.c
samtools-1.12/htslib-1.12/cram/cram_codecs.h
samtools-1.12/htslib-1.12/cram/cram_decode.c
samtools-1.12/htslib-1.12/cram/cram_decode.h
samtools-1.12/htslib-1.12/cram/cram_encode.c
samtools-1.12/htslib-1.12/cram/cram_encode.h
samtools-1.12/htslib-1.12/cram/cram_external.c
samtools-1.12/htslib-1.12/cram/cram_index.c
samtools-1.12/htslib-1.12/cram/cram_index.h
samtools-1.12/htslib-1.12/cram/cram_io.c
samtools-1.12/htslib-1.12/cram/cram_io.h
samtools-1.12/htslib-1.12/cram/cram_samtools.h
samtools-1.12/htslib-1.12/cram/cram_stats.c
samtools-1.12/htslib-1.12/cram/cram_stats.h
samtools-1.12/htslib-1.12/cram/cram_structs.h
samtools-1.12/htslib-1.12/cram/mFILE.c
samtools-1.12/htslib-1.12/cram/mFILE.h
samtools-1.12/htslib-1.12/cram/misc.h
samtools-1.12/htslib-1.12/cram/open_trace_file.c
samtools-1.12/htslib-1.12/cram/open_trace_file.h
samtools-1.12/htslib-1.12/cram/os.h
samtools-1.12/htslib-1.12/cram/pooled_alloc.c
samtools-1.12/htslib-1.12/cram/pooled_alloc.h
samtools-1.12/htslib-1.12/cram/string_alloc.c
samtools-1.12/htslib-1.12/cram/string_alloc.h
samtools-1.12/htslib-1.12/errmod.c
samtools-1.12/htslib-1.12/faidx.5
samtools-1.12/htslib-1.12/faidx.c
samtools-1.12/htslib-1.12/header.c
samtools-1.12/htslib-1.12/header.h
samtools-1.12/htslib-1.12/hfile.c
samtools-1.12/htslib-1.12/hfile_gcs.c
samtools-1.12/htslib-1.12/hfile_internal.h
samtools-1.12/htslib-1.12/hfile_libcurl.c
samtools-1.12/htslib-1.12/hfile_s3.c
samtools-1.12/htslib-1.12/hfile_s3_write.c
samtools-1.12/htslib-1.12/hts.c
samtools-1.12/htslib-1.12/hts_expr.c
samtools-1.12/htslib-1.12/hts_internal.h
samtools-1.12/htslib-1.12/hts_os.c
samtools-1.12/htslib-1.12/htscodecs/
samtools-1.12/htslib-1.12/htscodecs/LICENSE.md
samtools-1.12/htslib-1.12/htscodecs/NEWS
samtools-1.12/htslib-1.12/htscodecs/htscodecs/
samtools-1.12/htslib-1.12/htscodecs/htscodecs/arith_dynamic.c
samtools-1.12/htslib-1.12/htscodecs/htscodecs/arith_dynamic.h
samtools-1.12/htslib-1.12/htscodecs/htscodecs/c_range_coder.h
samtools-1.12/htslib-1.12/htscodecs/htscodecs/c_simple_model.h
samtools-1.12/htslib-1.12/htscodecs/htscodecs/fqzcomp_qual.c
samtools-1.12/htslib-1.12/htscodecs/htscodecs/fqzcomp_qual.h
samtools-1.12/htslib-1.12/htscodecs/htscodecs/htscodecs.c
samtools-1.12/htslib-1.12/htscodecs/htscodecs/htscodecs.h
samtools-1.12/htslib-1.12/htscodecs/htscodecs/htscodecs_endian.h
samtools-1.12/htslib-1.12/htscodecs/htscodecs/pack.c
samtools-1.12/htslib-1.12/htscodecs/htscodecs/pack.h
samtools-1.12/htslib-1.12/htscodecs/htscodecs/pooled_alloc.h
samtools-1.12/htslib-1.12/htscodecs/htscodecs/rANS_byte.h
samtools-1.12/htslib-1.12/htscodecs/htscodecs/rANS_static.c
samtools-1.12/htslib-1.12/htscodecs/htscodecs/rANS_static.h
samtools-1.12/htslib-1.12/htscodecs/htscodecs/rANS_static4x16.h
samtools-1.12/htslib-1.12/htscodecs/htscodecs/rANS_static4x16pr.c
samtools-1.12/htslib-1.12/htscodecs/htscodecs/rANS_word.h
samtools-1.12/htslib-1.12/htscodecs/htscodecs/rle.c
samtools-1.12/htslib-1.12/htscodecs/htscodecs/rle.h
samtools-1.12/htslib-1.12/htscodecs/htscodecs/tokenise_name3.c
samtools-1.12/htslib-1.12/htscodecs/htscodecs/tokenise_name3.h
samtools-1.12/htslib-1.12/htscodecs/htscodecs/utils.h
samtools-1.12/htslib-1.12/htscodecs/htscodecs/varint.h
samtools-1.12/htslib-1.12/htscodecs/htscodecs/varint2.h
samtools-1.12/htslib-1.12/htscodecs/htscodecs/version.h
samtools-1.12/htslib-1.12/htscodecs/tests/
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samtools-1.12/doc/samtools-mpileup.1
samtools-1.12/doc/samtools-phase.1
samtools-1.12/doc/samtools-quickcheck.1
samtools-1.12/doc/samtools-reheader.1
samtools-1.12/doc/samtools-rmdup.1
samtools-1.12/doc/samtools-sort.1
samtools-1.12/doc/samtools-split.1
samtools-1.12/doc/samtools-stats.1
samtools-1.12/doc/samtools-targetcut.1
samtools-1.12/doc/samtools-tview.1
samtools-1.12/doc/samtools-view.1
samtools-1.12/doc/samtools.1
samtools-1.12/examples/
samtools-1.12/examples/00README.txt
samtools-1.12/examples/ex1.fa
samtools-1.12/examples/ex1.sam.gz
samtools-1.12/examples/toy.fa
samtools-1.12/examples/toy.sam
samtools-1.12/faidx.c
samtools-1.12/install-sh
samtools-1.12/lz4/
samtools-1.12/lz4/LICENSE
samtools-1.12/lz4/lz4.c
samtools-1.12/lz4/lz4.h
samtools-1.12/m4/
samtools-1.12/m4/ax_with_htslib.m4
samtools-1.12/m4/hts_prog_cc_warnings.m4
samtools-1.12/m4/hts_with_curses.m4
samtools-1.12/misc/
samtools-1.12/misc/HmmGlocal.java
samtools-1.12/misc/ace2sam.c
samtools-1.12/misc/blast2sam.pl
samtools-1.12/misc/bowtie2sam.pl
samtools-1.12/misc/export2sam.pl
samtools-1.12/misc/fasta-sanitize.pl
samtools-1.12/misc/interpolate_sam.pl
samtools-1.12/misc/maq2sam.c
samtools-1.12/misc/md5fa.c
samtools-1.12/misc/md5sum-lite.c
samtools-1.12/misc/novo2sam.pl
samtools-1.12/misc/plot-ampliconstats
samtools-1.12/misc/plot-bamstats
samtools-1.12/misc/psl2sam.pl
samtools-1.12/misc/r2plot.lua
samtools-1.12/misc/sam2vcf.pl
samtools-1.12/misc/samtools.pl
samtools-1.12/misc/samtools_tab_completion
samtools-1.12/misc/seq_cache_populate.pl
samtools-1.12/misc/soap2sam.pl
samtools-1.12/misc/vcfutils.lua
samtools-1.12/misc/wgsim.1
samtools-1.12/misc/wgsim.c
samtools-1.12/misc/wgsim_eval.pl
samtools-1.12/misc/zoom2sam.pl
samtools-1.12/padding.c
samtools-1.12/phase.c
samtools-1.12/sam.c
samtools-1.12/sam.h
samtools-1.12/sam_opts.c
samtools-1.12/sam_opts.h
samtools-1.12/sam_utils.c
samtools-1.12/sam_view.c
samtools-1.12/sample.c
samtools-1.12/sample.h
samtools-1.12/samtools.h
samtools-1.12/stats.c
samtools-1.12/stats_isize.c
samtools-1.12/stats_isize.h
samtools-1.12/test/
samtools-1.12/test/addrprg/
samtools-1.12/test/addrprg/1_fixup.sam
samtools-1.12/test/addrprg/1_fixup.sam.expected
samtools-1.12/test/addrprg/1_fixup.sam.expected.err
samtools-1.12/test/addrprg/2_fixup_orphan.sam
samtools-1.12/test/addrprg/2_fixup_orphan.sam.expected
samtools-1.12/test/addrprg/2_fixup_orphan.sam.expected.err
samtools-1.12/test/addrprg/3_fixup.sam.expected
samtools-1.12/test/addrprg/3_fixup.sam.expected.err
samtools-1.12/test/addrprg/4_fixup_norg.sam
samtools-1.12/test/addrprg/4_fixup_norg.sam.expected
samtools-1.12/test/addrprg/4_fixup_norg.sam.expected.err
samtools-1.12/test/ampliconclip/
samtools-1.12/test/ampliconclip/1_delete_tag.expected.sam
samtools-1.12/test/ampliconclip/1_fail.expected.sam
samtools-1.12/test/ampliconclip/1_filter.expected.sam
samtools-1.12/test/ampliconclip/1_hard_clipped.expected.sam
samtools-1.12/test/ampliconclip/1_original_tag.expected.sam
samtools-1.12/test/ampliconclip/1_soft_clipped.expected.sam
samtools-1.12/test/ampliconclip/1_soft_clipped_strand.expected.sam
samtools-1.12/test/ampliconclip/1_test_data.sam
samtools-1.12/test/ampliconclip/2_both_clipped.expected.sam
samtools-1.12/test/ampliconclip/2_both_test_data.sam
samtools-1.12/test/ampliconclip/ac_test.bed
samtools-1.12/test/ampliconstats/
samtools-1.12/test/ampliconstats/stats.expected.txt
samtools-1.12/test/bam2fq/
samtools-1.12/test/bam2fq/1.1.fq.expected
samtools-1.12/test/bam2fq/1.2.fq.expected
samtools-1.12/test/bam2fq/1.stdout.expected
samtools-1.12/test/bam2fq/10.1.fq.expected
samtools-1.12/test/bam2fq/10.2.fq.expected
samtools-1.12/test/bam2fq/10.s.fq.expected
samtools-1.12/test/bam2fq/11.fq.expected
samtools-1.12/test/bam2fq/12.1.fq.expected
samtools-1.12/test/bam2fq/12.2.fq.expected
samtools-1.12/test/bam2fq/12.i.fq.expected
samtools-1.12/test/bam2fq/12.s.fq.expected
samtools-1.12/test/bam2fq/13.fq.expected
samtools-1.12/test/bam2fq/2.1.fq.expected
samtools-1.12/test/bam2fq/2.2.fq.expected
samtools-1.12/test/bam2fq/2.s.fq.expected
samtools-1.12/test/bam2fq/2.stdout.expected
samtools-1.12/test/bam2fq/3.1.fq.expected
samtools-1.12/test/bam2fq/3.2.fq.expected
samtools-1.12/test/bam2fq/3.s.fq.expected
samtools-1.12/test/bam2fq/3.stdout.expected
samtools-1.12/test/bam2fq/4.1.fq.expected
samtools-1.12/test/bam2fq/4.2.fq.expected
samtools-1.12/test/bam2fq/4.s.fq.expected
samtools-1.12/test/bam2fq/4.stdout.expected
samtools-1.12/test/bam2fq/5.1.fq.expected
samtools-1.12/test/bam2fq/5.2.fq.expected
samtools-1.12/test/bam2fq/5.s.fq.expected
samtools-1.12/test/bam2fq/6.1.fq.expected
samtools-1.12/test/bam2fq/6.2.fq.expected
samtools-1.12/test/bam2fq/6.s.fq.expected
samtools-1.12/test/bam2fq/7.1.fq.expected
samtools-1.12/test/bam2fq/7.2.fq.expected
samtools-1.12/test/bam2fq/7.s.fq.expected
samtools-1.12/test/bam2fq/8.1.fq.expected
samtools-1.12/test/bam2fq/8.2.fq.expected
samtools-1.12/test/bam2fq/8.i.fq.expected
samtools-1.12/test/bam2fq/8.s.fq.expected
samtools-1.12/test/bam2fq/9.1.fq.expected
samtools-1.12/test/bam2fq/9.2.fq.expected
samtools-1.12/test/bam2fq/bc.fq.expected
samtools-1.12/test/bam2fq/bc10.fq.expected
samtools-1.12/test/bam2fq/bc_split.fq.expected
samtools-1.12/test/bedcov/
samtools-1.12/test/bedcov/bedcov.bam
samtools-1.12/test/bedcov/bedcov.bam.bai
samtools-1.12/test/bedcov/bedcov.bed
samtools-1.12/test/bedcov/bedcov.expected
samtools-1.12/test/bedcov/bedcov_gG.bed
samtools-1.12/test/bedcov/bedcov_gG.expected
samtools-1.12/test/bedcov/bedcov_j.expected
samtools-1.12/test/collate/
samtools-1.12/test/collate/1_fast_collate.sam.expected
samtools-1.12/test/collate/2_fast_collate_with_tmp_used.sam.expected
samtools-1.12/test/collate/collate.expected.sam
samtools-1.12/test/collate/fast_collate.sam
samtools-1.12/test/dat/
samtools-1.12/test/dat/bam2fq.001.sam
samtools-1.12/test/dat/bam2fq.002.sam
samtools-1.12/test/dat/bam2fq.003.sam
samtools-1.12/test/dat/bam2fq.004.sam
samtools-1.12/test/dat/bam2fq.005.sam
samtools-1.12/test/dat/bam2fq.010.sam
samtools-1.12/test/dat/bam2fq.013.sam
samtools-1.12/test/dat/bam2fq.703.sam
samtools-1.12/test/dat/cat.hdr
samtools-1.12/test/dat/cram_md5/
samtools-1.12/test/dat/cram_md5/08c04d512d4797d9ba2a156c1daba468
samtools-1.12/test/dat/cram_md5/7c35feac7036c1cdef3bee0cc4b21437
samtools-1.12/test/dat/cram_md5/89b96de7acc5918c2858ef92710be7d4
samtools-1.12/test/dat/cram_md5/8a3d8deb9edd4ce3346b6061fcee6d0b
samtools-1.12/test/dat/depad.001.fa
samtools-1.12/test/dat/depad.001.fa.fai
samtools-1.12/test/dat/depad.001p.sam
samtools-1.12/test/dat/depad.001u.sam
samtools-1.12/test/dat/dict.alias.fa
samtools-1.12/test/dat/dict.alias.out
samtools-1.12/test/dat/dict.fa
samtools-1.12/test/dat/dict.out
samtools-1.12/test/dat/empty.expected
samtools-1.12/test/dat/large_chrom.out
samtools-1.12/test/dat/large_chrom.sam
samtools-1.12/test/dat/large_chrom_bai_index.err
samtools-1.12/test/dat/mpileup.1.sam
samtools-1.12/test/dat/mpileup.2.sam
samtools-1.12/test/dat/mpileup.3.sam
samtools-1.12/test/dat/mpileup.err.1
samtools-1.12/test/dat/mpileup.out.1
samtools-1.12/test/dat/mpileup.out.2
samtools-1.12/test/dat/mpileup.out.3
samtools-1.12/test/dat/mpileup.out.4
samtools-1.12/test/dat/mpileup.out.5
samtools-1.12/test/dat/mpileup.ref.fa
samtools-1.12/test/dat/mpileup.ref.fa.fai
samtools-1.12/test/dat/test_input_1_a.bam
samtools-1.12/test/dat/test_input_1_a.bam.bai.expected
samtools-1.12/test/dat/test_input_1_a.cram
samtools-1.12/test/dat/test_input_1_a.sam
samtools-1.12/test/dat/test_input_1_a_regex.sam
samtools-1.12/test/dat/test_input_1_ab.X.expected
samtools-1.12/test/dat/test_input_1_b.X.expected
samtools-1.12/test/dat/test_input_1_b.bam
samtools-1.12/test/dat/test_input_1_b.sam
samtools-1.12/test/dat/test_input_1_b_regex.sam
samtools-1.12/test/dat/test_input_1_c.bam
samtools-1.12/test/dat/test_input_1_c.sam
samtools-1.12/test/dat/test_input_1_d.sam
samtools-1.12/test/dat/view.001.01.bed
samtools-1.12/test/dat/view.001.02.bed
samtools-1.12/test/dat/view.001.fa
samtools-1.12/test/dat/view.001.fa.fai
samtools-1.12/test/dat/view.001.sam
samtools-1.12/test/dat/view.002.01.bed
samtools-1.12/test/dat/view.002.02.bed
samtools-1.12/test/dat/view.002.fa
samtools-1.12/test/dat/view.002.fa.fai
samtools-1.12/test/dat/view.002.sam
samtools-1.12/test/dat/view.003.expected.sam
samtools-1.12/test/dat/view.003.sam
samtools-1.12/test/dat/view.004.expected.sam
samtools-1.12/test/fixmate/
samtools-1.12/test/fixmate/1_coord_sort.sam
samtools-1.12/test/fixmate/1_coord_sort.sam.expected
samtools-1.12/test/fixmate/1_coord_sort.sam.expected.err
samtools-1.12/test/fixmate/2_isize_overflow.sam
samtools-1.12/test/fixmate/2_isize_overflow.sam.expected
samtools-1.12/test/fixmate/3_reverse_read_pp_lt.sam
samtools-1.12/test/fixmate/3_reverse_read_pp_lt.sam.expected
samtools-1.12/test/fixmate/4_reverse_read_pp_equal.sam
samtools-1.12/test/fixmate/4_reverse_read_pp_equal.sam.expected
samtools-1.12/test/fixmate/5_ct.sam
samtools-1.12/test/fixmate/5_ct.sam.expected
samtools-1.12/test/fixmate/6_ct_replace.sam
samtools-1.12/test/fixmate/6_ct_replace.sam.expected
samtools-1.12/test/fixmate/7_two_read_mapped.sam
samtools-1.12/test/fixmate/7_two_read_mapped.sam.expected
samtools-1.12/test/fixmate/8_isize_overflow_64bit.sam
samtools-1.12/test/fixmate/8_isize_overflow_64bit.sam.expected
samtools-1.12/test/idxstats/
samtools-1.12/test/idxstats/test_input_1_a.bam.expected
samtools-1.12/test/idxstats/test_input_1_a.bam.expected.err
samtools-1.12/test/large_pos/
samtools-1.12/test/large_pos/depth.expected.out
samtools-1.12/test/large_pos/depth_bed.expected.out
samtools-1.12/test/large_pos/longref.sam
samtools-1.12/test/large_pos/longref2.sam
samtools-1.12/test/large_pos/longref3.expected.sam
samtools-1.12/test/large_pos/longref3.sam
samtools-1.12/test/large_pos/longref_idx.expected.sam
samtools-1.12/test/large_pos/longref_name.sam
samtools-1.12/test/large_pos/merge.expected.sam
samtools-1.12/test/large_pos/test.bed
samtools-1.12/test/large_pos/tview.expected.out
samtools-1.12/test/maintainer/
samtools-1.12/test/maintainer/check_copyright.pl
samtools-1.12/test/maintainer/check_spaces.pl
samtools-1.12/test/markdup/
samtools-1.12/test/markdup/1_name_sort.expected.sam
samtools-1.12/test/markdup/1_name_sort.expected.sam.err
samtools-1.12/test/markdup/1_name_sort.sam
samtools-1.12/test/markdup/2_bad_order.expected.sam
samtools-1.12/test/markdup/2_bad_order.expected.sam.err
samtools-1.12/test/markdup/2_bad_order.sam
samtools-1.12/test/markdup/3_missing_mc.expected.sam
samtools-1.12/test/markdup/3_missing_mc.expected.sam.err
samtools-1.12/test/markdup/3_missing_mc.sam
samtools-1.12/test/markdup/4_missing_ms.expected.sam
samtools-1.12/test/markdup/4_missing_ms.expected.sam.err
samtools-1.12/test/markdup/4_missing_ms.sam
samtools-1.12/test/markdup/5_markdup.expected.sam
samtools-1.12/test/markdup/5_markdup.sam
samtools-1.12/test/markdup/6_remove_dups.expected.sam
samtools-1.12/test/markdup/6_remove_dups.sam
samtools-1.12/test/markdup/7_mark_supp_dup.expected.sam
samtools-1.12/test/markdup/7_mark_supp_dup.sam
samtools-1.12/test/markdup/8_optical_dup.expected.sam
samtools-1.12/test/markdup/8_optical_dup.sam
samtools-1.12/test/markdup/9_optical_dup_qcfail.expected.sam
samtools-1.12/test/markdup/9_optical_dup_qcfail.sam
samtools-1.12/test/merge/
samtools-1.12/test/merge/2.merge.expected.sam
samtools-1.12/test/merge/3.merge.expected.err
samtools-1.12/test/merge/3.merge.expected.sam
samtools-1.12/test/merge/4.merge.expected.sam
samtools-1.12/test/merge/5.merge.expected.sam
samtools-1.12/test/merge/6.merge.expected.sam
samtools-1.12/test/merge/7.merge.expected.sam
samtools-1.12/test/merge/merge.bed
samtools-1.12/test/merge/merge.bed.1.sam
samtools-1.12/test/merge/merge.bed.2.sam
samtools-1.12/test/merge/merge.bed.expected.sam
samtools-1.12/test/merge/tag.pg.merge.expected.sam
samtools-1.12/test/merge/tag.pg.n.merge.expected.sam
samtools-1.12/test/merge/test_3.fofn
samtools-1.12/test/merge/test_bam_translate.c
samtools-1.12/test/merge/test_header.sam
samtools-1.12/test/merge/test_no_pg_rg_co.sam
samtools-1.12/test/merge/test_rtrans_build.c
samtools-1.12/test/merge/test_trans_tbl_init.c
samtools-1.12/test/mpileup/
samtools-1.12/test/mpileup/1read.bam
samtools-1.12/test/mpileup/1read.sam
samtools-1.12/test/mpileup/anomalous.sam
samtools-1.12/test/mpileup/c1#clip.bam
samtools-1.12/test/mpileup/c1#pad1.bam
samtools-1.12/test/mpileup/c1#pad2.bam
samtools-1.12/test/mpileup/c1#pad3.bam
samtools-1.12/test/mpileup/c1.fa
samtools-1.12/test/mpileup/c1.fa.fai
samtools-1.12/test/mpileup/ce#5b.bam
samtools-1.12/test/mpileup/ce#5b.bam.bai
samtools-1.12/test/mpileup/ce#5b.cram
samtools-1.12/test/mpileup/ce#5b.cram.crai
samtools-1.12/test/mpileup/ce#5b.sam
samtools-1.12/test/mpileup/ce#large_seq.bam
samtools-1.12/test/mpileup/ce#unmap.bam
samtools-1.12/test/mpileup/ce#unmap1.bam
samtools-1.12/test/mpileup/ce#unmap2.bam
samtools-1.12/test/mpileup/ce.fa
samtools-1.12/test/mpileup/ce.fa.fai
samtools-1.12/test/mpileup/deep.sam
samtools-1.12/test/mpileup/depth.reg
samtools-1.12/test/mpileup/depth_del.sam
samtools-1.12/test/mpileup/expected/
samtools-1.12/test/mpileup/expected/1.out.f3-6.gz
samtools-1.12/test/mpileup/expected/10.out
samtools-1.12/test/mpileup/expected/11.out
samtools-1.12/test/mpileup/expected/12.out
samtools-1.12/test/mpileup/expected/13.out
samtools-1.12/test/mpileup/expected/14.out
samtools-1.12/test/mpileup/expected/15.out
samtools-1.12/test/mpileup/expected/16.out
samtools-1.12/test/mpileup/expected/17.out
samtools-1.12/test/mpileup/expected/18.out
samtools-1.12/test/mpileup/expected/19.out
samtools-1.12/test/mpileup/expected/2.out
samtools-1.12/test/mpileup/expected/20.out
samtools-1.12/test/mpileup/expected/21.out
samtools-1.12/test/mpileup/expected/22.out
samtools-1.12/test/mpileup/expected/23.out
samtools-1.12/test/mpileup/expected/24.out
samtools-1.12/test/mpileup/expected/25.out
samtools-1.12/test/mpileup/expected/26.out
samtools-1.12/test/mpileup/expected/27.out
samtools-1.12/test/mpileup/expected/28.out
samtools-1.12/test/mpileup/expected/29.out
samtools-1.12/test/mpileup/expected/3.out
samtools-1.12/test/mpileup/expected/30.out
samtools-1.12/test/mpileup/expected/31.out
samtools-1.12/test/mpileup/expected/32.out
samtools-1.12/test/mpileup/expected/33.out
samtools-1.12/test/mpileup/expected/34.out
samtools-1.12/test/mpileup/expected/35.out
samtools-1.12/test/mpileup/expected/37.out
samtools-1.12/test/mpileup/expected/38.out
samtools-1.12/test/mpileup/expected/39.out
samtools-1.12/test/mpileup/expected/4.out
samtools-1.12/test/mpileup/expected/40.out
samtools-1.12/test/mpileup/expected/41.out
samtools-1.12/test/mpileup/expected/42.out
samtools-1.12/test/mpileup/expected/43.out
samtools-1.12/test/mpileup/expected/44.out
samtools-1.12/test/mpileup/expected/45.out
samtools-1.12/test/mpileup/expected/46.out
samtools-1.12/test/mpileup/expected/47.out
samtools-1.12/test/mpileup/expected/48.out
samtools-1.12/test/mpileup/expected/49.out
samtools-1.12/test/mpileup/expected/5.out
samtools-1.12/test/mpileup/expected/50.out
samtools-1.12/test/mpileup/expected/51.out
samtools-1.12/test/mpileup/expected/52.out
samtools-1.12/test/mpileup/expected/53.out
samtools-1.12/test/mpileup/expected/54.out
samtools-1.12/test/mpileup/expected/55.out
samtools-1.12/test/mpileup/expected/56.out
samtools-1.12/test/mpileup/expected/57.out
samtools-1.12/test/mpileup/expected/58.out
samtools-1.12/test/mpileup/expected/59.out
samtools-1.12/test/mpileup/expected/6.out
samtools-1.12/test/mpileup/expected/60.out
samtools-1.12/test/mpileup/expected/61.out
samtools-1.12/test/mpileup/expected/62.out
samtools-1.12/test/mpileup/expected/63.out
samtools-1.12/test/mpileup/expected/64.out
samtools-1.12/test/mpileup/expected/65.out
samtools-1.12/test/mpileup/expected/66.out
samtools-1.12/test/mpileup/expected/67.out
samtools-1.12/test/mpileup/expected/68.out
samtools-1.12/test/mpileup/expected/69.out
samtools-1.12/test/mpileup/expected/7.out
samtools-1.12/test/mpileup/expected/70.out
samtools-1.12/test/mpileup/expected/71.out
samtools-1.12/test/mpileup/expected/72.out
samtools-1.12/test/mpileup/expected/73.out
samtools-1.12/test/mpileup/expected/74.out
samtools-1.12/test/mpileup/expected/75.out
samtools-1.12/test/mpileup/expected/76.out
samtools-1.12/test/mpileup/expected/77.out
samtools-1.12/test/mpileup/expected/78.out
samtools-1.12/test/mpileup/expected/79.out
samtools-1.12/test/mpileup/expected/8.out
samtools-1.12/test/mpileup/expected/9.out
samtools-1.12/test/mpileup/expected/a0.out
samtools-1.12/test/mpileup/expected/a1.out
samtools-1.12/test/mpileup/expected/a10.out
samtools-1.12/test/mpileup/expected/a11.out
samtools-1.12/test/mpileup/expected/a13.out
samtools-1.12/test/mpileup/expected/a14.out
samtools-1.12/test/mpileup/expected/a15.out
samtools-1.12/test/mpileup/expected/a16.out
samtools-1.12/test/mpileup/expected/a17.out
samtools-1.12/test/mpileup/expected/a2.out
samtools-1.12/test/mpileup/expected/a3.out
samtools-1.12/test/mpileup/expected/a4.out
samtools-1.12/test/mpileup/expected/a5.out
samtools-1.12/test/mpileup/expected/a6.out
samtools-1.12/test/mpileup/expected/a8.out
samtools-1.12/test/mpileup/expected/a9.out
samtools-1.12/test/mpileup/expected/d1_1.out
samtools-1.12/test/mpileup/expected/d1_12.out
samtools-1.12/test/mpileup/expected/d1_2.out
samtools-1.12/test/mpileup/expected/d2_12r.out
samtools-1.12/test/mpileup/expected/d3_12.out
samtools-1.12/test/mpileup/expected/d3_12r1a.out
samtools-1.12/test/mpileup/expected/d3_12r2a.out
samtools-1.12/test/mpileup/expected/d3_3.out
samtools-1.12/test/mpileup/expected/d4_12.out
samtools-1.12/test/mpileup/expected/d4_12b.out
samtools-1.12/test/mpileup/expected/d4_12r.out
samtools-1.12/test/mpileup/expected/d5_all1.out
samtools-1.12/test/mpileup/expected/d5_all2.out
samtools-1.12/test/mpileup/expected/d5_all3.out
samtools-1.12/test/mpileup/expected/d5_all4.out
samtools-1.12/test/mpileup/expected/d5_b3.out
samtools-1.12/test/mpileup/expected/d5_b3a.out
samtools-1.12/test/mpileup/expected/d5_b3aa.out
samtools-1.12/test/mpileup/expected/d5_blank.out
samtools-1.12/test/mpileup/expected/d5_xx1.out
samtools-1.12/test/mpileup/expected/d5_xx2.out
samtools-1.12/test/mpileup/expected/d5_xx3.out
samtools-1.12/test/mpileup/expected/d5_xy1.out
samtools-1.12/test/mpileup/expected/d6_nodel.out
samtools-1.12/test/mpileup/expected/d6_wdel.out
samtools-1.12/test/mpileup/expected/d7_nodup.out
samtools-1.12/test/mpileup/expected/m5_all1.out
samtools-1.12/test/mpileup/expected/m5_all2.out
samtools-1.12/test/mpileup/expected/m5_all3.out
samtools-1.12/test/mpileup/expected/m5_b3.out
samtools-1.12/test/mpileup/expected/m5_b3a.out
samtools-1.12/test/mpileup/expected/m5_b3aa.out
samtools-1.12/test/mpileup/expected/m5_blank.out
samtools-1.12/test/mpileup/expected/m5_xx1.out
samtools-1.12/test/mpileup/expected/m5_xx2.out
samtools-1.12/test/mpileup/expected/m5_xx3.out
samtools-1.12/test/mpileup/expected/m5_xy1.out
samtools-1.12/test/mpileup/expected/mp_D.out
samtools-1.12/test/mpileup/expected/mp_DI.out
samtools-1.12/test/mpileup/expected/mp_I.out
samtools-1.12/test/mpileup/expected/mp_ID.out
samtools-1.12/test/mpileup/expected/mp_ID_rev.out
samtools-1.12/test/mpileup/expected/mp_N.out
samtools-1.12/test/mpileup/expected/mp_N2.out
samtools-1.12/test/mpileup/expected/mp_P.out
samtools-1.12/test/mpileup/indels.sam
samtools-1.12/test/mpileup/md5/
samtools-1.12/test/mpileup/md5/02099b2aad2cfe707759353724fb40ae
samtools-1.12/test/mpileup/md5/0d4dfc45807d6a11439e858605cb364d
samtools-1.12/test/mpileup/md5/351f64d4f4f9ddd45b35336ad97aa6de
samtools-1.12/test/mpileup/md5/6ec590eb82c361a61e6baabce20109bc
samtools-1.12/test/mpileup/md5/6f60cdf4c739651ae72d53e2e94825c1
samtools-1.12/test/mpileup/md5/73d180d5cb3860a2713927b6812eab0e
samtools-1.12/test/mpileup/mp.fa
samtools-1.12/test/mpileup/mp.fa.fai
samtools-1.12/test/mpileup/mp_D.sam
samtools-1.12/test/mpileup/mp_DI.sam
samtools-1.12/test/mpileup/mp_I.sam
samtools-1.12/test/mpileup/mp_ID.sam
samtools-1.12/test/mpileup/mp_ID_rev.sam
samtools-1.12/test/mpileup/mp_N.sam
samtools-1.12/test/mpileup/mp_N2.sam
samtools-1.12/test/mpileup/mp_P.sam
samtools-1.12/test/mpileup/mpileup-E.bam
samtools-1.12/test/mpileup/mpileup.1.bam
samtools-1.12/test/mpileup/mpileup.1.bam.bai
samtools-1.12/test/mpileup/mpileup.2.bam
samtools-1.12/test/mpileup/mpileup.3.bam
samtools-1.12/test/mpileup/mpileup.ref.fa
samtools-1.12/test/mpileup/mpileup.ref.fa.fai
samtools-1.12/test/mpileup/mpileup.reg
samtools-1.12/test/mpileup/overlap.bam
samtools-1.12/test/mpileup/overlap50.sam
samtools-1.12/test/mpileup/overlapIllumina.bam
samtools-1.12/test/mpileup/regions
samtools-1.12/test/mpileup/regression.sh
samtools-1.12/test/mpileup/xx#depth1.sam
samtools-1.12/test/mpileup/xx#depth2.sam
samtools-1.12/test/mpileup/xx#depth3.sam
samtools-1.12/test/mpileup/xx#depth4.sam
samtools-1.12/test/mpileup/xx#minimal.bam
samtools-1.12/test/mpileup/xx#triplet.bam
samtools-1.12/test/mpileup/xx.bed
samtools-1.12/test/mpileup/xx.bed2
samtools-1.12/test/mpileup/xx.bed3
samtools-1.12/test/mpileup/xx.fa
samtools-1.12/test/mpileup/xx.fa.fai
samtools-1.12/test/quickcheck/
samtools-1.12/test/quickcheck/1.quickcheck.badeof.bam
samtools-1.12/test/quickcheck/10.quickcheck.notargets.bam
samtools-1.12/test/quickcheck/2.quickcheck.badheader.bam
samtools-1.12/test/quickcheck/3.quickcheck.ok.bam
samtools-1.12/test/quickcheck/4.quickcheck.ok.bam
samtools-1.12/test/quickcheck/5.quickcheck.scramble30.truncated.cram
samtools-1.12/test/quickcheck/6.quickcheck.cram21.ok.cram
samtools-1.12/test/quickcheck/7.quickcheck.cram30.ok.cram
samtools-1.12/test/quickcheck/8.quickcheck.cram21.truncated.cram
samtools-1.12/test/quickcheck/9.quickcheck.cram30.truncated.cram
samtools-1.12/test/quickcheck/all.expected
samtools-1.12/test/reheader/
samtools-1.12/test/reheader/1_view1.sam.expected
samtools-1.12/test/reheader/1_view1.sam.expected.err
samtools-1.12/test/reheader/2_view1.sam.expected
samtools-1.12/test/reheader/2_view1.sam.expected.err
samtools-1.12/test/reheader/3_view1.sam.expected
samtools-1.12/test/reheader/3_view1.sam.expected.err
samtools-1.12/test/reheader/4_view1.sam.expected
samtools-1.12/test/reheader/5_view1.sam.expected
samtools-1.12/test/reheader/hdr.sam
samtools-1.12/test/sort/
samtools-1.12/test/sort/name.sort.expected.sam
samtools-1.12/test/sort/pos.sort.expected.sam
samtools-1.12/test/sort/tag.as.sort.expected.sam
samtools-1.12/test/sort/tag.fi.sort.expected.sam
samtools-1.12/test/sort/tag.rg.n.sort.expected.sam
samtools-1.12/test/sort/tag.rg.sort.expected.sam
samtools-1.12/test/split/
samtools-1.12/test/split/split.expected.grp1.sam
samtools-1.12/test/split/split.expected.grp2.sam
samtools-1.12/test/split/split.expected.unk.sam
samtools-1.12/test/split/split.sam
samtools-1.12/test/split/test_count_rg.c
samtools-1.12/test/split/test_expand_format_string.c
samtools-1.12/test/split/test_filter_header_rg.c
samtools-1.12/test/split/test_parse_args.c
samtools-1.12/test/stat/
samtools-1.12/test/stat/1.stats.expected
samtools-1.12/test/stat/1.stats.large.expected
samtools-1.12/test/stat/10.stats.expected
samtools-1.12/test/stat/10_map_cigar.sam
samtools-1.12/test/stat/10_map_cigar.sam_s1_a_1.expected.bamstat
samtools-1.12/test/stat/10_map_cigar.sam_s1_b_1.expected.bamstat
samtools-1.12/test/stat/11.stats.expected
samtools-1.12/test/stat/11.stats.g4.expected
samtools-1.12/test/stat/11.stats.targets
samtools-1.12/test/stat/11_target.bam
samtools-1.12/test/stat/11_target.bam.bai
samtools-1.12/test/stat/11_target.sam
samtools-1.12/test/stat/12.2reads.nooverlap.expected
samtools-1.12/test/stat/12.2reads.overlap.expected
samtools-1.12/test/stat/12.3reads.nooverlap.expected
samtools-1.12/test/stat/12.3reads.overlap.expected
samtools-1.12/test/stat/12_2reads.bed
samtools-1.12/test/stat/12_3reads.bed
samtools-1.12/test/stat/12_overlaps.bam
samtools-1.12/test/stat/13.barcodes.bc.ok.expected
samtools-1.12/test/stat/13.barcodes.ox.ok.expected
samtools-1.12/test/stat/13_barcodes_fail_bc_length.sam
samtools-1.12/test/stat/13_barcodes_fail_hyphen.sam
samtools-1.12/test/stat/13_barcodes_fail_qt_length.sam
samtools-1.12/test/stat/13_barcodes_ok.sam
samtools-1.12/test/stat/13_barcodes_ok_ox_bz.sam
samtools-1.12/test/stat/1_map_cigar.sam
samtools-1.12/test/stat/1_map_cigar.sam_s1_a_1.expected.bamstat
samtools-1.12/test/stat/1_map_cigar_large.sam
samtools-1.12/test/stat/2.stats.expected
samtools-1.12/test/stat/2.stats.large.expected
samtools-1.12/test/stat/2_equal_cigar_full_seq.sam
samtools-1.12/test/stat/2_equal_cigar_full_seq_large.sam
samtools-1.12/test/stat/3.stats.expected
samtools-1.12/test/stat/3.stats.large.expected
samtools-1.12/test/stat/3_map_cigar_equal_seq.sam
samtools-1.12/test/stat/3_map_cigar_equal_seq_large.sam
samtools-1.12/test/stat/4.stats.expected
samtools-1.12/test/stat/4.stats.large.expected
samtools-1.12/test/stat/4_X_cigar_full_seq.sam
samtools-1.12/test/stat/4_X_cigar_full_seq_large.sam
samtools-1.12/test/stat/5.stats.expected
samtools-1.12/test/stat/5.stats.large.expected
samtools-1.12/test/stat/5_insert_cigar.sam
samtools-1.12/test/stat/5_insert_cigar_large.sam
samtools-1.12/test/stat/6.stats.expected
samtools-1.12/test/stat/7.stats.expected
samtools-1.12/test/stat/7.stats.large.expected
samtools-1.12/test/stat/7_supp.sam
samtools-1.12/test/stat/7_supp_large.sam
samtools-1.12/test/stat/8.stats.expected
samtools-1.12/test/stat/8.stats.large.expected
samtools-1.12/test/stat/8_secondary.sam
samtools-1.12/test/stat/8_secondary_large.sam
samtools-1.12/test/stat/9.stats.expected
samtools-1.12/test/stat/test.fa
samtools-1.12/test/stat/test.fa.fai
samtools-1.12/test/test.c
samtools-1.12/test/test.h
samtools-1.12/test/test.pl
samtools-1.12/test/tview/
samtools-1.12/test/tview/test_get_rg_sample.c
samtools-1.12/test/vcf-miniview.c
samtools-1.12/tmp_file.c
samtools-1.12/tmp_file.h
samtools-1.12/version.sh
source is under 'samtools-1.12'