[med-svn] samtools branch develop updated (b7c4b4d -> 8a06c51)
Andreas Tille
tille at debian.org
Fri Aug 4 16:57:00 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch develop
in repository samtools.
from b7c4b4d Ensure usage tests have a terminal on stdin
adds 8a06c51 New upstream version 1.5
No new revisions were added by this update.
Summary of changes:
.gitattributes | 10 -
.gitignore | 20 -
.travis.yml | 18 -
INSTALL | 153 +-
Makefile | 287 +-
NEWS | 239 +-
README | 51 +-
README.md | 13 -
bam.c | 85 +-
bam.h | 14 +-
bam2bcf.c | 79 +-
bam2bcf.h | 15 +-
bam2bcf_indel.c | 78 +-
bam2depth.c | 162 +-
bam_addrprg.c | 482 ++
bam_aux.c | 20 +-
bam_cat.c | 547 +-
bam_color.c | 2 +
bam_flags.c | 2 +
bam_import.c | 2 +
bam_index.c | 63 +-
bam_lpileup.c | 2 +
bam_mate.c | 200 +-
bam_md.c | 366 +-
bam_plbuf.c | 2 +
bam_plcmd.c | 383 +-
bam_quickcheck.c | 170 +
bam_reheader.c | 485 +-
bam_rmdup.c | 173 +-
bam_rmdupse.c | 79 +-
bam_sort.c | 1947 +++--
bam_split.c | 224 +-
bam_stat.c | 104 +-
bam_tview.c | 97 +-
bam_tview.h | 6 +-
bam_tview_curses.c | 114 +-
bam_tview_html.c | 12 +-
bamshuf.c | 243 +-
bamtk.c | 116 +-
bedcov.c | 35 +-
bedidx.c | 2 +
config.h.in | 50 +
config.mk.in | 54 +
configure.ac | 111 +
cut_target.c | 79 +-
dict.c | 154 +
errmod.c | 193 -
errmod.h | 49 -
examples/.gitignore | 9 -
examples/00README.txt | 2 +-
faidx.c | 78 +-
install-sh | 501 ++
kaln.c | 486 --
kaln.h | 67 -
kprobaln.c | 280 -
kprobaln.h | 49 -
m4/ax_with_curses.m4 | 518 ++
m4/ax_with_htslib.m4 | 154 +
misc/ace2sam.c | 9 +-
misc/maq2sam.c | 2 +
misc/md5.c | 298 -
misc/md5.h | 57 -
misc/md5fa.c | 49 +-
bam_plbuf.c => misc/md5sum-lite.c | 69 +-
misc/plot-bamstats | 38 +-
misc/samtools_tab_completion | 77 +
misc/seq_cache_populate.pl | 5 +
misc/wgsim.1 | 55 +
misc/wgsim.c | 145 +-
misc/wgsim_eval.pl | 376 +-
padding.c | 319 +-
phase.c | 121 +-
sam.c | 51 +-
sam.h | 27 +-
sam_header.c | 2 +
sam_opts.c | 161 +
sam_opts.h | 102 +
test/test.c => sam_utils.c | 53 +-
sam_view.c | 1296 +++-
sample.c | 2 +
samtools.1 | 1719 +++-
samtools.h | 12 +-
stats.c | 1082 +--
stats_isize.c | 2 +
test/addrprg/1_fixup.sam | 30 +
test/addrprg/1_fixup.sam.expected | 30 +
.../1_fixup.sam.expected.err} | 0
test/addrprg/2_fixup_orphan.sam | 30 +
test/addrprg/2_fixup_orphan.sam.expected | 30 +
.../2_fixup_orphan.sam.expected.err} | 0
.../3_fixup.sam.expected} | 0
test/addrprg/3_fixup.sam.expected.err | 1 +
test/addrprg/4_fixup_norg.sam | 29 +
test/addrprg/4_fixup_norg.sam.expected | 30 +
.../4_fixup_norg.sam.expected.err} | 0
test/bam2fq/1.1.fq.expected | 72 +
test/bam2fq/1.2.fq.expected | 72 +
.../empty.expected => bam2fq/1.stdout.expected} | 0
test/bam2fq/2.1.fq.expected | 72 +
test/bam2fq/2.2.fq.expected | 72 +
.../{dat/empty.expected => bam2fq/2.s.fq.expected} | 0
.../empty.expected => bam2fq/2.stdout.expected} | 0
test/bam2fq/3.1.fq.expected | 72 +
test/bam2fq/3.2.fq.expected | 72 +
test/bam2fq/3.s.fq.expected | 4 +
.../empty.expected => bam2fq/3.stdout.expected} | 0
test/bam2fq/4.1.fq.expected | 68 +
test/bam2fq/4.2.fq.expected | 68 +
test/bam2fq/4.s.fq.expected | 8 +
.../empty.expected => bam2fq/4.stdout.expected} | 0
test/bam2fq/5.1.fq.expected | 68 +
test/bam2fq/5.2.fq.expected | 68 +
test/bam2fq/5.s.fq.expected | 8 +
test/bam2fq/6.1.fq.expected | 68 +
test/bam2fq/6.2.fq.expected | 68 +
test/bam2fq/6.s.fq.expected | 8 +
test/bam2fq/7.1.fq.expected | 68 +
test/bam2fq/7.2.fq.expected | 68 +
test/bam2fq/7.s.fq.expected | 8 +
test/bam2fq/8.1.fq.expected | 68 +
test/bam2fq/8.2.fq.expected | 68 +
test/bam2fq/8.i.fq.expected | 12 +
test/bam2fq/8.s.fq.expected | 8 +
test/bam2fq/bc.fq.expected | 12 +
test/bam2fq/bc_split.fq.expected | 12 +
test/dat/bam2fq.001.sam | 9 +-
test/dat/{bam2fq.001.sam => bam2fq.002.sam} | 10 +-
test/dat/{bam2fq.001.sam => bam2fq.003.sam} | 11 +-
test/dat/{bam2fq.001.sam => bam2fq.004.sam} | 11 +-
test/dat/{bam2fq.001.sam => bam2fq.005.sam} | 15 +-
test/dat/depad.001p.sam | 12 +-
test/dat/depad.001u.sam | 14 +-
test/dat/dict.fa | 46 +
test/dat/dict.out | 10 +
test/dat/mpileup.1.sam | 44 +-
test/dat/mpileup.2.sam | 10 +-
test/dat/mpileup.3.sam | 14 +-
test/dat/mpileup.out.2 | 1006 +--
test/dat/mpileup.out.4 | 1008 +--
test/dat/test_input_1_a.bam | Bin 758 -> 759 bytes
...1_a.bam.bai => test_input_1_a.bam.bai.expected} | Bin
test/dat/test_input_1_a_regex.sam | 28 +
test/dat/test_input_1_b.bam | Bin 687 -> 686 bytes
test/dat/test_input_1_b.bam.bai | Bin 192 -> 0 bytes
test/dat/test_input_1_b.sam | 2 +-
test/dat/test_input_1_b_regex.sam | 24 +
test/dat/test_input_1_c.bam | Bin 655 -> 692 bytes
test/dat/test_input_1_c.bam.bai | Bin 176 -> 0 bytes
test/dat/test_input_1_c.sam | 1 +
.../dat/{test_input_1_b.sam => test_input_1_d.sam} | 26 +-
test/dat/view.001.fa | 2 +
test/dat/view.001.fa.fai | 1 +
test/dat/view.001.sam | 3 +-
test/fixmate/1_coord_sort.sam | 2 +
test/fixmate/2_isize_overflow.sam | 2 +
test/fixmate/2_isize_overflow.sam.expected | 14 +-
test/fixmate/3_reverse_read_pp_lt.sam.expected | 4 +-
test/fixmate/4_reverse_read_pp_equal.sam.expected | 4 +-
test/fixmate/5_ct.sam.expected | 4 +-
test/fixmate/6_ct_replace.sam.expected | 4 +-
...{2_isize_overflow.sam => 7_two_read_mapped.sam} | 6 +-
...sam.expected => 7_two_read_mapped.sam.expected} | 18 +-
test/merge/.gitignore | 6 -
test/merge/2.merge.expected.bam | Bin 1181 -> 1228 bytes
test/merge/3.merge.expected.bam | Bin 1199 -> 1233 bytes
test/merge/3.merge.expected.err | 6 +-
test/merge/4.merge.expected.bam | Bin 0 -> 689 bytes
test/merge/5.merge.expected.bam | Bin 0 -> 1115 bytes
test/merge/5.merge.expected.sam | 61 +
test/merge/6.merge.expected.bam | Bin 0 -> 899 bytes
test/merge/7.merge.expected.bam | Bin 0 -> 1056 bytes
test/merge/tag.pg.merge.expected.sam | 37 +
test/merge/tag.pg.n.merge.expected.sam | 39 +
test/merge/test_bam_translate.c | 37 +-
test/merge/test_pretty_header.c | 87 -
test/merge/test_rtrans_build.c | 6 +-
test/merge/test_trans_tbl_init.c | 419 +-
test/mpileup/.gitignore | 11 -
test/mpileup/depth.reg | 88 +
test/mpileup/expected/1.out.f3-6.gz | Bin 0 -> 596114 bytes
test/mpileup/expected/1.out.xz | Bin 1336220 -> 0 bytes
test/mpileup/expected/11.out | 18 +-
test/mpileup/expected/12.out | 18 +-
test/mpileup/expected/14.out | 32 +-
test/mpileup/expected/15.out | 32 +-
test/mpileup/expected/16.out | 182 +-
test/mpileup/expected/19.out | 182 +-
test/mpileup/expected/20.out | 6796 ++++++++--------
test/mpileup/expected/21.out | 182 +-
test/mpileup/expected/22.out | 182 +-
test/mpileup/expected/23.out | 6 +-
test/mpileup/expected/24.out | 6 +-
test/mpileup/expected/25.out | 6 +-
test/mpileup/expected/30.out | 2 +-
test/mpileup/expected/32.out | 2 +-
test/mpileup/expected/33.out | 4 +-
test/mpileup/expected/34.out | 4 +-
test/mpileup/expected/35.out | 60 +-
test/mpileup/expected/4.out | 56 +-
test/mpileup/expected/43.out | 4 +-
test/mpileup/expected/44.out | 4 +-
test/mpileup/expected/48.out | 8202 ++++++++++----------
test/mpileup/expected/49.out | 8202 ++++++++++----------
test/mpileup/expected/50.out | 8202 ++++++++++----------
test/mpileup/expected/51.out | 8202 ++++++++++----------
test/mpileup/expected/52.out | 4209 +++++++++-
test/mpileup/expected/6.out | 2 +-
test/mpileup/expected/7.out | 2 +-
test/mpileup/expected/76.out | 182 +-
test/mpileup/expected/77.out | 182 +-
test/mpileup/expected/9.out | 20 +-
test/mpileup/expected/a0.out | 4200 ++++++++++
test/mpileup/expected/a1.out | 20 +
test/mpileup/expected/a10.out | 6 +
test/mpileup/expected/a11.out | 6 +
test/mpileup/expected/a13.out | 12 +
test/mpileup/expected/a14.out | 17 +
test/mpileup/expected/a15.out | 20 +
test/mpileup/expected/a16.out | 20 +
test/mpileup/expected/a17.out | 20 +
test/mpileup/expected/a2.out | 20 +
test/mpileup/expected/a3.out | 20 +
test/mpileup/expected/a4.out | 60 +
test/mpileup/expected/a5.out | 60 +
test/mpileup/expected/a6.out | 60 +
test/mpileup/expected/a8.out | 12 +
test/mpileup/expected/a9.out | 12 +
test/mpileup/expected/d1_1.out | 6 +
test/mpileup/expected/d1_12.out | 9 +
test/mpileup/expected/d1_2.out | 6 +
test/mpileup/expected/d2_12r.out | 5 +
test/mpileup/expected/d3_12.out | 20 +
test/mpileup/expected/d3_12r1a.out | 12 +
test/mpileup/expected/d3_12r2a.out | 6 +
test/mpileup/expected/d3_3.out | 40 +
test/mpileup/expected/d4_12.out | 60 +
test/mpileup/expected/d4_12b.out | 17 +
test/mpileup/expected/d4_12r.out | 12 +
test/mpileup/expected/d5_all1.out | 6 +
test/mpileup/expected/d5_all2.out | 40 +
test/mpileup/expected/d5_all3.out | 80 +
test/mpileup/expected/d5_b3.out | 3 +
test/mpileup/expected/d5_b3a.out | 7 +
test/mpileup/expected/d5_b3aa.out | 14 +
.../expected/d5_blank.out} | 0
test/mpileup/expected/d5_xx1.out | 3 +
test/mpileup/expected/d5_xx2.out | 7 +
test/mpileup/expected/d5_xx3.out | 12 +
test/mpileup/expected/d5_xy1.out | 2 +
test/mpileup/expected/m5_all1.out | 6 +
test/mpileup/expected/m5_all2.out | 40 +
test/mpileup/expected/m5_all3.out | 80 +
test/mpileup/expected/m5_b3.out | 3 +
test/mpileup/expected/m5_b3a.out | 7 +
test/mpileup/expected/m5_b3aa.out | 14 +
.../expected/m5_blank.out} | 0
test/mpileup/expected/m5_xx1.out | 3 +
test/mpileup/expected/m5_xx2.out | 7 +
test/mpileup/expected/m5_xx3.out | 12 +
test/mpileup/expected/m5_xy1.out | 2 +
test/mpileup/mpileup.reg | 62 +-
test/mpileup/regression.sh | 133 +-
test/mpileup/xx#depth1.sam | 6 +
test/mpileup/xx#depth2.sam | 6 +
test/mpileup/xx#depth3.sam | 7 +
test/mpileup/xx.bed | 2 +
test/mpileup/xx.bed2 | 1 +
test/mpileup/xx.bed3 | 3 +
test/mpileup/xx.fa | 1 -
test/quickcheck/1.quickcheck.badeof.bam | Bin 0 -> 1228 bytes
test/quickcheck/2.quickcheck.badheader.bam | Bin 0 -> 1233 bytes
test/quickcheck/3.quickcheck.ok.bam | Bin 0 -> 1228 bytes
test/quickcheck/4.quickcheck.ok.bam | Bin 0 -> 1233 bytes
.../5.quickcheck.scramble30.truncated.cram | Bin 0 -> 11960 bytes
test/quickcheck/6.quickcheck.cram21.ok.cram | Bin 0 -> 154443 bytes
test/quickcheck/7.quickcheck.cram30.ok.cram | Bin 0 -> 49122 bytes
test/quickcheck/8.quickcheck.cram21.truncated.cram | Bin 0 -> 154413 bytes
test/quickcheck/9.quickcheck.cram30.truncated.cram | Bin 0 -> 49084 bytes
test/quickcheck/all.expected | 5 +
.../view.001.sam => reheader/1_view1.sam.expected} | 11 +-
.../1_view1.sam.expected.err} | 0
.../2_view1.sam.expected} | 61 +-
.../2_view1.sam.expected.err} | 0
.../3_view1.sam.expected} | 57 +-
.../3_view1.sam.expected.err} | 0
test/{dat/cat.hdr => reheader/hdr.sam} | 7 +-
.../name.sort.expected.sam} | 8 +-
.../pos.sort.expected.sam} | 2 +-
.../tag.as.sort.expected.sam} | 28 +-
.../tag.fi.sort.expected.sam} | 28 +-
.../tag.rg.n.sort.expected.sam} | 16 +-
.../tag.rg.sort.expected.sam} | 16 +-
test/split/.gitignore | 4 -
test/split/test_count_rg.c | 11 +-
test/split/test_expand_format_string.c | 15 +-
test/split/test_filter_header_rg.c | 32 +-
test/split/test_parse_args.c | 34 +-
test/stat/1.stats.expected | 74 +-
test/stat/{5.stats.expected => 10.stats.expected} | 252 +-
test/stat/{1_map_cigar.sam => 10_map_cigar.sam} | 3 +
...ed => 10_map_cigar.sam_s1_a_1.expected.bamstat} | 74 +-
...ed => 10_map_cigar.sam_s1_b_1.expected.bamstat} | 74 +-
...ted => 1_map_cigar.sam_s1_a_1.expected.bamstat} | 74 +-
test/stat/2.stats.expected | 74 +-
test/stat/3.stats.expected | 4 +-
test/stat/4.stats.expected | 74 +-
test/stat/5.stats.expected | 74 +-
test/stat/6.stats.expected | 74 +-
test/stat/{5.stats.expected => 7.stats.expected} | 85 +-
test/stat/7_supp.sam | 6 +
test/stat/{5.stats.expected => 8.stats.expected} | 78 +-
test/stat/{5_insert_cigar.sam => 8_secondary.sam} | 1 +
test/stat/{1.stats.expected => 9.stats.expected} | 74 +-
test/test.c | 10 +-
test/test.pl | 438 +-
test/tview/test_get_rg_sample.c | 2 +
test/vcf-miniview.c | 14 +-
317 files changed, 45657 insertions(+), 27346 deletions(-)
delete mode 100644 .gitattributes
delete mode 100644 .gitignore
delete mode 100644 .travis.yml
delete mode 100644 README.md
create mode 100644 bam_addrprg.c
create mode 100644 bam_quickcheck.c
create mode 100644 config.h.in
create mode 100644 config.mk.in
create mode 100644 configure.ac
create mode 100644 dict.c
delete mode 100644 errmod.c
delete mode 100644 errmod.h
delete mode 100644 examples/.gitignore
create mode 100755 install-sh
delete mode 100644 kaln.c
delete mode 100644 kaln.h
delete mode 100644 kprobaln.c
delete mode 100644 kprobaln.h
create mode 100644 m4/ax_with_curses.m4
create mode 100644 m4/ax_with_htslib.m4
delete mode 100644 misc/md5.c
delete mode 100644 misc/md5.h
copy bam_plbuf.c => misc/md5sum-lite.c (53%)
create mode 100644 misc/samtools_tab_completion
create mode 100644 misc/wgsim.1
create mode 100644 sam_opts.c
create mode 100644 sam_opts.h
copy test/test.c => sam_utils.c (51%)
create mode 100644 test/addrprg/1_fixup.sam
create mode 100644 test/addrprg/1_fixup.sam.expected
copy test/{dat/empty.expected => addrprg/1_fixup.sam.expected.err} (100%)
create mode 100644 test/addrprg/2_fixup_orphan.sam
create mode 100644 test/addrprg/2_fixup_orphan.sam.expected
copy test/{dat/empty.expected => addrprg/2_fixup_orphan.sam.expected.err} (100%)
copy test/{dat/empty.expected => addrprg/3_fixup.sam.expected} (100%)
create mode 100644 test/addrprg/3_fixup.sam.expected.err
create mode 100644 test/addrprg/4_fixup_norg.sam
create mode 100644 test/addrprg/4_fixup_norg.sam.expected
copy test/{dat/empty.expected => addrprg/4_fixup_norg.sam.expected.err} (100%)
create mode 100644 test/bam2fq/1.1.fq.expected
create mode 100644 test/bam2fq/1.2.fq.expected
copy test/{dat/empty.expected => bam2fq/1.stdout.expected} (100%)
create mode 100644 test/bam2fq/2.1.fq.expected
create mode 100644 test/bam2fq/2.2.fq.expected
copy test/{dat/empty.expected => bam2fq/2.s.fq.expected} (100%)
copy test/{dat/empty.expected => bam2fq/2.stdout.expected} (100%)
create mode 100644 test/bam2fq/3.1.fq.expected
create mode 100644 test/bam2fq/3.2.fq.expected
create mode 100644 test/bam2fq/3.s.fq.expected
copy test/{dat/empty.expected => bam2fq/3.stdout.expected} (100%)
create mode 100644 test/bam2fq/4.1.fq.expected
create mode 100644 test/bam2fq/4.2.fq.expected
create mode 100644 test/bam2fq/4.s.fq.expected
copy test/{dat/empty.expected => bam2fq/4.stdout.expected} (100%)
create mode 100644 test/bam2fq/5.1.fq.expected
create mode 100644 test/bam2fq/5.2.fq.expected
create mode 100644 test/bam2fq/5.s.fq.expected
create mode 100644 test/bam2fq/6.1.fq.expected
create mode 100644 test/bam2fq/6.2.fq.expected
create mode 100644 test/bam2fq/6.s.fq.expected
create mode 100644 test/bam2fq/7.1.fq.expected
create mode 100644 test/bam2fq/7.2.fq.expected
create mode 100644 test/bam2fq/7.s.fq.expected
create mode 100644 test/bam2fq/8.1.fq.expected
create mode 100644 test/bam2fq/8.2.fq.expected
create mode 100644 test/bam2fq/8.i.fq.expected
create mode 100644 test/bam2fq/8.s.fq.expected
create mode 100644 test/bam2fq/bc.fq.expected
create mode 100644 test/bam2fq/bc_split.fq.expected
copy test/dat/{bam2fq.001.sam => bam2fq.002.sam} (90%)
copy test/dat/{bam2fq.001.sam => bam2fq.003.sam} (90%)
copy test/dat/{bam2fq.001.sam => bam2fq.004.sam} (89%)
copy test/dat/{bam2fq.001.sam => bam2fq.005.sam} (82%)
create mode 100644 test/dat/dict.fa
create mode 100644 test/dat/dict.out
rename test/dat/{test_input_1_a.bam.bai => test_input_1_a.bam.bai.expected} (100%)
create mode 100644 test/dat/test_input_1_a_regex.sam
delete mode 100644 test/dat/test_input_1_b.bam.bai
create mode 100644 test/dat/test_input_1_b_regex.sam
delete mode 100644 test/dat/test_input_1_c.bam.bai
copy test/dat/{test_input_1_b.sam => test_input_1_d.sam} (55%)
copy test/fixmate/{2_isize_overflow.sam => 7_two_read_mapped.sam} (82%)
copy test/fixmate/{2_isize_overflow.sam.expected => 7_two_read_mapped.sam.expected} (60%)
delete mode 100644 test/merge/.gitignore
create mode 100644 test/merge/4.merge.expected.bam
create mode 100644 test/merge/5.merge.expected.bam
create mode 100644 test/merge/5.merge.expected.sam
create mode 100644 test/merge/6.merge.expected.bam
create mode 100644 test/merge/7.merge.expected.bam
create mode 100644 test/merge/tag.pg.merge.expected.sam
create mode 100644 test/merge/tag.pg.n.merge.expected.sam
delete mode 100644 test/merge/test_pretty_header.c
delete mode 100644 test/mpileup/.gitignore
create mode 100644 test/mpileup/depth.reg
create mode 100644 test/mpileup/expected/1.out.f3-6.gz
delete mode 100644 test/mpileup/expected/1.out.xz
create mode 100644 test/mpileup/expected/a0.out
create mode 100644 test/mpileup/expected/a1.out
create mode 100644 test/mpileup/expected/a10.out
create mode 100644 test/mpileup/expected/a11.out
create mode 100644 test/mpileup/expected/a13.out
create mode 100644 test/mpileup/expected/a14.out
create mode 100644 test/mpileup/expected/a15.out
create mode 100644 test/mpileup/expected/a16.out
create mode 100644 test/mpileup/expected/a17.out
create mode 100644 test/mpileup/expected/a2.out
create mode 100644 test/mpileup/expected/a3.out
create mode 100644 test/mpileup/expected/a4.out
create mode 100644 test/mpileup/expected/a5.out
create mode 100644 test/mpileup/expected/a6.out
create mode 100644 test/mpileup/expected/a8.out
create mode 100644 test/mpileup/expected/a9.out
create mode 100644 test/mpileup/expected/d1_1.out
create mode 100644 test/mpileup/expected/d1_12.out
create mode 100644 test/mpileup/expected/d1_2.out
create mode 100644 test/mpileup/expected/d2_12r.out
create mode 100644 test/mpileup/expected/d3_12.out
create mode 100644 test/mpileup/expected/d3_12r1a.out
create mode 100644 test/mpileup/expected/d3_12r2a.out
create mode 100644 test/mpileup/expected/d3_3.out
create mode 100644 test/mpileup/expected/d4_12.out
create mode 100644 test/mpileup/expected/d4_12b.out
create mode 100644 test/mpileup/expected/d4_12r.out
create mode 100644 test/mpileup/expected/d5_all1.out
create mode 100644 test/mpileup/expected/d5_all2.out
create mode 100644 test/mpileup/expected/d5_all3.out
create mode 100644 test/mpileup/expected/d5_b3.out
create mode 100644 test/mpileup/expected/d5_b3a.out
create mode 100644 test/mpileup/expected/d5_b3aa.out
copy test/{dat/empty.expected => mpileup/expected/d5_blank.out} (100%)
create mode 100644 test/mpileup/expected/d5_xx1.out
create mode 100644 test/mpileup/expected/d5_xx2.out
create mode 100644 test/mpileup/expected/d5_xx3.out
create mode 100644 test/mpileup/expected/d5_xy1.out
create mode 100644 test/mpileup/expected/m5_all1.out
create mode 100644 test/mpileup/expected/m5_all2.out
create mode 100644 test/mpileup/expected/m5_all3.out
create mode 100644 test/mpileup/expected/m5_b3.out
create mode 100644 test/mpileup/expected/m5_b3a.out
create mode 100644 test/mpileup/expected/m5_b3aa.out
copy test/{dat/empty.expected => mpileup/expected/m5_blank.out} (100%)
create mode 100644 test/mpileup/expected/m5_xx1.out
create mode 100644 test/mpileup/expected/m5_xx2.out
create mode 100644 test/mpileup/expected/m5_xx3.out
create mode 100644 test/mpileup/expected/m5_xy1.out
create mode 100644 test/mpileup/xx#depth1.sam
create mode 100644 test/mpileup/xx#depth2.sam
create mode 100644 test/mpileup/xx#depth3.sam
create mode 100644 test/mpileup/xx.bed
create mode 100644 test/mpileup/xx.bed2
create mode 100644 test/mpileup/xx.bed3
create mode 100644 test/quickcheck/1.quickcheck.badeof.bam
create mode 100644 test/quickcheck/2.quickcheck.badheader.bam
create mode 100644 test/quickcheck/3.quickcheck.ok.bam
create mode 100644 test/quickcheck/4.quickcheck.ok.bam
create mode 100644 test/quickcheck/5.quickcheck.scramble30.truncated.cram
create mode 100644 test/quickcheck/6.quickcheck.cram21.ok.cram
create mode 100644 test/quickcheck/7.quickcheck.cram30.ok.cram
create mode 100644 test/quickcheck/8.quickcheck.cram21.truncated.cram
create mode 100644 test/quickcheck/9.quickcheck.cram30.truncated.cram
create mode 100644 test/quickcheck/all.expected
copy test/{dat/view.001.sam => reheader/1_view1.sam.expected} (95%)
copy test/{dat/empty.expected => reheader/1_view1.sam.expected.err} (100%)
copy test/{dat/bam2fq.001.sam => reheader/2_view1.sam.expected} (62%)
copy test/{dat/empty.expected => reheader/2_view1.sam.expected.err} (100%)
copy test/{dat/bam2fq.001.sam => reheader/3_view1.sam.expected} (62%)
copy test/{dat/empty.expected => reheader/3_view1.sam.expected.err} (100%)
copy test/{dat/cat.hdr => reheader/hdr.sam} (83%)
copy test/{dat/test_input_1_a.sam => sort/name.sort.expected.sam} (98%)
copy test/{dat/test_input_1_a.sam => sort/pos.sort.expected.sam} (98%)
copy test/{dat/test_input_1_b.sam => sort/tag.as.sort.expected.sam} (54%)
copy test/{dat/test_input_1_b.sam => sort/tag.fi.sort.expected.sam} (54%)
copy test/{dat/test_input_1_a.sam => sort/tag.rg.n.sort.expected.sam} (98%)
copy test/{dat/test_input_1_a.sam => sort/tag.rg.sort.expected.sam} (98%)
delete mode 100644 test/split/.gitignore
copy test/stat/{5.stats.expected => 10.stats.expected} (95%)
copy test/stat/{1_map_cigar.sam => 10_map_cigar.sam} (53%)
copy test/stat/{1.stats.expected => 10_map_cigar.sam_s1_a_1.expected.bamstat} (97%)
copy test/stat/{1.stats.expected => 10_map_cigar.sam_s1_b_1.expected.bamstat} (97%)
copy test/stat/{1.stats.expected => 1_map_cigar.sam_s1_a_1.expected.bamstat} (97%)
copy test/stat/{5.stats.expected => 7.stats.expected} (97%)
create mode 100644 test/stat/7_supp.sam
copy test/stat/{5.stats.expected => 8.stats.expected} (97%)
copy test/stat/{5_insert_cigar.sam => 8_secondary.sam} (71%)
copy test/stat/{1.stats.expected => 9.stats.expected} (97%)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/samtools.git
More information about the debian-med-commit
mailing list