packagesFile list of package samtools-test in questing of architecture all
/usr/share/doc/samtools-test/changelog.Debian.gz /usr/share/doc/samtools-test/copyright /usr/share/doc/samtools/run-unit-test /usr/share/samtools/test/addrprg/1_fixup.sam /usr/share/samtools/test/addrprg/1_fixup.sam.expected /usr/share/samtools/test/addrprg/1_fixup.sam.expected.err /usr/share/samtools/test/addrprg/2_fixup_orphan.sam /usr/share/samtools/test/addrprg/2_fixup_orphan.sam.expected /usr/share/samtools/test/addrprg/2_fixup_orphan.sam.expected.err /usr/share/samtools/test/addrprg/3_fixup.sam.expected /usr/share/samtools/test/addrprg/3_fixup.sam.expected.err /usr/share/samtools/test/addrprg/4_fixup_norg.sam /usr/share/samtools/test/addrprg/4_fixup_norg.sam.expected /usr/share/samtools/test/addrprg/4_fixup_norg.sam.expected.err /usr/share/samtools/test/addrprg/5_editrg.sam.expected /usr/share/samtools/test/ampliconclip/1_delete_tag.expected.sam /usr/share/samtools/test/ampliconclip/1_fail.expected.sam /usr/share/samtools/test/ampliconclip/1_filter.expected.sam /usr/share/samtools/test/ampliconclip/1_hard_clipped.expected.sam /usr/share/samtools/test/ampliconclip/1_original_tag.expected.sam /usr/share/samtools/test/ampliconclip/1_soft_clipped.expected.sam /usr/share/samtools/test/ampliconclip/1_soft_clipped_primer_counts.expected.tsv /usr/share/samtools/test/ampliconclip/1_soft_clipped_strand.expected.sam /usr/share/samtools/test/ampliconclip/1_soft_clipped_strand_primer_counts.expected.tsv /usr/share/samtools/test/ampliconclip/1_test_data.sam /usr/share/samtools/test/ampliconclip/2_both_clipped.expected.sam /usr/share/samtools/test/ampliconclip/2_both_test_data.sam /usr/share/samtools/test/ampliconclip/3_multi_ref_both_clip.expected.sam /usr/share/samtools/test/ampliconclip/3_multi_ref_clip.expected.sam /usr/share/samtools/test/ampliconclip/3_multi_ref_data.sam /usr/share/samtools/test/ampliconclip/3_multi_ref_data_primer_counts.expected.tsv /usr/share/samtools/test/ampliconclip/4_total_hc_data.expected.sam /usr/share/samtools/test/ampliconclip/4_total_hc_data.sam /usr/share/samtools/test/ampliconclip/ac_test.bed /usr/share/samtools/test/ampliconclip/ac_test2.bed /usr/share/samtools/test/ampliconclip/multi_ref.bed /usr/share/samtools/test/ampliconstats/mixed_clipped.sam /usr/share/samtools/test/ampliconstats/stats.expected.txt /usr/share/samtools/test/ampliconstats/stats_mixed.expected.txt /usr/share/samtools/test/ampliconstats/stats_partial.expected.txt /usr/share/samtools/test/bam2fq/1.1.fq.expected /usr/share/samtools/test/bam2fq/1.2.fq.expected /usr/share/samtools/test/bam2fq/10.1.fq.expected /usr/share/samtools/test/bam2fq/10.2.fq.expected /usr/share/samtools/test/bam2fq/10.s.fq.expected /usr/share/samtools/test/bam2fq/11.fa.expected /usr/share/samtools/test/bam2fq/11.fq.expected /usr/share/samtools/test/bam2fq/12.1.fq.expected /usr/share/samtools/test/bam2fq/12.2.fq.expected /usr/share/samtools/test/bam2fq/12.i.fq.expected /usr/share/samtools/test/bam2fq/12.s.fq.expected /usr/share/samtools/test/bam2fq/13.fq.expected /usr/share/samtools/test/bam2fq/14.0.fq.expected /usr/share/samtools/test/bam2fq/14.i1.fq.expected /usr/share/samtools/test/bam2fq/14.i2.fq.expected /usr/share/samtools/test/bam2fq/15.fq.expected /usr/share/samtools/test/bam2fq/16.fq.expected /usr/share/samtools/test/bam2fq/17.fq.expected /usr/share/samtools/test/bam2fq/18.fq.expected /usr/share/samtools/test/bam2fq/19.fq.expected /usr/share/samtools/test/bam2fq/2.1.fq.expected /usr/share/samtools/test/bam2fq/2.2.fq.expected /usr/share/samtools/test/bam2fq/2.s.fq.expected /usr/share/samtools/test/bam2fq/20.fq.expected /usr/share/samtools/test/bam2fq/3.1.fq.expected /usr/share/samtools/test/bam2fq/3.2.fq.expected /usr/share/samtools/test/bam2fq/3.s.fq.expected /usr/share/samtools/test/bam2fq/4.1.fq.expected /usr/share/samtools/test/bam2fq/4.2.fq.expected /usr/share/samtools/test/bam2fq/4.s.fq.expected /usr/share/samtools/test/bam2fq/5.1.fq.expected /usr/share/samtools/test/bam2fq/5.2.fq.expected /usr/share/samtools/test/bam2fq/5.s.fq.expected /usr/share/samtools/test/bam2fq/6.1.fq.expected /usr/share/samtools/test/bam2fq/6.2.fq.expected /usr/share/samtools/test/bam2fq/6.s.fq.expected /usr/share/samtools/test/bam2fq/7.1.fq.expected /usr/share/samtools/test/bam2fq/7.2.fq.expected /usr/share/samtools/test/bam2fq/7.s.fq.expected /usr/share/samtools/test/bam2fq/8.1.fq.expected /usr/share/samtools/test/bam2fq/8.2.fq.expected /usr/share/samtools/test/bam2fq/8.i.fq.expected /usr/share/samtools/test/bam2fq/8.s.fq.expected /usr/share/samtools/test/bam2fq/9.1.fq.expected /usr/share/samtools/test/bam2fq/9.2.fq.expected /usr/share/samtools/test/bam2fq/bc.fq.expected /usr/share/samtools/test/bam2fq/bc10.fq.expected /usr/share/samtools/test/bam2fq/bc_split.fq.expected /usr/share/samtools/test/bedcov/bedcov.bam /usr/share/samtools/test/bedcov/bedcov.bam.bai /usr/share/samtools/test/bedcov/bedcov.bed /usr/share/samtools/test/bedcov/bedcov.expected /usr/share/samtools/test/bedcov/bedcov_c.expected /usr/share/samtools/test/bedcov/bedcov_gG.bed /usr/share/samtools/test/bedcov/bedcov_gG.expected /usr/share/samtools/test/bedcov/bedcov_j.expected /usr/share/samtools/test/collate/1_fast_collate.sam.expected /usr/share/samtools/test/collate/2_fast_collate_with_tmp_used.sam.expected /usr/share/samtools/test/collate/collate.expected.sam /usr/share/samtools/test/collate/fast_collate.sam /usr/share/samtools/test/consensus/consen1.sam /usr/share/samtools/test/consensus/consen2.sam /usr/share/samtools/test/consensus/consen3.sam /usr/share/samtools/test/consensus/consensus.reg /usr/share/samtools/test/consensus/expected/1.out /usr/share/samtools/test/consensus/expected/10.1q.out /usr/share/samtools/test/consensus/expected/10q.out /usr/share/samtools/test/consensus/expected/11.3p.out /usr/share/samtools/test/consensus/expected/11.3q.out /usr/share/samtools/test/consensus/expected/11.6p.out /usr/share/samtools/test/consensus/expected/11.6q.out /usr/share/samtools/test/consensus/expected/12p.out /usr/share/samtools/test/consensus/expected/12q.out /usr/share/samtools/test/consensus/expected/13p.out /usr/share/samtools/test/consensus/expected/13q.out /usr/share/samtools/test/consensus/expected/14p.out /usr/share/samtools/test/consensus/expected/14q.out /usr/share/samtools/test/consensus/expected/15p.out /usr/share/samtools/test/consensus/expected/16p.out /usr/share/samtools/test/consensus/expected/16q.out /usr/share/samtools/test/consensus/expected/17q.out /usr/share/samtools/test/consensus/expected/18p.out /usr/share/samtools/test/consensus/expected/18q.out /usr/share/samtools/test/consensus/expected/19p.out /usr/share/samtools/test/consensus/expected/19q.out /usr/share/samtools/test/consensus/expected/1p.out /usr/share/samtools/test/consensus/expected/1q.out /usr/share/samtools/test/consensus/expected/2.out /usr/share/samtools/test/consensus/expected/20p.out /usr/share/samtools/test/consensus/expected/21p.out /usr/share/samtools/test/consensus/expected/22p.out /usr/share/samtools/test/consensus/expected/23p.out /usr/share/samtools/test/consensus/expected/24p.out /usr/share/samtools/test/consensus/expected/25p.out /usr/share/samtools/test/consensus/expected/26p.out /usr/share/samtools/test/consensus/expected/2p.out /usr/share/samtools/test/consensus/expected/2q.out /usr/share/samtools/test/consensus/expected/3.out /usr/share/samtools/test/consensus/expected/3q.out /usr/share/samtools/test/consensus/expected/4.out /usr/share/samtools/test/consensus/expected/4p.out /usr/share/samtools/test/consensus/expected/4q.out /usr/share/samtools/test/consensus/expected/5p.out /usr/share/samtools/test/consensus/expected/5q.out /usr/share/samtools/test/consensus/expected/6p.out /usr/share/samtools/test/consensus/expected/6q.out /usr/share/samtools/test/consensus/expected/7p.out /usr/share/samtools/test/consensus/expected/7q.out /usr/share/samtools/test/consensus/expected/8p.out /usr/share/samtools/test/consensus/expected/8q.out /usr/share/samtools/test/consensus/expected/9.1p.out /usr/share/samtools/test/consensus/expected/9.1q.out /usr/share/samtools/test/consensus/expected/9p.out /usr/share/samtools/test/consensus/expected/9q.out /usr/share/samtools/test/consensus/expected/empty.out /usr/share/samtools/test/cram_size/cram_size.reg /usr/share/samtools/test/cram_size/expected/encodings.out /usr/share/samtools/test/cram_size/expected/normal.out /usr/share/samtools/test/cram_size/expected/verbose.out /usr/share/samtools/test/cram_size/mpileup.1.cram /usr/share/samtools/test/dat/bam2fq.001.sam /usr/share/samtools/test/dat/bam2fq.002.sam /usr/share/samtools/test/dat/bam2fq.003.sam /usr/share/samtools/test/dat/bam2fq.004.sam /usr/share/samtools/test/dat/bam2fq.005.sam /usr/share/samtools/test/dat/bam2fq.010.sam /usr/share/samtools/test/dat/bam2fq.013.sam /usr/share/samtools/test/dat/bam2fq.014.sam /usr/share/samtools/test/dat/bam2fq.703.sam /usr/share/samtools/test/dat/bam2fq.MD-D /usr/share/samtools/test/dat/bam2fq.NM-D /usr/share/samtools/test/dat/cat.hdr /usr/share/samtools/test/dat/cram_md5/08c04d512d4797d9ba2a156c1daba468 /usr/share/samtools/test/dat/cram_md5/7c35feac7036c1cdef3bee0cc4b21437 /usr/share/samtools/test/dat/cram_md5/89b96de7acc5918c2858ef92710be7d4 /usr/share/samtools/test/dat/cram_md5/8a3d8deb9edd4ce3346b6061fcee6d0b /usr/share/samtools/test/dat/depad.001.fa /usr/share/samtools/test/dat/depad.001.fa.fai /usr/share/samtools/test/dat/depad.001p.sam /usr/share/samtools/test/dat/depad.001u.sam /usr/share/samtools/test/dat/dict.alias.fa /usr/share/samtools/test/dat/dict.alias.out /usr/share/samtools/test/dat/dict.alt /usr/share/samtools/test/dat/dict.alt.out /usr/share/samtools/test/dat/dict.fa /usr/share/samtools/test/dat/dict.out /usr/share/samtools/test/dat/empty.expected /usr/share/samtools/test/dat/large_chrom.out /usr/share/samtools/test/dat/large_chrom.sam /usr/share/samtools/test/dat/large_chrom_bai_index.err /usr/share/samtools/test/dat/mpileup.1.sam /usr/share/samtools/test/dat/mpileup.2.sam /usr/share/samtools/test/dat/mpileup.3.sam /usr/share/samtools/test/dat/mpileup.err.1 /usr/share/samtools/test/dat/mpileup.out.1 /usr/share/samtools/test/dat/mpileup.out.2 /usr/share/samtools/test/dat/mpileup.out.3 /usr/share/samtools/test/dat/mpileup.out.4 /usr/share/samtools/test/dat/mpileup.out.5 /usr/share/samtools/test/dat/mpileup.ref.fa /usr/share/samtools/test/dat/mpileup.ref.fa.fai /usr/share/samtools/test/dat/nested.bed /usr/share/samtools/test/dat/nested.expected.sam /usr/share/samtools/test/dat/sort_name_input_1.sam /usr/share/samtools/test/dat/test_input_1_a.bam /usr/share/samtools/test/dat/test_input_1_a.bam.bai.expected /usr/share/samtools/test/dat/test_input_1_a.cram /usr/share/samtools/test/dat/test_input_1_a.sam /usr/share/samtools/test/dat/test_input_1_a_regex.sam /usr/share/samtools/test/dat/test_input_1_ab.X.expected /usr/share/samtools/test/dat/test_input_1_b.X.expected /usr/share/samtools/test/dat/test_input_1_b.X2.expected /usr/share/samtools/test/dat/test_input_1_b.bam /usr/share/samtools/test/dat/test_input_1_b.sam /usr/share/samtools/test/dat/test_input_1_b_regex.sam /usr/share/samtools/test/dat/test_input_1_c.bam /usr/share/samtools/test/dat/test_input_1_c.sam /usr/share/samtools/test/dat/test_input_1_d.sam /usr/share/samtools/test/dat/view.001.01.bed /usr/share/samtools/test/dat/view.001.02.bed /usr/share/samtools/test/dat/view.001.03.bed /usr/share/samtools/test/dat/view.001.fa /usr/share/samtools/test/dat/view.001.fa.fai /usr/share/samtools/test/dat/view.001.sam /usr/share/samtools/test/dat/view.002.01.bed /usr/share/samtools/test/dat/view.002.02.bed /usr/share/samtools/test/dat/view.002.fa /usr/share/samtools/test/dat/view.002.fa.fai /usr/share/samtools/test/dat/view.002.sam /usr/share/samtools/test/dat/view.003.expected.sam /usr/share/samtools/test/dat/view.003.sam /usr/share/samtools/test/dat/view.004.expected.sam /usr/share/samtools/test/dat/view.005.expected.sam /usr/share/samtools/test/dat/view.005.sam /usr/share/samtools/test/dat/view.005.unmap.expected.sam /usr/share/samtools/test/dat/view.fetch-pairs.bam /usr/share/samtools/test/dat/view.fetch-pairs.expected.sam /usr/share/samtools/test/dat/view.fetch-pairs.filter0.expected.sam /usr/share/samtools/test/dat/view.fetch-pairs.filter1.expected.sam /usr/share/samtools/test/fixmate/1_coord_sort.sam /usr/share/samtools/test/fixmate/1_coord_sort.sam.expected /usr/share/samtools/test/fixmate/1_coord_sort.sam.expected.err /usr/share/samtools/test/fixmate/2_isize_overflow.sam /usr/share/samtools/test/fixmate/2_isize_overflow.sam.expected /usr/share/samtools/test/fixmate/3_reverse_read_pp_lt.sam /usr/share/samtools/test/fixmate/3_reverse_read_pp_lt.sam.expected /usr/share/samtools/test/fixmate/4_reverse_read_pp_equal.sam /usr/share/samtools/test/fixmate/4_reverse_read_pp_equal.sam.expected /usr/share/samtools/test/fixmate/5_ct.sam /usr/share/samtools/test/fixmate/5_ct.sam.expected /usr/share/samtools/test/fixmate/6_ct_replace.sam /usr/share/samtools/test/fixmate/6_ct_replace.sam.expected /usr/share/samtools/test/fixmate/7_two_read_mapped.sam /usr/share/samtools/test/fixmate/7_two_read_mapped.sam.expected /usr/share/samtools/test/fixmate/8_isize_overflow_64bit.sam /usr/share/samtools/test/fixmate/8_isize_overflow_64bit.sam.expected /usr/share/samtools/test/fixmate/mod_ML_only.sam /usr/share/samtools/test/fixmate/mod_ML_only.sam.expected /usr/share/samtools/test/fixmate/mod_ML_wrong_len.sam /usr/share/samtools/test/fixmate/mod_ML_wrong_len.sam.expected /usr/share/samtools/test/fixmate/mod_MN_only.sam /usr/share/samtools/test/fixmate/mod_MN_only.sam.expected /usr/share/samtools/test/fixmate/mod_bad_MN.sam /usr/share/samtools/test/fixmate/mod_bad_MN.sam.expected /usr/share/samtools/test/fixmate/mod_bounds.sam /usr/share/samtools/test/fixmate/mod_bounds.sam.expected /usr/share/samtools/test/fixmate/mod_draft.sam /usr/share/samtools/test/fixmate/mod_draft.sam.expected /usr/share/samtools/test/fixmate/mod_noseq.sam /usr/share/samtools/test/fixmate/mod_noseq.sam.expected /usr/share/samtools/test/fixmate/mod_not_updated.sam /usr/share/samtools/test/fixmate/mod_not_updated.sam.expected /usr/share/samtools/test/fixmate/mod_not_updated_noML.sam /usr/share/samtools/test/fixmate/mod_not_updated_noML.sam.expected /usr/share/samtools/test/fixmate/mod_not_updated_noMN.sam /usr/share/samtools/test/fixmate/mod_not_updated_noMN.sam.expected /usr/share/samtools/test/fixmate/mod_not_updated_noseq.sam /usr/share/samtools/test/fixmate/mod_ok+.sam /usr/share/samtools/test/fixmate/mod_ok+.sam.expected /usr/share/samtools/test/fixmate/mod_ok-.sam /usr/share/samtools/test/fixmate/mod_ok-.sam.expected /usr/share/samtools/test/fixmate/sanitize.sam /usr/share/samtools/test/fixmate/sanitize.sam.expected /usr/share/samtools/test/idxstats/test_input_1_a.bam.expected /usr/share/samtools/test/idxstats/test_input_1_a.bam.expected.err /usr/share/samtools/test/import/1.expected.sam /usr/share/samtools/test/import/2.expected.sam /usr/share/samtools/test/import/2.interleaved.fq /usr/share/samtools/test/import/3.interleaved.fq /usr/share/samtools/test/import/4.aux.fq /usr/share/samtools/test/import/4.expected-XZ,XA,AA.sam /usr/share/samtools/test/import/4.expected.sam /usr/share/samtools/test/import/5-BC.expected.sam /usr/share/samtools/test/import/5-OX.expected.sam /usr/share/samtools/test/import/5-i1.fq /usr/share/samtools/test/import/5-i2.fq /usr/share/samtools/test/import/5-r1.fq /usr/share/samtools/test/import/5-r2.fq /usr/share/samtools/test/large_pos/depth.expected.out /usr/share/samtools/test/large_pos/depth_bed.expected.out /usr/share/samtools/test/large_pos/longref.sam /usr/share/samtools/test/large_pos/longref2.sam /usr/share/samtools/test/large_pos/longref3.expected.sam /usr/share/samtools/test/large_pos/longref3.sam /usr/share/samtools/test/large_pos/longref_idx.expected.sam /usr/share/samtools/test/large_pos/longref_name.sam /usr/share/samtools/test/large_pos/merge.expected.sam /usr/share/samtools/test/large_pos/test.bed /usr/share/samtools/test/large_pos/tview.expected.out /usr/share/samtools/test/maintainer/check_copyright.pl /usr/share/samtools/test/maintainer/check_spaces.pl /usr/share/samtools/test/markdup/10_optical_chain.expected.sam /usr/share/samtools/test/markdup/10_optical_chain.sam /usr/share/samtools/test/markdup/11_optical_dup_regex.expected.sam /usr/share/samtools/test/markdup/11_optical_dup_regex.sam /usr/share/samtools/test/markdup/12_optical_chain_regex.expected.sam /usr/share/samtools/test/markdup/12_optical_chain_regex.sam /usr/share/samtools/test/markdup/13_optical_barcode_tag.expected.sam /usr/share/samtools/test/markdup/13_optical_barcode_tag.sam /usr/share/samtools/test/markdup/14_optical_barcode_name.expected.sam /usr/share/samtools/test/markdup/14_optical_barcode_name.sam /usr/share/samtools/test/markdup/15_optical_barcode_rgx_name.expected.sam /usr/share/samtools/test/markdup/15_optical_barcode_rgx_name.sam /usr/share/samtools/test/markdup/16_optical_barcode_rgx_name_test_2.expected.sam /usr/share/samtools/test/markdup/16_optical_barcode_rgx_name_test_2.sam /usr/share/samtools/test/markdup/17_read_group.expected.sam /usr/share/samtools/test/markdup/17_read_group.sam /usr/share/samtools/test/markdup/18_primary_duplicate_count.expected.sam /usr/share/samtools/test/markdup/18_primary_duplicate_count.sam /usr/share/samtools/test/markdup/1_name_sort.expected.sam /usr/share/samtools/test/markdup/1_name_sort.expected.sam.err /usr/share/samtools/test/markdup/1_name_sort.sam /usr/share/samtools/test/markdup/2_bad_order.expected.sam /usr/share/samtools/test/markdup/2_bad_order.expected.sam.err /usr/share/samtools/test/markdup/2_bad_order.sam /usr/share/samtools/test/markdup/3_missing_mc.expected.sam /usr/share/samtools/test/markdup/3_missing_mc.expected.sam.err /usr/share/samtools/test/markdup/3_missing_mc.sam /usr/share/samtools/test/markdup/4_missing_ms.expected.sam /usr/share/samtools/test/markdup/4_missing_ms.expected.sam.err /usr/share/samtools/test/markdup/4_missing_ms.sam /usr/share/samtools/test/markdup/5_markdup.expected.sam /usr/share/samtools/test/markdup/5_markdup.sam /usr/share/samtools/test/markdup/6_remove_dups.expected.sam /usr/share/samtools/test/markdup/6_remove_dups.sam /usr/share/samtools/test/markdup/7_mark_supp_dup.expected.sam /usr/share/samtools/test/markdup/7_mark_supp_dup.sam /usr/share/samtools/test/markdup/8_optical_dup.expected.sam /usr/share/samtools/test/markdup/8_optical_dup.sam /usr/share/samtools/test/markdup/9_optical_dup_qcfail.expected.sam /usr/share/samtools/test/markdup/9_optical_dup_qcfail.sam /usr/share/samtools/test/merge/2.merge.expected.sam /usr/share/samtools/test/merge/3.merge.expected.err /usr/share/samtools/test/merge/3.merge.expected.sam /usr/share/samtools/test/merge/4.merge.expected.sam /usr/share/samtools/test/merge/5.merge.expected.sam /usr/share/samtools/test/merge/6.merge.expected.sam /usr/share/samtools/test/merge/7.merge.expected.sam /usr/share/samtools/test/merge/merge.bed /usr/share/samtools/test/merge/merge.bed.1.sam /usr/share/samtools/test/merge/merge.bed.2.sam /usr/share/samtools/test/merge/merge.bed.expected.sam /usr/share/samtools/test/merge/rg_from_r_mode.expected.sam /usr/share/samtools/test/merge/tag.pg.merge.expected.sam /usr/share/samtools/test/merge/tag.pg.n.merge.expected.sam /usr/share/samtools/test/merge/test_3.fofn /usr/share/samtools/test/merge/test_bam_translate.c /usr/share/samtools/test/merge/test_header.sam /usr/share/samtools/test/merge/test_no_pg_rg_co.sam /usr/share/samtools/test/merge/test_rtrans_build.c /usr/share/samtools/test/merge/test_template_coordinate.1.sam /usr/share/samtools/test/merge/test_template_coordinate.2.sam /usr/share/samtools/test/merge/test_template_coordinate.expected.sam /usr/share/samtools/test/merge/test_trans_tbl_init.c /usr/share/samtools/test/mpileup/1read.bam /usr/share/samtools/test/mpileup/1read.sam /usr/share/samtools/test/mpileup/anomalous.sam /usr/share/samtools/test/mpileup/c1#clip.bam /usr/share/samtools/test/mpileup/c1#pad1.bam /usr/share/samtools/test/mpileup/c1#pad2.bam /usr/share/samtools/test/mpileup/c1#pad3.bam /usr/share/samtools/test/mpileup/c1.fa /usr/share/samtools/test/mpileup/ce#5b.bam /usr/share/samtools/test/mpileup/ce#5b.bam.bai /usr/share/samtools/test/mpileup/ce#5b.cram /usr/share/samtools/test/mpileup/ce#5b.cram.crai /usr/share/samtools/test/mpileup/ce#5b.sam /usr/share/samtools/test/mpileup/ce#large_seq.bam /usr/share/samtools/test/mpileup/ce#unmap.bam /usr/share/samtools/test/mpileup/ce#unmap1.bam /usr/share/samtools/test/mpileup/ce#unmap2.bam /usr/share/samtools/test/mpileup/ce.fa /usr/share/samtools/test/mpileup/cram-size.reg /usr/share/samtools/test/mpileup/deep.sam /usr/share/samtools/test/mpileup/depth.reg /usr/share/samtools/test/mpileup/depth_del.sam /usr/share/samtools/test/mpileup/expected/1.out.f3-6.gz /usr/share/samtools/test/mpileup/expected/10.out /usr/share/samtools/test/mpileup/expected/11.out /usr/share/samtools/test/mpileup/expected/12.out /usr/share/samtools/test/mpileup/expected/13.out /usr/share/samtools/test/mpileup/expected/14.out /usr/share/samtools/test/mpileup/expected/15.out /usr/share/samtools/test/mpileup/expected/16.out /usr/share/samtools/test/mpileup/expected/17.out /usr/share/samtools/test/mpileup/expected/18.out /usr/share/samtools/test/mpileup/expected/19.out /usr/share/samtools/test/mpileup/expected/2.out /usr/share/samtools/test/mpileup/expected/20.out /usr/share/samtools/test/mpileup/expected/21.out /usr/share/samtools/test/mpileup/expected/22.out /usr/share/samtools/test/mpileup/expected/23.out /usr/share/samtools/test/mpileup/expected/24.out /usr/share/samtools/test/mpileup/expected/25.out /usr/share/samtools/test/mpileup/expected/26.out /usr/share/samtools/test/mpileup/expected/27.out /usr/share/samtools/test/mpileup/expected/28.out /usr/share/samtools/test/mpileup/expected/29.out /usr/share/samtools/test/mpileup/expected/3.out /usr/share/samtools/test/mpileup/expected/30.out /usr/share/samtools/test/mpileup/expected/31.out /usr/share/samtools/test/mpileup/expected/32.out /usr/share/samtools/test/mpileup/expected/33.out /usr/share/samtools/test/mpileup/expected/34.out /usr/share/samtools/test/mpileup/expected/35.out /usr/share/samtools/test/mpileup/expected/37.out /usr/share/samtools/test/mpileup/expected/38.out /usr/share/samtools/test/mpileup/expected/39.out /usr/share/samtools/test/mpileup/expected/4.out /usr/share/samtools/test/mpileup/expected/40.out /usr/share/samtools/test/mpileup/expected/41.out /usr/share/samtools/test/mpileup/expected/42.out /usr/share/samtools/test/mpileup/expected/43.out /usr/share/samtools/test/mpileup/expected/44.out /usr/share/samtools/test/mpileup/expected/45.out /usr/share/samtools/test/mpileup/expected/46.out /usr/share/samtools/test/mpileup/expected/47.out /usr/share/samtools/test/mpileup/expected/48.out /usr/share/samtools/test/mpileup/expected/49.out /usr/share/samtools/test/mpileup/expected/5.out /usr/share/samtools/test/mpileup/expected/50.out /usr/share/samtools/test/mpileup/expected/51.out /usr/share/samtools/test/mpileup/expected/52.out /usr/share/samtools/test/mpileup/expected/53.out /usr/share/samtools/test/mpileup/expected/54.out /usr/share/samtools/test/mpileup/expected/55.out /usr/share/samtools/test/mpileup/expected/56.out /usr/share/samtools/test/mpileup/expected/57.out /usr/share/samtools/test/mpileup/expected/58.out /usr/share/samtools/test/mpileup/expected/59.out /usr/share/samtools/test/mpileup/expected/6.out /usr/share/samtools/test/mpileup/expected/60.out /usr/share/samtools/test/mpileup/expected/61.out /usr/share/samtools/test/mpileup/expected/62.out /usr/share/samtools/test/mpileup/expected/63.out /usr/share/samtools/test/mpileup/expected/64.out /usr/share/samtools/test/mpileup/expected/65.out /usr/share/samtools/test/mpileup/expected/66.out /usr/share/samtools/test/mpileup/expected/67.out /usr/share/samtools/test/mpileup/expected/68.out /usr/share/samtools/test/mpileup/expected/69.out /usr/share/samtools/test/mpileup/expected/7.out /usr/share/samtools/test/mpileup/expected/70.out /usr/share/samtools/test/mpileup/expected/71.out /usr/share/samtools/test/mpileup/expected/72.out /usr/share/samtools/test/mpileup/expected/73.out /usr/share/samtools/test/mpileup/expected/74.out /usr/share/samtools/test/mpileup/expected/75.out /usr/share/samtools/test/mpileup/expected/76.out /usr/share/samtools/test/mpileup/expected/77.out /usr/share/samtools/test/mpileup/expected/78.out /usr/share/samtools/test/mpileup/expected/79.out /usr/share/samtools/test/mpileup/expected/8.out /usr/share/samtools/test/mpileup/expected/80.out /usr/share/samtools/test/mpileup/expected/81.out /usr/share/samtools/test/mpileup/expected/9.out /usr/share/samtools/test/mpileup/expected/a0.out /usr/share/samtools/test/mpileup/expected/a1.out /usr/share/samtools/test/mpileup/expected/a10.out /usr/share/samtools/test/mpileup/expected/a11.out /usr/share/samtools/test/mpileup/expected/a13.out /usr/share/samtools/test/mpileup/expected/a14.out /usr/share/samtools/test/mpileup/expected/a15.out /usr/share/samtools/test/mpileup/expected/a16.out /usr/share/samtools/test/mpileup/expected/a17.out /usr/share/samtools/test/mpileup/expected/a2.out /usr/share/samtools/test/mpileup/expected/a3.out /usr/share/samtools/test/mpileup/expected/a4.out /usr/share/samtools/test/mpileup/expected/a5.out /usr/share/samtools/test/mpileup/expected/a6.out /usr/share/samtools/test/mpileup/expected/a8.out /usr/share/samtools/test/mpileup/expected/a9.out /usr/share/samtools/test/mpileup/expected/csize.out /usr/share/samtools/test/mpileup/expected/d1_1.out /usr/share/samtools/test/mpileup/expected/d1_12.out /usr/share/samtools/test/mpileup/expected/d1_2.out /usr/share/samtools/test/mpileup/expected/d2_12r.out /usr/share/samtools/test/mpileup/expected/d3_12.out /usr/share/samtools/test/mpileup/expected/d3_12r1a.out /usr/share/samtools/test/mpileup/expected/d3_12r2a.out /usr/share/samtools/test/mpileup/expected/d3_3.out /usr/share/samtools/test/mpileup/expected/d4_12.out /usr/share/samtools/test/mpileup/expected/d4_12b.out /usr/share/samtools/test/mpileup/expected/d4_12r.out /usr/share/samtools/test/mpileup/expected/d5_all1.out /usr/share/samtools/test/mpileup/expected/d5_all2.out /usr/share/samtools/test/mpileup/expected/d5_all3.out /usr/share/samtools/test/mpileup/expected/d5_all4.out /usr/share/samtools/test/mpileup/expected/d5_b3.out /usr/share/samtools/test/mpileup/expected/d5_b3a.out /usr/share/samtools/test/mpileup/expected/d5_b3aa.out /usr/share/samtools/test/mpileup/expected/d5_blank.out /usr/share/samtools/test/mpileup/expected/d5_xx1.out /usr/share/samtools/test/mpileup/expected/d5_xx2.out /usr/share/samtools/test/mpileup/expected/d5_xx3.out /usr/share/samtools/test/mpileup/expected/d5_xy1.out /usr/share/samtools/test/mpileup/expected/d6_nodel.out /usr/share/samtools/test/mpileup/expected/d6_wdel.out /usr/share/samtools/test/mpileup/expected/d7_nodup.out /usr/share/samtools/test/mpileup/expected/d8_PROPER.out /usr/share/samtools/test/mpileup/expected/d8_PROSUP.out /usr/share/samtools/test/mpileup/expected/d8_QC.out /usr/share/samtools/test/mpileup/expected/d8_R1PROP.out /usr/share/samtools/test/mpileup/expected/d8_noQC.out /usr/share/samtools/test/mpileup/expected/d8_noSUPP.out /usr/share/samtools/test/mpileup/expected/m5_all1.out /usr/share/samtools/test/mpileup/expected/m5_all2.out /usr/share/samtools/test/mpileup/expected/m5_all3.out /usr/share/samtools/test/mpileup/expected/m5_b3.out /usr/share/samtools/test/mpileup/expected/m5_b3a.out /usr/share/samtools/test/mpileup/expected/m5_b3aa.out /usr/share/samtools/test/mpileup/expected/m5_blank.out /usr/share/samtools/test/mpileup/expected/m5_xx1.out /usr/share/samtools/test/mpileup/expected/m5_xx2.out /usr/share/samtools/test/mpileup/expected/m5_xx3.out /usr/share/samtools/test/mpileup/expected/m5_xy1.out /usr/share/samtools/test/mpileup/expected/mp1_d.out /usr/share/samtools/test/mpileup/expected/mp1_dd.out /usr/share/samtools/test/mpileup/expected/mp1_ends.out /usr/share/samtools/test/mpileup/expected/mp1_i.out /usr/share/samtools/test/mpileup/expected/mp1_ii.out /usr/share/samtools/test/mpileup/expected/mp1_iidd.out /usr/share/samtools/test/mpileup/expected/mp2-noins.out /usr/share/samtools/test/mpileup/expected/mp2.out /usr/share/samtools/test/mpileup/expected/mp_2018a.out /usr/share/samtools/test/mpileup/expected/mp_2018aa.out /usr/share/samtools/test/mpileup/expected/mp_D.out /usr/share/samtools/test/mpileup/expected/mp_DI.out /usr/share/samtools/test/mpileup/expected/mp_I.out /usr/share/samtools/test/mpileup/expected/mp_ID.out /usr/share/samtools/test/mpileup/expected/mp_ID_rev.out /usr/share/samtools/test/mpileup/expected/mp_N.out /usr/share/samtools/test/mpileup/expected/mp_N2.out /usr/share/samtools/test/mpileup/expected/mp_P.out /usr/share/samtools/test/mpileup/indels.sam /usr/share/samtools/test/mpileup/md5/02099b2aad2cfe707759353724fb40ae /usr/share/samtools/test/mpileup/md5/0d4dfc45807d6a11439e858605cb364d /usr/share/samtools/test/mpileup/md5/351f64d4f4f9ddd45b35336ad97aa6de /usr/share/samtools/test/mpileup/md5/6ec590eb82c361a61e6baabce20109bc /usr/share/samtools/test/mpileup/md5/6f60cdf4c739651ae72d53e2e94825c1 /usr/share/samtools/test/mpileup/md5/73d180d5cb3860a2713927b6812eab0e /usr/share/samtools/test/mpileup/mod1.sam /usr/share/samtools/test/mpileup/mp.fa /usr/share/samtools/test/mpileup/mp_2018.fa /usr/share/samtools/test/mpileup/mp_2018.sam /usr/share/samtools/test/mpileup/mp_D.sam /usr/share/samtools/test/mpileup/mp_DI.sam /usr/share/samtools/test/mpileup/mp_I.sam /usr/share/samtools/test/mpileup/mp_ID.sam /usr/share/samtools/test/mpileup/mp_ID_rev.sam /usr/share/samtools/test/mpileup/mp_N.sam /usr/share/samtools/test/mpileup/mp_N2.sam /usr/share/samtools/test/mpileup/mp_P.sam /usr/share/samtools/test/mpileup/mpileup-E.bam /usr/share/samtools/test/mpileup/mpileup.1.bam /usr/share/samtools/test/mpileup/mpileup.1.bam.bai /usr/share/samtools/test/mpileup/mpileup.2.bam /usr/share/samtools/test/mpileup/mpileup.3.bam /usr/share/samtools/test/mpileup/mpileup.ref.fa /usr/share/samtools/test/mpileup/mpileup.reg /usr/share/samtools/test/mpileup/output-BP.sam /usr/share/samtools/test/mpileup/overlap.bam /usr/share/samtools/test/mpileup/overlap50.sam /usr/share/samtools/test/mpileup/overlapIllumina.bam /usr/share/samtools/test/mpileup/regions /usr/share/samtools/test/mpileup/xx#depth1.sam /usr/share/samtools/test/mpileup/xx#depth2.sam /usr/share/samtools/test/mpileup/xx#depth3.sam /usr/share/samtools/test/mpileup/xx#depth4.sam /usr/share/samtools/test/mpileup/xx#minimal.bam /usr/share/samtools/test/mpileup/xx#triplet.bam /usr/share/samtools/test/mpileup/xx.bed /usr/share/samtools/test/mpileup/xx.bed2 /usr/share/samtools/test/mpileup/xx.bed3 /usr/share/samtools/test/mpileup/xx.fa /usr/share/samtools/test/quickcheck/1.quickcheck.badeof.bam /usr/share/samtools/test/quickcheck/10.quickcheck.notargets.bam /usr/share/samtools/test/quickcheck/2.quickcheck.badheader.bam /usr/share/samtools/test/quickcheck/3.quickcheck.ok.bam /usr/share/samtools/test/quickcheck/4.quickcheck.ok.bam /usr/share/samtools/test/quickcheck/5.quickcheck.scramble30.truncated.cram /usr/share/samtools/test/quickcheck/6.quickcheck.cram21.ok.cram /usr/share/samtools/test/quickcheck/7.quickcheck.cram30.ok.cram /usr/share/samtools/test/quickcheck/8.quickcheck.cram21.truncated.cram /usr/share/samtools/test/quickcheck/9.quickcheck.cram30.truncated.cram /usr/share/samtools/test/quickcheck/all.expected /usr/share/samtools/test/reference/mpileup.MD.fa.expected /usr/share/samtools/test/reference/mpileup.embed.fa.expected /usr/share/samtools/test/regression.sh /usr/share/samtools/test/reheader/1_view1.sam.expected /usr/share/samtools/test/reheader/1_view1.sam.expected.err /usr/share/samtools/test/reheader/2_view1.sam.expected /usr/share/samtools/test/reheader/2_view1.sam.expected.err /usr/share/samtools/test/reheader/3_view1.sam.expected /usr/share/samtools/test/reheader/3_view1.sam.expected.err /usr/share/samtools/test/reheader/4_view1.sam.expected /usr/share/samtools/test/reheader/5_view1.sam.expected /usr/share/samtools/test/reheader/hdr.sam /usr/share/samtools/test/reset/basic.1.mp.1.expected /usr/share/samtools/test/reset/basic.bam.input.expected /usr/share/samtools/test/reset/basic.cram.input.expected /usr/share/samtools/test/reset/basic.output.mp.1.expected /usr/share/samtools/test/reset/empty.expected /usr/share/samtools/test/reset/output.flg.1.expected /usr/share/samtools/test/reset/output.flg.2.expected /usr/share/samtools/test/reset/output.keep.1.expected /usr/share/samtools/test/reset/output.keep.2.expected /usr/share/samtools/test/reset/output.keep.3.expected /usr/share/samtools/test/reset/output.nRG.1.expected /usr/share/samtools/test/reset/output.nRG.2.expected /usr/share/samtools/test/reset/reject.1.expected /usr/share/samtools/test/reset/reject.2.expected /usr/share/samtools/test/reset/seq.sam /usr/share/samtools/test/sort/minimiser-basic.sam /usr/share/samtools/test/sort/minimiser-indexed-poly.sam /usr/share/samtools/test/sort/minimiser-indexed.sam /usr/share/samtools/test/sort/name.sort.expected.sam /usr/share/samtools/test/sort/name2.sort.expected.sam /usr/share/samtools/test/sort/name3.sort.expected.sam /usr/share/samtools/test/sort/pos.sort.expected.sam /usr/share/samtools/test/sort/tag.as.sort.expected.sam /usr/share/samtools/test/sort/tag.fi.sort.expected.sam /usr/share/samtools/test/sort/tag.rg.n.sort.expected.sam /usr/share/samtools/test/sort/tag.rg.sort.expected.sam /usr/share/samtools/test/sort/template-coordinate.sort.expected.sam /usr/share/samtools/test/sort/template-coordinate.sort.sam /usr/share/samtools/test/split/split.expected.grp1.sam /usr/share/samtools/test/split/split.expected.grp2.sam /usr/share/samtools/test/split/split.expected.unk.sam /usr/share/samtools/test/split/split.expected_d_RG.grp3.sam /usr/share/samtools/test/split/split.expected_d_RG.unk.sam /usr/share/samtools/test/split/split.expected_d_an.aardvark.sam /usr/share/samtools/test/split/split.expected_d_an.badger.sam /usr/share/samtools/test/split/split.expected_d_an.cat.sam /usr/share/samtools/test/split/split.expected_d_an.dog.sam /usr/share/samtools/test/split/split.expected_d_an.unk.sam /usr/share/samtools/test/split/split.expected_d_an_M_3.unk.sam /usr/share/samtools/test/split/split.expected_d_nn.-1.sam /usr/share/samtools/test/split/split.expected_d_nn.-2.sam /usr/share/samtools/test/split/split.expected_d_nn.1.sam /usr/share/samtools/test/split/split.expected_d_nn.2.sam /usr/share/samtools/test/split/split.expected_d_nn.unk.sam /usr/share/samtools/test/split/split.sam /usr/share/samtools/test/split/split_d_nn.sam /usr/share/samtools/test/split/test_count_rg.c /usr/share/samtools/test/split/test_expand_format_string.c /usr/share/samtools/test/split/test_filter_header_rg.c /usr/share/samtools/test/split/test_parse_args.c /usr/share/samtools/test/stat/1.stats.expected /usr/share/samtools/test/stat/1.stats.large.expected /usr/share/samtools/test/stat/10.stats.expected /usr/share/samtools/test/stat/10_map_cigar.sam /usr/share/samtools/test/stat/10_map_cigar.sam_s1_a_1.expected.bamstat /usr/share/samtools/test/stat/10_map_cigar.sam_s1_b_1.expected.bamstat /usr/share/samtools/test/stat/11.stats.expected /usr/share/samtools/test/stat/11.stats.g4.expected /usr/share/samtools/test/stat/11.stats.targets /usr/share/samtools/test/stat/11_target.bam /usr/share/samtools/test/stat/11_target.bam.bai /usr/share/samtools/test/stat/11_target.sam /usr/share/samtools/test/stat/12.2reads.nooverlap.expected /usr/share/samtools/test/stat/12.2reads.overlap.expected /usr/share/samtools/test/stat/12.3reads.nooverlap.expected /usr/share/samtools/test/stat/12.3reads.overlap.expected /usr/share/samtools/test/stat/12_2reads.bed /usr/share/samtools/test/stat/12_3reads.bed /usr/share/samtools/test/stat/12_overlaps.bam /usr/share/samtools/test/stat/13.barcodes.bc.ok.expected /usr/share/samtools/test/stat/13.barcodes.ox.ok.expected /usr/share/samtools/test/stat/13_barcodes_fail_bc_length.sam /usr/share/samtools/test/stat/13_barcodes_fail_hyphen.sam /usr/share/samtools/test/stat/13_barcodes_fail_qt_length.sam /usr/share/samtools/test/stat/13_barcodes_ok.sam /usr/share/samtools/test/stat/13_barcodes_ok_ox_bz.sam /usr/share/samtools/test/stat/14.rg.Sample.expected /usr/share/samtools/test/stat/14.rg.grp2.expected /usr/share/samtools/test/stat/14.rg.grp3.expected /usr/share/samtools/test/stat/14.rg.s1.expected /usr/share/samtools/test/stat/15.big_del.sam /usr/share/samtools/test/stat/15.stats.expected /usr/share/samtools/test/stat/1_map_cigar.sam /usr/share/samtools/test/stat/1_map_cigar.sam_s1_a_1.expected.bamstat /usr/share/samtools/test/stat/1_map_cigar_large.sam /usr/share/samtools/test/stat/2.stats.expected /usr/share/samtools/test/stat/2.stats.large.expected /usr/share/samtools/test/stat/2_equal_cigar_full_seq.sam /usr/share/samtools/test/stat/2_equal_cigar_full_seq_large.sam /usr/share/samtools/test/stat/3.stats.expected /usr/share/samtools/test/stat/3.stats.large.expected /usr/share/samtools/test/stat/3_map_cigar_equal_seq.sam /usr/share/samtools/test/stat/3_map_cigar_equal_seq_large.sam /usr/share/samtools/test/stat/4.stats.expected /usr/share/samtools/test/stat/4.stats.large.expected /usr/share/samtools/test/stat/4_X_cigar_full_seq.sam /usr/share/samtools/test/stat/4_X_cigar_full_seq_large.sam /usr/share/samtools/test/stat/5.stats.expected /usr/share/samtools/test/stat/5.stats.large.expected /usr/share/samtools/test/stat/5_insert_cigar.sam /usr/share/samtools/test/stat/5_insert_cigar_large.sam /usr/share/samtools/test/stat/6.stats.expected /usr/share/samtools/test/stat/7.stats.expected /usr/share/samtools/test/stat/7.stats.large.expected /usr/share/samtools/test/stat/7_supp.sam /usr/share/samtools/test/stat/7_supp_large.sam /usr/share/samtools/test/stat/8.stats.expected /usr/share/samtools/test/stat/8.stats.large.expected /usr/share/samtools/test/stat/8_secondary.sam /usr/share/samtools/test/stat/8_secondary_large.sam /usr/share/samtools/test/stat/9.stats.expected /usr/share/samtools/test/stat/test.fa /usr/share/samtools/test/stat/test.fa.fai /usr/share/samtools/test/test.c /usr/share/samtools/test/test.h /usr/share/samtools/test/test.pl /usr/share/samtools/test/tview/test_get_rg_sample.c /usr/share/samtools/test/vcf-miniview.c