The following packages will be installed: samtools Fetching README... 0%100%100%100%100%100%Done Fetching README.references... 0%100%100%100%100%100%Done Fetching samtools.SlackBuild... 0%100%100%100%100%100%Done Fetching samtools.info... 0%100%100%100%100%100%Done Fetching slack-desc... 0%100%100%100%100%100%Done samtools-1.15.1/ samtools-1.15.1/AUTHORS samtools-1.15.1/ChangeLog.old samtools-1.15.1/INSTALL samtools-1.15.1/LICENSE samtools-1.15.1/Makefile samtools-1.15.1/NEWS samtools-1.15.1/README samtools-1.15.1/amplicon_stats.c samtools-1.15.1/bam.c samtools-1.15.1/bam.h samtools-1.15.1/bam2bcf.c samtools-1.15.1/bam2bcf.h samtools-1.15.1/bam2depth.c samtools-1.15.1/bam_addrprg.c samtools-1.15.1/bam_ampliconclip.c samtools-1.15.1/bam_ampliconclip.h samtools-1.15.1/bam_aux.c samtools-1.15.1/bam_cat.c samtools-1.15.1/bam_color.c samtools-1.15.1/bam_consensus.c samtools-1.15.1/bam_fastq.c samtools-1.15.1/bam_flags.c samtools-1.15.1/bam_import.c samtools-1.15.1/bam_index.c samtools-1.15.1/bam_lpileup.c samtools-1.15.1/bam_lpileup.h samtools-1.15.1/bam_markdup.c samtools-1.15.1/bam_mate.c samtools-1.15.1/bam_md.c samtools-1.15.1/bam_plbuf.c samtools-1.15.1/bam_plbuf.h samtools-1.15.1/bam_plcmd.c samtools-1.15.1/bam_quickcheck.c samtools-1.15.1/bam_reheader.c samtools-1.15.1/bam_rmdup.c samtools-1.15.1/bam_rmdupse.c samtools-1.15.1/bam_samples.c samtools-1.15.1/bam_sort.c samtools-1.15.1/bam_split.c samtools-1.15.1/bam_stat.c samtools-1.15.1/bam_tview.c samtools-1.15.1/bam_tview.h samtools-1.15.1/bam_tview_curses.c samtools-1.15.1/bam_tview_html.c samtools-1.15.1/bamshuf.c samtools-1.15.1/bamtk.c samtools-1.15.1/bedcov.c samtools-1.15.1/bedidx.c samtools-1.15.1/bedidx.h samtools-1.15.1/config.mk.in samtools-1.15.1/configure.ac samtools-1.15.1/consensus_pileup.c samtools-1.15.1/consensus_pileup.h samtools-1.15.1/coverage.c samtools-1.15.1/cut_target.c samtools-1.15.1/dict.c samtools-1.15.1/doc/ samtools-1.15.1/doc/samtools-addreplacerg.1 samtools-1.15.1/doc/samtools-ampliconclip.1 samtools-1.15.1/doc/samtools-ampliconstats.1 samtools-1.15.1/doc/samtools-bedcov.1 samtools-1.15.1/doc/samtools-calmd.1 samtools-1.15.1/doc/samtools-cat.1 samtools-1.15.1/doc/samtools-collate.1 samtools-1.15.1/doc/samtools-consensus.1 samtools-1.15.1/doc/samtools-coverage.1 samtools-1.15.1/doc/samtools-depad.1 samtools-1.15.1/doc/samtools-depth.1 samtools-1.15.1/doc/samtools-dict.1 samtools-1.15.1/doc/samtools-faidx.1 samtools-1.15.1/doc/samtools-fasta.1 samtools-1.15.1/doc/samtools-fastq.1 samtools-1.15.1/doc/samtools-fixmate.1 samtools-1.15.1/doc/samtools-flags.1 samtools-1.15.1/doc/samtools-flagstat.1 samtools-1.15.1/doc/samtools-fqidx.1 samtools-1.15.1/doc/samtools-head.1 samtools-1.15.1/doc/samtools-idxstats.1 samtools-1.15.1/doc/samtools-import.1 samtools-1.15.1/doc/samtools-index.1 samtools-1.15.1/doc/samtools-markdup.1 samtools-1.15.1/doc/samtools-merge.1 samtools-1.15.1/doc/samtools-mpileup.1 samtools-1.15.1/doc/samtools-phase.1 samtools-1.15.1/doc/samtools-quickcheck.1 samtools-1.15.1/doc/samtools-reheader.1 samtools-1.15.1/doc/samtools-rmdup.1 samtools-1.15.1/doc/samtools-samples.1 samtools-1.15.1/doc/samtools-sort.1 samtools-1.15.1/doc/samtools-split.1 samtools-1.15.1/doc/samtools-stats.1 samtools-1.15.1/doc/samtools-targetcut.1 samtools-1.15.1/doc/samtools-tview.1 samtools-1.15.1/doc/samtools-view.1 samtools-1.15.1/doc/samtools.1 samtools-1.15.1/examples/ samtools-1.15.1/examples/00README.txt samtools-1.15.1/examples/ex1.fa samtools-1.15.1/examples/ex1.sam.gz samtools-1.15.1/examples/toy.fa samtools-1.15.1/examples/toy.sam samtools-1.15.1/faidx.c samtools-1.15.1/install-sh samtools-1.15.1/lz4/ samtools-1.15.1/lz4/LICENSE samtools-1.15.1/lz4/lz4.c samtools-1.15.1/lz4/lz4.h samtools-1.15.1/m4/ samtools-1.15.1/m4/ax_with_htslib.m4 samtools-1.15.1/m4/hts_prog_cc_warnings.m4 samtools-1.15.1/m4/hts_with_curses.m4 samtools-1.15.1/misc/ samtools-1.15.1/misc/HmmGlocal.java samtools-1.15.1/misc/ace2sam.c samtools-1.15.1/misc/blast2sam.pl samtools-1.15.1/misc/bowtie2sam.pl samtools-1.15.1/misc/export2sam.pl samtools-1.15.1/misc/fasta-sanitize.pl samtools-1.15.1/misc/interpolate_sam.pl samtools-1.15.1/misc/maq2sam.c samtools-1.15.1/misc/md5fa.c samtools-1.15.1/misc/md5sum-lite.c samtools-1.15.1/misc/novo2sam.pl samtools-1.15.1/misc/plot-ampliconstats samtools-1.15.1/misc/plot-bamstats samtools-1.15.1/misc/psl2sam.pl samtools-1.15.1/misc/r2plot.lua samtools-1.15.1/misc/sam2vcf.pl samtools-1.15.1/misc/samtools.pl samtools-1.15.1/misc/samtools_tab_completion samtools-1.15.1/misc/seq_cache_populate.pl samtools-1.15.1/misc/soap2sam.pl samtools-1.15.1/misc/vcfutils.lua samtools-1.15.1/misc/wgsim.1 samtools-1.15.1/misc/wgsim.c samtools-1.15.1/misc/wgsim_eval.pl samtools-1.15.1/misc/zoom2sam.pl samtools-1.15.1/padding.c samtools-1.15.1/phase.c samtools-1.15.1/sam_opts.c samtools-1.15.1/sam_opts.h samtools-1.15.1/sam_utils.c samtools-1.15.1/sam_view.c samtools-1.15.1/sample.c samtools-1.15.1/sample.h samtools-1.15.1/samtools.h samtools-1.15.1/splaysort.h samtools-1.15.1/stats.c samtools-1.15.1/stats_isize.c samtools-1.15.1/stats_isize.h samtools-1.15.1/test/ samtools-1.15.1/test/addrprg/ samtools-1.15.1/test/addrprg/1_fixup.sam samtools-1.15.1/test/addrprg/1_fixup.sam.expected samtools-1.15.1/test/addrprg/1_fixup.sam.expected.err samtools-1.15.1/test/addrprg/2_fixup_orphan.sam samtools-1.15.1/test/addrprg/2_fixup_orphan.sam.expected samtools-1.15.1/test/addrprg/2_fixup_orphan.sam.expected.err samtools-1.15.1/test/addrprg/3_fixup.sam.expected samtools-1.15.1/test/addrprg/3_fixup.sam.expected.err samtools-1.15.1/test/addrprg/4_fixup_norg.sam samtools-1.15.1/test/addrprg/4_fixup_norg.sam.expected samtools-1.15.1/test/addrprg/4_fixup_norg.sam.expected.err samtools-1.15.1/test/addrprg/5_editrg.sam.expected samtools-1.15.1/test/ampliconclip/ samtools-1.15.1/test/ampliconclip/1_delete_tag.expected.sam samtools-1.15.1/test/ampliconclip/1_fail.expected.sam samtools-1.15.1/test/ampliconclip/1_filter.expected.sam samtools-1.15.1/test/ampliconclip/1_hard_clipped.expected.sam samtools-1.15.1/test/ampliconclip/1_original_tag.expected.sam samtools-1.15.1/test/ampliconclip/1_soft_clipped.expected.sam samtools-1.15.1/test/ampliconclip/1_soft_clipped_strand.expected.sam samtools-1.15.1/test/ampliconclip/1_test_data.sam samtools-1.15.1/test/ampliconclip/2_both_clipped.expected.sam samtools-1.15.1/test/ampliconclip/2_both_test_data.sam samtools-1.15.1/test/ampliconclip/3_multi_ref_both_clip.expected.sam samtools-1.15.1/test/ampliconclip/3_multi_ref_clip.expected.sam samtools-1.15.1/test/ampliconclip/3_multi_ref_data.sam samtools-1.15.1/test/ampliconclip/ac_test.bed samtools-1.15.1/test/ampliconclip/multi_ref.bed samtools-1.15.1/test/ampliconstats/ samtools-1.15.1/test/ampliconstats/mixed_clipped.sam samtools-1.15.1/test/ampliconstats/stats.expected.txt samtools-1.15.1/test/ampliconstats/stats_mixed.expected.txt samtools-1.15.1/test/bam2fq/ samtools-1.15.1/test/bam2fq/1.1.fq.expected samtools-1.15.1/test/bam2fq/1.2.fq.expected samtools-1.15.1/test/bam2fq/10.1.fq.expected samtools-1.15.1/test/bam2fq/10.2.fq.expected samtools-1.15.1/test/bam2fq/10.s.fq.expected samtools-1.15.1/test/bam2fq/11.fa.expected samtools-1.15.1/test/bam2fq/11.fq.expected samtools-1.15.1/test/bam2fq/12.1.fq.expected samtools-1.15.1/test/bam2fq/12.2.fq.expected samtools-1.15.1/test/bam2fq/12.i.fq.expected samtools-1.15.1/test/bam2fq/12.s.fq.expected samtools-1.15.1/test/bam2fq/13.fq.expected samtools-1.15.1/test/bam2fq/14.0.fq.expected samtools-1.15.1/test/bam2fq/14.i1.fq.expected samtools-1.15.1/test/bam2fq/14.i2.fq.expected samtools-1.15.1/test/bam2fq/2.1.fq.expected samtools-1.15.1/test/bam2fq/2.2.fq.expected samtools-1.15.1/test/bam2fq/2.s.fq.expected samtools-1.15.1/test/bam2fq/3.1.fq.expected samtools-1.15.1/test/bam2fq/3.2.fq.expected samtools-1.15.1/test/bam2fq/3.s.fq.expected samtools-1.15.1/test/bam2fq/4.1.fq.expected samtools-1.15.1/test/bam2fq/4.2.fq.expected samtools-1.15.1/test/bam2fq/4.s.fq.expected samtools-1.15.1/test/bam2fq/5.1.fq.expected samtools-1.15.1/test/bam2fq/5.2.fq.expected samtools-1.15.1/test/bam2fq/5.s.fq.expected samtools-1.15.1/test/bam2fq/6.1.fq.expected samtools-1.15.1/test/bam2fq/6.2.fq.expected samtools-1.15.1/test/bam2fq/6.s.fq.expected samtools-1.15.1/test/bam2fq/7.1.fq.expected samtools-1.15.1/test/bam2fq/7.2.fq.expected samtools-1.15.1/test/bam2fq/7.s.fq.expected samtools-1.15.1/test/bam2fq/8.1.fq.expected samtools-1.15.1/test/bam2fq/8.2.fq.expected samtools-1.15.1/test/bam2fq/8.i.fq.expected samtools-1.15.1/test/bam2fq/8.s.fq.expected samtools-1.15.1/test/bam2fq/9.1.fq.expected samtools-1.15.1/test/bam2fq/9.2.fq.expected samtools-1.15.1/test/bam2fq/bc.fq.expected samtools-1.15.1/test/bam2fq/bc10.fq.expected samtools-1.15.1/test/bam2fq/bc_split.fq.expected samtools-1.15.1/test/bedcov/ samtools-1.15.1/test/bedcov/bedcov.bam samtools-1.15.1/test/bedcov/bedcov.bam.bai samtools-1.15.1/test/bedcov/bedcov.bed samtools-1.15.1/test/bedcov/bedcov.expected samtools-1.15.1/test/bedcov/bedcov_gG.bed samtools-1.15.1/test/bedcov/bedcov_gG.expected samtools-1.15.1/test/bedcov/bedcov_j.expected samtools-1.15.1/test/collate/ samtools-1.15.1/test/collate/1_fast_collate.sam.expected samtools-1.15.1/test/collate/2_fast_collate_with_tmp_used.sam.expected samtools-1.15.1/test/collate/collate.expected.sam samtools-1.15.1/test/collate/fast_collate.sam samtools-1.15.1/test/consensus/ samtools-1.15.1/test/consensus/consen1.sam samtools-1.15.1/test/consensus/consen2.sam samtools-1.15.1/test/consensus/consen3.sam samtools-1.15.1/test/consensus/consensus.reg samtools-1.15.1/test/consensus/expected/ samtools-1.15.1/test/consensus/expected/1.out samtools-1.15.1/test/consensus/expected/10.1q.out samtools-1.15.1/test/consensus/expected/10q.out samtools-1.15.1/test/consensus/expected/11.3p.out samtools-1.15.1/test/consensus/expected/11.3q.out samtools-1.15.1/test/consensus/expected/11.4p.out samtools-1.15.1/test/consensus/expected/11.4q.out samtools-1.15.1/test/consensus/expected/11.6p.out samtools-1.15.1/test/consensus/expected/11.6q.out samtools-1.15.1/test/consensus/expected/12p.out samtools-1.15.1/test/consensus/expected/12q.out samtools-1.15.1/test/consensus/expected/13p.out samtools-1.15.1/test/consensus/expected/13q.out samtools-1.15.1/test/consensus/expected/14p.out samtools-1.15.1/test/consensus/expected/14q.out samtools-1.15.1/test/consensus/expected/15p.out samtools-1.15.1/test/consensus/expected/16p.out samtools-1.15.1/test/consensus/expected/16q.out samtools-1.15.1/test/consensus/expected/17q.out samtools-1.15.1/test/consensus/expected/18p.out samtools-1.15.1/test/consensus/expected/18q.out samtools-1.15.1/test/consensus/expected/19p.out samtools-1.15.1/test/consensus/expected/19q.out samtools-1.15.1/test/consensus/expected/1p.out samtools-1.15.1/test/consensus/expected/1q.out samtools-1.15.1/test/consensus/expected/2.out samtools-1.15.1/test/consensus/expected/20p.out samtools-1.15.1/test/consensus/expected/21p.out samtools-1.15.1/test/consensus/expected/2p.out samtools-1.15.1/test/consensus/expected/2q.out samtools-1.15.1/test/consensus/expected/3.out samtools-1.15.1/test/consensus/expected/3q.out samtools-1.15.1/test/consensus/expected/4.out samtools-1.15.1/test/consensus/expected/4p.out samtools-1.15.1/test/consensus/expected/4q.out samtools-1.15.1/test/consensus/expected/5p.out samtools-1.15.1/test/consensus/expected/5q.out samtools-1.15.1/test/consensus/expected/6p.out samtools-1.15.1/test/consensus/expected/6q.out samtools-1.15.1/test/consensus/expected/7p.out samtools-1.15.1/test/consensus/expected/7q.out samtools-1.15.1/test/consensus/expected/8p.out samtools-1.15.1/test/consensus/expected/8q.out samtools-1.15.1/test/consensus/expected/9.1p.out samtools-1.15.1/test/consensus/expected/9.1q.out samtools-1.15.1/test/consensus/expected/9p.out samtools-1.15.1/test/consensus/expected/9q.out samtools-1.15.1/test/consensus/expected/empty.out samtools-1.15.1/test/dat/ samtools-1.15.1/test/dat/bam2fq.001.sam samtools-1.15.1/test/dat/bam2fq.002.sam samtools-1.15.1/test/dat/bam2fq.003.sam samtools-1.15.1/test/dat/bam2fq.004.sam samtools-1.15.1/test/dat/bam2fq.005.sam samtools-1.15.1/test/dat/bam2fq.010.sam samtools-1.15.1/test/dat/bam2fq.013.sam samtools-1.15.1/test/dat/bam2fq.014.sam samtools-1.15.1/test/dat/bam2fq.703.sam samtools-1.15.1/test/dat/cat.hdr samtools-1.15.1/test/dat/cram_md5/ samtools-1.15.1/test/dat/cram_md5/08c04d512d4797d9ba2a156c1daba468 samtools-1.15.1/test/dat/cram_md5/7c35feac7036c1cdef3bee0cc4b21437 samtools-1.15.1/test/dat/cram_md5/89b96de7acc5918c2858ef92710be7d4 samtools-1.15.1/test/dat/cram_md5/8a3d8deb9edd4ce3346b6061fcee6d0b samtools-1.15.1/test/dat/depad.001.fa samtools-1.15.1/test/dat/depad.001.fa.fai samtools-1.15.1/test/dat/depad.001p.sam samtools-1.15.1/test/dat/depad.001u.sam samtools-1.15.1/test/dat/dict.alias.fa samtools-1.15.1/test/dat/dict.alias.out samtools-1.15.1/test/dat/dict.fa samtools-1.15.1/test/dat/dict.out samtools-1.15.1/test/dat/empty.expected samtools-1.15.1/test/dat/large_chrom.out samtools-1.15.1/test/dat/large_chrom.sam samtools-1.15.1/test/dat/large_chrom_bai_index.err samtools-1.15.1/test/dat/mpileup.1.sam samtools-1.15.1/test/dat/mpileup.2.sam samtools-1.15.1/test/dat/mpileup.3.sam samtools-1.15.1/test/dat/mpileup.err.1 samtools-1.15.1/test/dat/mpileup.out.1 samtools-1.15.1/test/dat/mpileup.out.2 samtools-1.15.1/test/dat/mpileup.out.3 samtools-1.15.1/test/dat/mpileup.out.4 samtools-1.15.1/test/dat/mpileup.out.5 samtools-1.15.1/test/dat/mpileup.ref.fa samtools-1.15.1/test/dat/mpileup.ref.fa.fai samtools-1.15.1/test/dat/test_input_1_a.bam samtools-1.15.1/test/dat/test_input_1_a.bam.bai.expected samtools-1.15.1/test/dat/test_input_1_a.cram samtools-1.15.1/test/dat/test_input_1_a.sam samtools-1.15.1/test/dat/test_input_1_a_regex.sam samtools-1.15.1/test/dat/test_input_1_ab.X.expected samtools-1.15.1/test/dat/test_input_1_b.X.expected samtools-1.15.1/test/dat/test_input_1_b.bam samtools-1.15.1/test/dat/test_input_1_b.sam samtools-1.15.1/test/dat/test_input_1_b_regex.sam samtools-1.15.1/test/dat/test_input_1_c.bam samtools-1.15.1/test/dat/test_input_1_c.sam samtools-1.15.1/test/dat/test_input_1_d.sam samtools-1.15.1/test/dat/view.001.01.bed samtools-1.15.1/test/dat/view.001.02.bed samtools-1.15.1/test/dat/view.001.fa samtools-1.15.1/test/dat/view.001.fa.fai samtools-1.15.1/test/dat/view.001.sam samtools-1.15.1/test/dat/view.002.01.bed samtools-1.15.1/test/dat/view.002.02.bed samtools-1.15.1/test/dat/view.002.fa samtools-1.15.1/test/dat/view.002.fa.fai samtools-1.15.1/test/dat/view.002.sam samtools-1.15.1/test/dat/view.003.expected.sam samtools-1.15.1/test/dat/view.003.sam samtools-1.15.1/test/dat/view.004.expected.sam samtools-1.15.1/test/dat/view.005.expected.sam samtools-1.15.1/test/dat/view.005.sam samtools-1.15.1/test/dat/view.005.unmap.expected.sam samtools-1.15.1/test/dat/view.fetch-pairs.bam samtools-1.15.1/test/dat/view.fetch-pairs.expected.sam samtools-1.15.1/test/dat/view.fetch-pairs.filter0.expected.sam samtools-1.15.1/test/dat/view.fetch-pairs.filter1.expected.sam samtools-1.15.1/test/fixmate/ samtools-1.15.1/test/fixmate/1_coord_sort.sam samtools-1.15.1/test/fixmate/1_coord_sort.sam.expected samtools-1.15.1/test/fixmate/1_coord_sort.sam.expected.err samtools-1.15.1/test/fixmate/2_isize_overflow.sam samtools-1.15.1/test/fixmate/2_isize_overflow.sam.expected samtools-1.15.1/test/fixmate/3_reverse_read_pp_lt.sam samtools-1.15.1/test/fixmate/3_reverse_read_pp_lt.sam.expected samtools-1.15.1/test/fixmate/4_reverse_read_pp_equal.sam samtools-1.15.1/test/fixmate/4_reverse_read_pp_equal.sam.expected samtools-1.15.1/test/fixmate/5_ct.sam samtools-1.15.1/test/fixmate/5_ct.sam.expected samtools-1.15.1/test/fixmate/6_ct_replace.sam samtools-1.15.1/test/fixmate/6_ct_replace.sam.expected samtools-1.15.1/test/fixmate/7_two_read_mapped.sam samtools-1.15.1/test/fixmate/7_two_read_mapped.sam.expected samtools-1.15.1/test/fixmate/8_isize_overflow_64bit.sam samtools-1.15.1/test/fixmate/8_isize_overflow_64bit.sam.expected samtools-1.15.1/test/idxstats/ samtools-1.15.1/test/idxstats/test_input_1_a.bam.expected samtools-1.15.1/test/idxstats/test_input_1_a.bam.expected.err samtools-1.15.1/test/import/ samtools-1.15.1/test/import/1.expected.sam samtools-1.15.1/test/import/2.expected.sam samtools-1.15.1/test/import/2.interleaved.fq samtools-1.15.1/test/import/3.interleaved.fq samtools-1.15.1/test/import/4.aux.fq samtools-1.15.1/test/import/4.expected-XZ,XA,AA.sam samtools-1.15.1/test/import/4.expected.sam samtools-1.15.1/test/import/5-BC.expected.sam samtools-1.15.1/test/import/5-OX.expected.sam samtools-1.15.1/test/import/5-i1.fq samtools-1.15.1/test/import/5-i2.fq samtools-1.15.1/test/import/5-r1.fq samtools-1.15.1/test/import/5-r2.fq samtools-1.15.1/test/large_pos/ samtools-1.15.1/test/large_pos/depth.expected.out samtools-1.15.1/test/large_pos/depth_bed.expected.out samtools-1.15.1/test/large_pos/longref.sam samtools-1.15.1/test/large_pos/longref2.sam samtools-1.15.1/test/large_pos/longref3.expected.sam samtools-1.15.1/test/large_pos/longref3.sam samtools-1.15.1/test/large_pos/longref_idx.expected.sam samtools-1.15.1/test/large_pos/longref_name.sam samtools-1.15.1/test/large_pos/merge.expected.sam samtools-1.15.1/test/large_pos/test.bed samtools-1.15.1/test/large_pos/tview.expected.out samtools-1.15.1/test/maintainer/ samtools-1.15.1/test/maintainer/check_copyright.pl samtools-1.15.1/test/maintainer/check_spaces.pl samtools-1.15.1/test/markdup/ samtools-1.15.1/test/markdup/10_optical_chain.expected.sam samtools-1.15.1/test/markdup/10_optical_chain.sam samtools-1.15.1/test/markdup/11_optical_dup_regex.expected.sam samtools-1.15.1/test/markdup/11_optical_dup_regex.sam samtools-1.15.1/test/markdup/12_optical_chain_regex.expected.sam samtools-1.15.1/test/markdup/12_optical_chain_regex.sam samtools-1.15.1/test/markdup/1_name_sort.expected.sam samtools-1.15.1/test/markdup/1_name_sort.expected.sam.err samtools-1.15.1/test/markdup/1_name_sort.sam samtools-1.15.1/test/markdup/2_bad_order.expected.sam samtools-1.15.1/test/markdup/2_bad_order.expected.sam.err samtools-1.15.1/test/markdup/2_bad_order.sam samtools-1.15.1/test/markdup/3_missing_mc.expected.sam samtools-1.15.1/test/markdup/3_missing_mc.expected.sam.err samtools-1.15.1/test/markdup/3_missing_mc.sam samtools-1.15.1/test/markdup/4_missing_ms.expected.sam samtools-1.15.1/test/markdup/4_missing_ms.expected.sam.err samtools-1.15.1/test/markdup/4_missing_ms.sam samtools-1.15.1/test/markdup/5_markdup.expected.sam samtools-1.15.1/test/markdup/5_markdup.sam samtools-1.15.1/test/markdup/6_remove_dups.expected.sam samtools-1.15.1/test/markdup/6_remove_dups.sam samtools-1.15.1/test/markdup/7_mark_supp_dup.expected.sam samtools-1.15.1/test/markdup/7_mark_supp_dup.sam samtools-1.15.1/test/markdup/8_optical_dup.expected.sam samtools-1.15.1/test/markdup/8_optical_dup.sam samtools-1.15.1/test/markdup/9_optical_dup_qcfail.expected.sam samtools-1.15.1/test/markdup/9_optical_dup_qcfail.sam samtools-1.15.1/test/merge/ samtools-1.15.1/test/merge/2.merge.expected.sam samtools-1.15.1/test/merge/3.merge.expected.err samtools-1.15.1/test/merge/3.merge.expected.sam samtools-1.15.1/test/merge/4.merge.expected.sam samtools-1.15.1/test/merge/5.merge.expected.sam samtools-1.15.1/test/merge/6.merge.expected.sam samtools-1.15.1/test/merge/7.merge.expected.sam samtools-1.15.1/test/merge/merge.bed samtools-1.15.1/test/merge/merge.bed.1.sam samtools-1.15.1/test/merge/merge.bed.2.sam samtools-1.15.1/test/merge/merge.bed.expected.sam samtools-1.15.1/test/merge/tag.pg.merge.expected.sam samtools-1.15.1/test/merge/tag.pg.n.merge.expected.sam samtools-1.15.1/test/merge/test_3.fofn samtools-1.15.1/test/merge/test_bam_translate.c samtools-1.15.1/test/merge/test_header.sam samtools-1.15.1/test/merge/test_no_pg_rg_co.sam samtools-1.15.1/test/merge/test_rtrans_build.c samtools-1.15.1/test/merge/test_trans_tbl_init.c samtools-1.15.1/test/mpileup/ samtools-1.15.1/test/mpileup/1read.bam samtools-1.15.1/test/mpileup/1read.sam samtools-1.15.1/test/mpileup/anomalous.sam samtools-1.15.1/test/mpileup/c1#clip.bam samtools-1.15.1/test/mpileup/c1#pad1.bam samtools-1.15.1/test/mpileup/c1#pad2.bam samtools-1.15.1/test/mpileup/c1#pad3.bam samtools-1.15.1/test/mpileup/c1.fa samtools-1.15.1/test/mpileup/c1.fa.fai samtools-1.15.1/test/mpileup/ce#5b.bam samtools-1.15.1/test/mpileup/ce#5b.bam.bai samtools-1.15.1/test/mpileup/ce#5b.cram samtools-1.15.1/test/mpileup/ce#5b.cram.crai samtools-1.15.1/test/mpileup/ce#5b.sam samtools-1.15.1/test/mpileup/ce#large_seq.bam samtools-1.15.1/test/mpileup/ce#unmap.bam samtools-1.15.1/test/mpileup/ce#unmap1.bam samtools-1.15.1/test/mpileup/ce#unmap2.bam samtools-1.15.1/test/mpileup/ce.fa samtools-1.15.1/test/mpileup/ce.fa.fai samtools-1.15.1/test/mpileup/deep.sam samtools-1.15.1/test/mpileup/depth.reg samtools-1.15.1/test/mpileup/depth_del.sam samtools-1.15.1/test/mpileup/expected/ samtools-1.15.1/test/mpileup/expected/1.out.f3-6.gz samtools-1.15.1/test/mpileup/expected/10.out samtools-1.15.1/test/mpileup/expected/11.out samtools-1.15.1/test/mpileup/expected/12.out samtools-1.15.1/test/mpileup/expected/13.out samtools-1.15.1/test/mpileup/expected/14.out samtools-1.15.1/test/mpileup/expected/15.out samtools-1.15.1/test/mpileup/expected/16.out samtools-1.15.1/test/mpileup/expected/17.out samtools-1.15.1/test/mpileup/expected/18.out samtools-1.15.1/test/mpileup/expected/19.out samtools-1.15.1/test/mpileup/expected/2.out samtools-1.15.1/test/mpileup/expected/20.out samtools-1.15.1/test/mpileup/expected/21.out samtools-1.15.1/test/mpileup/expected/22.out samtools-1.15.1/test/mpileup/expected/23.out samtools-1.15.1/test/mpileup/expected/24.out samtools-1.15.1/test/mpileup/expected/25.out samtools-1.15.1/test/mpileup/expected/26.out samtools-1.15.1/test/mpileup/expected/27.out samtools-1.15.1/test/mpileup/expected/28.out samtools-1.15.1/test/mpileup/expected/29.out samtools-1.15.1/test/mpileup/expected/3.out samtools-1.15.1/test/mpileup/expected/30.out samtools-1.15.1/test/mpileup/expected/31.out samtools-1.15.1/test/mpileup/expected/32.out samtools-1.15.1/test/mpileup/expected/33.out samtools-1.15.1/test/mpileup/expected/34.out samtools-1.15.1/test/mpileup/expected/35.out samtools-1.15.1/test/mpileup/expected/37.out samtools-1.15.1/test/mpileup/expected/38.out samtools-1.15.1/test/mpileup/expected/39.out samtools-1.15.1/test/mpileup/expected/4.out samtools-1.15.1/test/mpileup/expected/40.out samtools-1.15.1/test/mpileup/expected/41.out samtools-1.15.1/test/mpileup/expected/42.out samtools-1.15.1/test/mpileup/expected/43.out samtools-1.15.1/test/mpileup/expected/44.out samtools-1.15.1/test/mpileup/expected/45.out samtools-1.15.1/test/mpileup/expected/46.out samtools-1.15.1/test/mpileup/expected/47.out samtools-1.15.1/test/mpileup/expected/48.out samtools-1.15.1/test/mpileup/expected/49.out samtools-1.15.1/test/mpileup/expected/5.out samtools-1.15.1/test/mpileup/expected/50.out samtools-1.15.1/test/mpileup/expected/51.out samtools-1.15.1/test/mpileup/expected/52.out samtools-1.15.1/test/mpileup/expected/53.out samtools-1.15.1/test/mpileup/expected/54.out samtools-1.15.1/test/mpileup/expected/55.out samtools-1.15.1/test/mpileup/expected/56.out samtools-1.15.1/test/mpileup/expected/57.out samtools-1.15.1/test/mpileup/expected/58.out samtools-1.15.1/test/mpileup/expected/59.out samtools-1.15.1/test/mpileup/expected/6.out samtools-1.15.1/test/mpileup/expected/60.out samtools-1.15.1/test/mpileup/expected/61.out samtools-1.15.1/test/mpileup/expected/62.out samtools-1.15.1/test/mpileup/expected/63.out samtools-1.15.1/test/mpileup/expected/64.out samtools-1.15.1/test/mpileup/expected/65.out samtools-1.15.1/test/mpileup/expected/66.out samtools-1.15.1/test/mpileup/expected/67.out samtools-1.15.1/test/mpileup/expected/68.out samtools-1.15.1/test/mpileup/expected/69.out samtools-1.15.1/test/mpileup/expected/7.out samtools-1.15.1/test/mpileup/expected/70.out samtools-1.15.1/test/mpileup/expected/71.out samtools-1.15.1/test/mpileup/expected/72.out samtools-1.15.1/test/mpileup/expected/73.out samtools-1.15.1/test/mpileup/expected/74.out samtools-1.15.1/test/mpileup/expected/75.out samtools-1.15.1/test/mpileup/expected/76.out samtools-1.15.1/test/mpileup/expected/77.out samtools-1.15.1/test/mpileup/expected/78.out samtools-1.15.1/test/mpileup/expected/79.out samtools-1.15.1/test/mpileup/expected/8.out samtools-1.15.1/test/mpileup/expected/80.out samtools-1.15.1/test/mpileup/expected/81.out samtools-1.15.1/test/mpileup/expected/9.out samtools-1.15.1/test/mpileup/expected/a0.out samtools-1.15.1/test/mpileup/expected/a1.out samtools-1.15.1/test/mpileup/expected/a10.out samtools-1.15.1/test/mpileup/expected/a11.out samtools-1.15.1/test/mpileup/expected/a13.out samtools-1.15.1/test/mpileup/expected/a14.out samtools-1.15.1/test/mpileup/expected/a15.out samtools-1.15.1/test/mpileup/expected/a16.out samtools-1.15.1/test/mpileup/expected/a17.out samtools-1.15.1/test/mpileup/expected/a2.out samtools-1.15.1/test/mpileup/expected/a3.out samtools-1.15.1/test/mpileup/expected/a4.out samtools-1.15.1/test/mpileup/expected/a5.out samtools-1.15.1/test/mpileup/expected/a6.out samtools-1.15.1/test/mpileup/expected/a8.out samtools-1.15.1/test/mpileup/expected/a9.out samtools-1.15.1/test/mpileup/expected/d1_1.out samtools-1.15.1/test/mpileup/expected/d1_12.out samtools-1.15.1/test/mpileup/expected/d1_2.out samtools-1.15.1/test/mpileup/expected/d2_12r.out samtools-1.15.1/test/mpileup/expected/d3_12.out samtools-1.15.1/test/mpileup/expected/d3_12r1a.out samtools-1.15.1/test/mpileup/expected/d3_12r2a.out samtools-1.15.1/test/mpileup/expected/d3_3.out samtools-1.15.1/test/mpileup/expected/d4_12.out samtools-1.15.1/test/mpileup/expected/d4_12b.out samtools-1.15.1/test/mpileup/expected/d4_12r.out samtools-1.15.1/test/mpileup/expected/d5_all1.out samtools-1.15.1/test/mpileup/expected/d5_all2.out samtools-1.15.1/test/mpileup/expected/d5_all3.out samtools-1.15.1/test/mpileup/expected/d5_all4.out samtools-1.15.1/test/mpileup/expected/d5_b3.out samtools-1.15.1/test/mpileup/expected/d5_b3a.out samtools-1.15.1/test/mpileup/expected/d5_b3aa.out samtools-1.15.1/test/mpileup/expected/d5_blank.out samtools-1.15.1/test/mpileup/expected/d5_xx1.out samtools-1.15.1/test/mpileup/expected/d5_xx2.out samtools-1.15.1/test/mpileup/expected/d5_xx3.out samtools-1.15.1/test/mpileup/expected/d5_xy1.out samtools-1.15.1/test/mpileup/expected/d6_nodel.out samtools-1.15.1/test/mpileup/expected/d6_wdel.out samtools-1.15.1/test/mpileup/expected/d7_nodup.out samtools-1.15.1/test/mpileup/expected/m5_all1.out samtools-1.15.1/test/mpileup/expected/m5_all2.out samtools-1.15.1/test/mpileup/expected/m5_all3.out samtools-1.15.1/test/mpileup/expected/m5_b3.out samtools-1.15.1/test/mpileup/expected/m5_b3a.out samtools-1.15.1/test/mpileup/expected/m5_b3aa.out samtools-1.15.1/test/mpileup/expected/m5_blank.out samtools-1.15.1/test/mpileup/expected/m5_xx1.out samtools-1.15.1/test/mpileup/expected/m5_xx2.out samtools-1.15.1/test/mpileup/expected/m5_xx3.out samtools-1.15.1/test/mpileup/expected/m5_xy1.out samtools-1.15.1/test/mpileup/expected/mp1_d.out samtools-1.15.1/test/mpileup/expected/mp1_dd.out samtools-1.15.1/test/mpileup/expected/mp1_ends.out samtools-1.15.1/test/mpileup/expected/mp1_i.out samtools-1.15.1/test/mpileup/expected/mp1_ii.out samtools-1.15.1/test/mpileup/expected/mp1_iidd.out samtools-1.15.1/test/mpileup/expected/mp2-noins.out samtools-1.15.1/test/mpileup/expected/mp2.out samtools-1.15.1/test/mpileup/expected/mp_D.out samtools-1.15.1/test/mpileup/expected/mp_DI.out samtools-1.15.1/test/mpileup/expected/mp_I.out samtools-1.15.1/test/mpileup/expected/mp_ID.out samtools-1.15.1/test/mpileup/expected/mp_ID_rev.out samtools-1.15.1/test/mpileup/expected/mp_N.out samtools-1.15.1/test/mpileup/expected/mp_N2.out samtools-1.15.1/test/mpileup/expected/mp_P.out samtools-1.15.1/test/mpileup/indels.sam samtools-1.15.1/test/mpileup/md5/ samtools-1.15.1/test/mpileup/md5/02099b2aad2cfe707759353724fb40ae samtools-1.15.1/test/mpileup/md5/0d4dfc45807d6a11439e858605cb364d samtools-1.15.1/test/mpileup/md5/351f64d4f4f9ddd45b35336ad97aa6de samtools-1.15.1/test/mpileup/md5/6ec590eb82c361a61e6baabce20109bc samtools-1.15.1/test/mpileup/md5/6f60cdf4c739651ae72d53e2e94825c1 samtools-1.15.1/test/mpileup/md5/73d180d5cb3860a2713927b6812eab0e samtools-1.15.1/test/mpileup/mod1.sam samtools-1.15.1/test/mpileup/mp.fa samtools-1.15.1/test/mpileup/mp.fa.fai samtools-1.15.1/test/mpileup/mp_D.sam samtools-1.15.1/test/mpileup/mp_DI.sam samtools-1.15.1/test/mpileup/mp_I.sam samtools-1.15.1/test/mpileup/mp_ID.sam samtools-1.15.1/test/mpileup/mp_ID_rev.sam samtools-1.15.1/test/mpileup/mp_N.sam samtools-1.15.1/test/mpileup/mp_N2.sam samtools-1.15.1/test/mpileup/mp_P.sam samtools-1.15.1/test/mpileup/mpileup-E.bam samtools-1.15.1/test/mpileup/mpileup.1.bam samtools-1.15.1/test/mpileup/mpileup.1.bam.bai samtools-1.15.1/test/mpileup/mpileup.2.bam samtools-1.15.1/test/mpileup/mpileup.3.bam samtools-1.15.1/test/mpileup/mpileup.ref.fa samtools-1.15.1/test/mpileup/mpileup.ref.fa.fai samtools-1.15.1/test/mpileup/mpileup.reg samtools-1.15.1/test/mpileup/output-BP.sam samtools-1.15.1/test/mpileup/overlap.bam samtools-1.15.1/test/mpileup/overlap50.sam samtools-1.15.1/test/mpileup/overlapIllumina.bam samtools-1.15.1/test/mpileup/regions samtools-1.15.1/test/mpileup/xx#depth1.sam samtools-1.15.1/test/mpileup/xx#depth2.sam samtools-1.15.1/test/mpileup/xx#depth3.sam samtools-1.15.1/test/mpileup/xx#depth4.sam samtools-1.15.1/test/mpileup/xx#minimal.bam samtools-1.15.1/test/mpileup/xx#triplet.bam samtools-1.15.1/test/mpileup/xx.bed samtools-1.15.1/test/mpileup/xx.bed2 samtools-1.15.1/test/mpileup/xx.bed3 samtools-1.15.1/test/mpileup/xx.fa samtools-1.15.1/test/mpileup/xx.fa.fai samtools-1.15.1/test/quickcheck/ samtools-1.15.1/test/quickcheck/1.quickcheck.badeof.bam samtools-1.15.1/test/quickcheck/10.quickcheck.notargets.bam samtools-1.15.1/test/quickcheck/2.quickcheck.badheader.bam samtools-1.15.1/test/quickcheck/3.quickcheck.ok.bam samtools-1.15.1/test/quickcheck/4.quickcheck.ok.bam samtools-1.15.1/test/quickcheck/5.quickcheck.scramble30.truncated.cram samtools-1.15.1/test/quickcheck/6.quickcheck.cram21.ok.cram samtools-1.15.1/test/quickcheck/7.quickcheck.cram30.ok.cram samtools-1.15.1/test/quickcheck/8.quickcheck.cram21.truncated.cram samtools-1.15.1/test/quickcheck/9.quickcheck.cram30.truncated.cram samtools-1.15.1/test/quickcheck/all.expected samtools-1.15.1/test/regression.sh samtools-1.15.1/test/reheader/ samtools-1.15.1/test/reheader/1_view1.sam.expected samtools-1.15.1/test/reheader/1_view1.sam.expected.err samtools-1.15.1/test/reheader/2_view1.sam.expected samtools-1.15.1/test/reheader/2_view1.sam.expected.err samtools-1.15.1/test/reheader/3_view1.sam.expected samtools-1.15.1/test/reheader/3_view1.sam.expected.err samtools-1.15.1/test/reheader/4_view1.sam.expected samtools-1.15.1/test/reheader/5_view1.sam.expected samtools-1.15.1/test/reheader/hdr.sam samtools-1.15.1/test/sort/ samtools-1.15.1/test/sort/name.sort.expected.sam samtools-1.15.1/test/sort/pos.sort.expected.sam samtools-1.15.1/test/sort/tag.as.sort.expected.sam samtools-1.15.1/test/sort/tag.fi.sort.expected.sam samtools-1.15.1/test/sort/tag.rg.n.sort.expected.sam samtools-1.15.1/test/sort/tag.rg.sort.expected.sam samtools-1.15.1/test/split/ samtools-1.15.1/test/split/split.expected.grp1.sam samtools-1.15.1/test/split/split.expected.grp2.sam samtools-1.15.1/test/split/split.expected.unk.sam samtools-1.15.1/test/split/split.sam samtools-1.15.1/test/split/test_count_rg.c samtools-1.15.1/test/split/test_expand_format_string.c samtools-1.15.1/test/split/test_filter_header_rg.c samtools-1.15.1/test/split/test_parse_args.c samtools-1.15.1/test/stat/ samtools-1.15.1/test/stat/1.stats.expected samtools-1.15.1/test/stat/1.stats.large.expected samtools-1.15.1/test/stat/10.stats.expected samtools-1.15.1/test/stat/10_map_cigar.sam samtools-1.15.1/test/stat/10_map_cigar.sam_s1_a_1.expected.bamstat samtools-1.15.1/test/stat/10_map_cigar.sam_s1_b_1.expected.bamstat samtools-1.15.1/test/stat/11.stats.expected samtools-1.15.1/test/stat/11.stats.g4.expected samtools-1.15.1/test/stat/11.stats.targets samtools-1.15.1/test/stat/11_target.bam samtools-1.15.1/test/stat/11_target.bam.bai samtools-1.15.1/test/stat/11_target.sam samtools-1.15.1/test/stat/12.2reads.nooverlap.expected samtools-1.15.1/test/stat/12.2reads.overlap.expected samtools-1.15.1/test/stat/12.3reads.nooverlap.expected samtools-1.15.1/test/stat/12.3reads.overlap.expected samtools-1.15.1/test/stat/12_2reads.bed samtools-1.15.1/test/stat/12_3reads.bed samtools-1.15.1/test/stat/12_overlaps.bam samtools-1.15.1/test/stat/13.barcodes.bc.ok.expected samtools-1.15.1/test/stat/13.barcodes.ox.ok.expected samtools-1.15.1/test/stat/13_barcodes_fail_bc_length.sam samtools-1.15.1/test/stat/13_barcodes_fail_hyphen.sam samtools-1.15.1/test/stat/13_barcodes_fail_qt_length.sam samtools-1.15.1/test/stat/13_barcodes_ok.sam samtools-1.15.1/test/stat/13_barcodes_ok_ox_bz.sam samtools-1.15.1/test/stat/14.rg.Sample.expected samtools-1.15.1/test/stat/14.rg.grp2.expected samtools-1.15.1/test/stat/14.rg.grp3.expected samtools-1.15.1/test/stat/14.rg.s1.expected samtools-1.15.1/test/stat/1_map_cigar.sam samtools-1.15.1/test/stat/1_map_cigar.sam_s1_a_1.expected.bamstat samtools-1.15.1/test/stat/1_map_cigar_large.sam samtools-1.15.1/test/stat/2.stats.expected samtools-1.15.1/test/stat/2.stats.large.expected samtools-1.15.1/test/stat/2_equal_cigar_full_seq.sam samtools-1.15.1/test/stat/2_equal_cigar_full_seq_large.sam samtools-1.15.1/test/stat/3.stats.expected samtools-1.15.1/test/stat/3.stats.large.expected samtools-1.15.1/test/stat/3_map_cigar_equal_seq.sam samtools-1.15.1/test/stat/3_map_cigar_equal_seq_large.sam samtools-1.15.1/test/stat/4.stats.expected samtools-1.15.1/test/stat/4.stats.large.expected samtools-1.15.1/test/stat/4_X_cigar_full_seq.sam samtools-1.15.1/test/stat/4_X_cigar_full_seq_large.sam samtools-1.15.1/test/stat/5.stats.expected samtools-1.15.1/test/stat/5.stats.large.expected samtools-1.15.1/test/stat/5_insert_cigar.sam samtools-1.15.1/test/stat/5_insert_cigar_large.sam samtools-1.15.1/test/stat/6.stats.expected samtools-1.15.1/test/stat/7.stats.expected samtools-1.15.1/test/stat/7.stats.large.expected samtools-1.15.1/test/stat/7_supp.sam samtools-1.15.1/test/stat/7_supp_large.sam samtools-1.15.1/test/stat/8.stats.expected samtools-1.15.1/test/stat/8.stats.large.expected samtools-1.15.1/test/stat/8_secondary.sam samtools-1.15.1/test/stat/8_secondary_large.sam samtools-1.15.1/test/stat/9.stats.expected samtools-1.15.1/test/stat/test.fa samtools-1.15.1/test/stat/test.fa.fai samtools-1.15.1/test/test.c samtools-1.15.1/test/test.h samtools-1.15.1/test/test.pl samtools-1.15.1/test/tview/ samtools-1.15.1/test/tview/test_get_rg_sample.c samtools-1.15.1/test/vcf-miniview.c samtools-1.15.1/tmp_file.c samtools-1.15.1/tmp_file.h samtools-1.15.1/version.sh samtools-1.15.1/config.h.in samtools-1.15.1/configure samtools-1.15.1/htslib-1.15.1/ samtools-1.15.1/htslib-1.15.1/INSTALL samtools-1.15.1/htslib-1.15.1/LICENSE samtools-1.15.1/htslib-1.15.1/Makefile samtools-1.15.1/htslib-1.15.1/NEWS samtools-1.15.1/htslib-1.15.1/README samtools-1.15.1/htslib-1.15.1/README.large_positions.md samtools-1.15.1/htslib-1.15.1/bcf_sr_sort.c samtools-1.15.1/htslib-1.15.1/bcf_sr_sort.h samtools-1.15.1/htslib-1.15.1/bgzf.c samtools-1.15.1/htslib-1.15.1/bgzip.1 samtools-1.15.1/htslib-1.15.1/bgzip.c samtools-1.15.1/htslib-1.15.1/builddir_vars.mk.in samtools-1.15.1/htslib-1.15.1/config.mk.in samtools-1.15.1/htslib-1.15.1/configure.ac samtools-1.15.1/htslib-1.15.1/cram/ samtools-1.15.1/htslib-1.15.1/cram/cram.h samtools-1.15.1/htslib-1.15.1/cram/cram_codecs.c samtools-1.15.1/htslib-1.15.1/cram/cram_codecs.h samtools-1.15.1/htslib-1.15.1/cram/cram_decode.c samtools-1.15.1/htslib-1.15.1/cram/cram_decode.h samtools-1.15.1/htslib-1.15.1/cram/cram_encode.c samtools-1.15.1/htslib-1.15.1/cram/cram_encode.h samtools-1.15.1/htslib-1.15.1/cram/cram_external.c samtools-1.15.1/htslib-1.15.1/cram/cram_index.c samtools-1.15.1/htslib-1.15.1/cram/cram_index.h samtools-1.15.1/htslib-1.15.1/cram/cram_io.c samtools-1.15.1/htslib-1.15.1/cram/cram_io.h samtools-1.15.1/htslib-1.15.1/cram/cram_samtools.h samtools-1.15.1/htslib-1.15.1/cram/cram_stats.c samtools-1.15.1/htslib-1.15.1/cram/cram_stats.h samtools-1.15.1/htslib-1.15.1/cram/cram_structs.h samtools-1.15.1/htslib-1.15.1/cram/mFILE.c samtools-1.15.1/htslib-1.15.1/cram/mFILE.h samtools-1.15.1/htslib-1.15.1/cram/misc.h samtools-1.15.1/htslib-1.15.1/cram/open_trace_file.c samtools-1.15.1/htslib-1.15.1/cram/open_trace_file.h samtools-1.15.1/htslib-1.15.1/cram/os.h samtools-1.15.1/htslib-1.15.1/cram/pooled_alloc.c samtools-1.15.1/htslib-1.15.1/cram/pooled_alloc.h samtools-1.15.1/htslib-1.15.1/cram/string_alloc.c samtools-1.15.1/htslib-1.15.1/cram/string_alloc.h samtools-1.15.1/htslib-1.15.1/errmod.c samtools-1.15.1/htslib-1.15.1/faidx.5 samtools-1.15.1/htslib-1.15.1/faidx.c samtools-1.15.1/htslib-1.15.1/header.c samtools-1.15.1/htslib-1.15.1/header.h samtools-1.15.1/htslib-1.15.1/hfile.c samtools-1.15.1/htslib-1.15.1/hfile_gcs.c samtools-1.15.1/htslib-1.15.1/hfile_internal.h samtools-1.15.1/htslib-1.15.1/hfile_libcurl.c samtools-1.15.1/htslib-1.15.1/hfile_s3.c samtools-1.15.1/htslib-1.15.1/hfile_s3_write.c samtools-1.15.1/htslib-1.15.1/hts.c samtools-1.15.1/htslib-1.15.1/hts_expr.c samtools-1.15.1/htslib-1.15.1/hts_internal.h samtools-1.15.1/htslib-1.15.1/hts_os.c samtools-1.15.1/htslib-1.15.1/htscodecs/ samtools-1.15.1/htslib-1.15.1/htscodecs/LICENSE.md samtools-1.15.1/htslib-1.15.1/htscodecs/MAINTAINERS.md samtools-1.15.1/htslib-1.15.1/htscodecs/NEWS samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/ samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/arith_dynamic.c samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/arith_dynamic.h samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/c_range_coder.h samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/c_simple_model.h samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/fqzcomp_qual.c samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/fqzcomp_qual.h samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/htscodecs.c samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/htscodecs.h samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/htscodecs_endian.h samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/pack.c samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/pack.h samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/pooled_alloc.h samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/rANS_byte.h samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/rANS_static.c samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/rANS_static.h samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/rANS_static4x16.h samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/rANS_static4x16pr.c samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/rANS_word.h samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/rle.c samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/rle.h samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/tokenise_name3.c samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/tokenise_name3.h samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/utils.h samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/varint.h samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/varint2.h samtools-1.15.1/htslib-1.15.1/htscodecs/htscodecs/version.h samtools-1.15.1/htslib-1.15.1/htscodecs/tests/ samtools-1.15.1/htslib-1.15.1/htscodecs/tests/arith.test samtools-1.15.1/htslib-1.15.1/htscodecs/tests/arith_dynamic_fuzz.c samtools-1.15.1/htslib-1.15.1/htscodecs/tests/arith_dynamic_test.c samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/ samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/ samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/q4.0 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/q4.1 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/q4.128 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/q4.129 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/q4.192 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/q4.193 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/q4.64 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/q4.65 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/q4.8 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/q4.9 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/q40+dir.0 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/q40+dir.1 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/q40+dir.64 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/q40+dir.65 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/q40+dir.8 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/q40+dir.9 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/q8.0 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/q8.1 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/q8.128 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/q8.129 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/q8.192 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/q8.193 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/q8.64 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/q8.65 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/qvar.0 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/qvar.1 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/qvar.64 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/arith/qvar.65 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/fqzcomp/ samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/fqzcomp/q4.0 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/fqzcomp/q4.1 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/fqzcomp/q4.2 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/fqzcomp/q4.3 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/fqzcomp/q40+dir.0 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/fqzcomp/q40+dir.1 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/fqzcomp/q40+dir.2 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/fqzcomp/q40+dir.3 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/fqzcomp/q8.0 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/fqzcomp/q8.1 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/fqzcomp/q8.2 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/fqzcomp/q8.3 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/fqzcomp/qvar.0 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/fqzcomp/qvar.1 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/fqzcomp/qvar.2 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/fqzcomp/qvar.3 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/q4 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/q40+dir samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/q8 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/qvar samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x16/ samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x16/q4.0 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x16/q4.1 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x16/q4.128 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x16/q4.129 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x16/q4.192 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x16/q4.193 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x16/q4.64 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x16/q4.65 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x16/q4.8 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x16/q4.9 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x16/q40+dir.0 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x16/q40+dir.1 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x16/q40+dir.8 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x16/q40+dir.9 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x16/q8.0 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x16/q8.1 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x16/q8.128 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x16/q8.129 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x16/q8.192 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x16/q8.193 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x16/q8.64 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x16/q8.65 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x16/qvar.0 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x16/qvar.1 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x8/ samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x8/q4.0 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x8/q4.1 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x8/q40+dir.0 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x8/q40+dir.1 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x8/q8.0 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x8/q8.1 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x8/qvar.0 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/dat/r4x8/qvar.1 samtools-1.15.1/htslib-1.15.1/htscodecs/tests/fqzcomp.test samtools-1.15.1/htslib-1.15.1/htscodecs/tests/fqzcomp_qual_fuzz.c samtools-1.15.1/htslib-1.15.1/htscodecs/tests/fqzcomp_qual_test.c 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samtools-1.15.1/htslib-1.15.1/test/thread_pool.md samtools-1.15.1/htslib-1.15.1/test/vcf_meta_meta.vcf samtools-1.15.1/htslib-1.15.1/test/with-shlib.sh samtools-1.15.1/htslib-1.15.1/test/xx#MD.sam samtools-1.15.1/htslib-1.15.1/test/xx#MD2.sam samtools-1.15.1/htslib-1.15.1/test/xx#blank.sam samtools-1.15.1/htslib-1.15.1/test/xx#large_aux.sam samtools-1.15.1/htslib-1.15.1/test/xx#large_aux2.sam samtools-1.15.1/htslib-1.15.1/test/xx#large_aux_java.cram samtools-1.15.1/htslib-1.15.1/test/xx#minimal.sam samtools-1.15.1/htslib-1.15.1/test/xx#pair.sam samtools-1.15.1/htslib-1.15.1/test/xx#repeated.sam samtools-1.15.1/htslib-1.15.1/test/xx#rg.sam samtools-1.15.1/htslib-1.15.1/test/xx#tlen.sam samtools-1.15.1/htslib-1.15.1/test/xx#tlen2.sam samtools-1.15.1/htslib-1.15.1/test/xx#triplet.sam samtools-1.15.1/htslib-1.15.1/test/xx#unsorted.sam samtools-1.15.1/htslib-1.15.1/test/xx.fa samtools-1.15.1/htslib-1.15.1/test/xx.fa.fai samtools-1.15.1/htslib-1.15.1/textutils.c samtools-1.15.1/htslib-1.15.1/textutils_internal.h samtools-1.15.1/htslib-1.15.1/thread_pool.c samtools-1.15.1/htslib-1.15.1/thread_pool_internal.h samtools-1.15.1/htslib-1.15.1/vcf.5 samtools-1.15.1/htslib-1.15.1/vcf.c samtools-1.15.1/htslib-1.15.1/vcf_sweep.c samtools-1.15.1/htslib-1.15.1/vcfutils.c samtools-1.15.1/htslib-1.15.1/version.sh samtools-1.15.1/htslib-1.15.1/config.h.in samtools-1.15.1/htslib-1.15.1/configure checking for gawk... gawk checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking for NcursesW wide-character library... yes checking for working ncursesw/curses.h... yes checking for library containing cbreak... none required checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam.o bam.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_aux.o bam_aux.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_index.o bam_index.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_plcmd.o bam_plcmd.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o sam_view.o sam_view.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_fastq.o bam_fastq.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_cat.o bam_cat.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_md.o bam_md.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_plbuf.o bam_plbuf.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_reheader.o bam_reheader.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_sort.o bam_sort.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_rmdup.o bam_rmdup.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_rmdupse.o bam_rmdupse.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_mate.o bam_mate.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_stat.o bam_stat.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_color.o bam_color.c echo '#define SAMTOOLS_VERSION "1.15.1"' > version.h echo '#define SAMTOOLS_CC "gcc"' >> version.h echo '#define SAMTOOLS_CPPFLAGS ""' >> version.h echo '#define SAMTOOLS_CFLAGS "-Wall -O2 -march=i586 -mtune=i686"' >> version.h echo '#define SAMTOOLS_LDFLAGS ""' >> version.h echo '#define SAMTOOLS_HTSDIR ""' >> version.h echo '#define SAMTOOLS_LIBS ""' >> version.h echo '#define SAMTOOLS_CURSES_LIB "-lncursesw"' >> version.h gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bamtk.o bamtk.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam2bcf.o bam2bcf.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o sample.o sample.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o cut_target.o cut_target.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o phase.o phase.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam2depth.o bam2depth.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o coverage.o coverage.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o padding.o padding.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bedcov.o bedcov.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bamshuf.o bamshuf.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o faidx.o faidx.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o dict.o dict.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o stats.o stats.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o stats_isize.o stats_isize.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_flags.o bam_flags.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_split.o bam_split.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_tview.o bam_tview.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_tview_curses.o bam_tview_curses.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_tview_html.o bam_tview_html.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_lpileup.o bam_lpileup.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_quickcheck.o bam_quickcheck.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_addrprg.o bam_addrprg.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_markdup.o bam_markdup.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o tmp_file.o tmp_file.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_ampliconclip.o bam_ampliconclip.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o amplicon_stats.o amplicon_stats.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_import.o bam_import.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_samples.o bam_samples.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bam_consensus.o bam_consensus.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o consensus_pileup.o consensus_pileup.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o lz4/lz4.o lz4/lz4.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o sam_opts.o sam_opts.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o sam_utils.o sam_utils.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o bedidx.o bedidx.c ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o gcc -L./lz4 -o samtools bam.o bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o ./lz4/lz4.o libst.a -lhts -lncursesw -lm -lz -lpthread gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o misc/ace2sam.o misc/ace2sam.c gcc -L./lz4 -o misc/ace2sam misc/ace2sam.o -lhts -lz gcc -Wall -O2 -march=i586 -mtune=i686 -DMAQ_LONGREADS -I. -I./lz4 -c -o misc/maq2sam-long.o misc/maq2sam.c gcc -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o misc/maq2sam-short.o misc/maq2sam.c gcc -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o misc/md5fa.o misc/md5fa.c gcc -L./lz4 -o misc/md5fa misc/md5fa.o -lhts -lz gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o misc/md5sum-lite.o misc/md5sum-lite.c gcc -L./lz4 -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o misc/wgsim.o misc/wgsim.c gcc -L./lz4 -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o test/test.o test/test.c gcc -L./lz4 -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c gcc -L./lz4 -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c gcc -L./lz4 -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o test/split/test_count_rg.o test/split/test_count_rg.c gcc -L./lz4 -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c gcc -L./lz4 -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c gcc -L./lz4 -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o test/split/test_parse_args.o test/split/test_parse_args.c gcc -L./lz4 -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread gcc -Wall -O2 -march=i586 -mtune=i686 -I. -I./lz4 -c -o test/vcf-miniview.o test/vcf-miniview.c gcc -L./lz4 -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread mkdir -p -m 755 /usr/src/slapt-src/academic/samtools/package-samtools/usr/bin /usr/src/slapt-src/academic/samtools/package-samtools/usr/bin /usr/src/slapt-src/academic/samtools/package-samtools/usr/man/man1 install -p samtools /usr/src/slapt-src/academic/samtools/package-samtools/usr/bin install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /usr/src/slapt-src/academic/samtools/package-samtools/usr/bin install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/fasta-sanitize.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-ampliconstats misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/wgsim_eval.pl misc/zoom2sam.pl /usr/src/slapt-src/academic/samtools/package-samtools/usr/bin install -p -m 644 doc/samtools*.1 misc/wgsim.1 /usr/src/slapt-src/academic/samtools/package-samtools/usr/man/man1 Slackware package maker, version 3.14159265. Searching for symbolic links: No symbolic links were found, so we won't make an installation script. You can make your own later in ./install/doinst.sh and rebuild the package if you like. This next step is optional - you can set the directories in your package to some sane permissions. If any of the directories in your package have special permissions, then DO NOT reset them here! Would you like to reset all directory permissions to 755 (drwxr-xr-x) and directory ownerships to root.root ([y]es, [n]o)? n Creating Slackware package: /usr/src/slapt-src/academic/samtools/samtools-1.15.1-i586-1salix15.0.txz ./ install/ install/slack-desc usr/ usr/bin/ usr/bin/ace2sam usr/bin/blast2sam.pl usr/bin/bowtie2sam.pl usr/bin/export2sam.pl usr/bin/fasta-sanitize.pl usr/bin/interpolate_sam.pl usr/bin/maq2sam-long usr/bin/maq2sam-short usr/bin/md5fa usr/bin/md5sum-lite usr/bin/novo2sam.pl usr/bin/plot-ampliconstats usr/bin/plot-bamstats usr/bin/psl2sam.pl usr/bin/sam2vcf.pl usr/bin/samtools usr/bin/samtools.pl usr/bin/seq_cache_populate.pl usr/bin/soap2sam.pl usr/bin/wgsim usr/bin/wgsim_eval.pl usr/bin/zoom2sam.pl usr/doc/ usr/doc/samtools-1.15.1/ usr/doc/samtools-1.15.1/AUTHORS usr/doc/samtools-1.15.1/INSTALL usr/doc/samtools-1.15.1/LICENSE usr/doc/samtools-1.15.1/NEWS usr/doc/samtools-1.15.1/README usr/doc/samtools-1.15.1/examples/ usr/doc/samtools-1.15.1/examples/00README.txt usr/doc/samtools-1.15.1/examples/ex1.fa usr/doc/samtools-1.15.1/examples/ex1.sam.gz usr/doc/samtools-1.15.1/examples/toy.fa usr/doc/samtools-1.15.1/examples/toy.sam usr/doc/samtools-1.15.1/samtools.SlackBuild usr/man/ usr/man/man1/ usr/man/man1/samtools-addreplacerg.1.gz usr/man/man1/samtools-ampliconclip.1.gz usr/man/man1/samtools-ampliconstats.1.gz usr/man/man1/samtools-bedcov.1.gz usr/man/man1/samtools-calmd.1.gz usr/man/man1/samtools-cat.1.gz usr/man/man1/samtools-collate.1.gz usr/man/man1/samtools-consensus.1.gz usr/man/man1/samtools-coverage.1.gz usr/man/man1/samtools-depad.1.gz usr/man/man1/samtools-depth.1.gz usr/man/man1/samtools-dict.1.gz usr/man/man1/samtools-faidx.1.gz usr/man/man1/samtools-fasta.1.gz usr/man/man1/samtools-fastq.1.gz usr/man/man1/samtools-fixmate.1.gz usr/man/man1/samtools-flags.1.gz usr/man/man1/samtools-flagstat.1.gz usr/man/man1/samtools-fqidx.1.gz usr/man/man1/samtools-head.1.gz usr/man/man1/samtools-idxstats.1.gz usr/man/man1/samtools-import.1.gz usr/man/man1/samtools-index.1.gz usr/man/man1/samtools-markdup.1.gz usr/man/man1/samtools-merge.1.gz usr/man/man1/samtools-mpileup.1.gz usr/man/man1/samtools-phase.1.gz usr/man/man1/samtools-quickcheck.1.gz usr/man/man1/samtools-reheader.1.gz usr/man/man1/samtools-rmdup.1.gz usr/man/man1/samtools-samples.1.gz usr/man/man1/samtools-sort.1.gz usr/man/man1/samtools-split.1.gz usr/man/man1/samtools-stats.1.gz usr/man/man1/samtools-targetcut.1.gz usr/man/man1/samtools-tview.1.gz usr/man/man1/samtools-view.1.gz usr/man/man1/samtools.1.gz usr/man/man1/wgsim.1.gz usr/share/ usr/share/samtools-1.15.1/ usr/share/samtools-1.15.1/r2plot.lua usr/share/samtools-1.15.1/vcfutils.lua Slackware package /usr/src/slapt-src/academic/samtools/samtools-1.15.1-i586-1salix15.0.txz created. Installing package samtools-1.15.1-i586-1salix15.0... | samtools (Sequence Alignment/Map Tools) | | SAM (Sequence Alignment/Map) format is a generic format for storing | large nucleotide sequence alignments. The original samtools package | has been split into three separate but tightly coordinated projects: | htslib (C-library for handling high-throughput sequencing data), | samtools (for handling SAM, BAM, CRAM), and bcftools (for handling | VCF and BCF). | | Homepage: http://www.htslib.org | | |