[med-svn] samtools 01/02: Merge branch 'debian/unstable' into debian/jessie-backports
Charles Plessy
plessy at moszumanska.debian.org
Fri Feb 12 04:03:58 UTC 2016
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to annotated tag 1.3-1_bpo8+1
in repository samtools.
commit 24274e5166b10317fa9bad2ff58af9374fc1d241
Merge: 032962f 096bc41
Author: Charles Plessy <plessy at debian.org>
Date: Fri Feb 12 12:54:49 2016 +0900
Merge branch 'debian/unstable' into debian/jessie-backports
Conflicts:
debian/changelog
.gitattributes | 2 +-
.gitignore | 9 +
.travis.yml | 14 +-
.travis/clone | 14 +
INSTALL | 144 +-
Makefile | 212 +-
NEWS | 104 +-
README | 31 +-
README.md | 25 +
bam.c | 67 +-
bam.h | 7 +-
bam2bcf.c | 75 +-
bam2bcf.h | 13 +-
bam2bcf_indel.c | 14 +-
bam2depth.c | 142 +-
bam_addrprg.c | 476 ++
bam_aux.c | 18 +-
bam_cat.c | 432 +-
bam_index.c | 29 +-
bam_mate.c | 58 +-
bam_md.c | 173 +-
bam_plcmd.c | 232 +-
bam_quickcheck.c | 134 +
bam_reheader.c | 437 +-
bam_rmdup.c | 94 +-
bam_rmdupse.c | 31 +-
bam_sort.c | 1472 +++-
bam_split.c | 99 +-
bam_stat.c | 66 +-
bam_tview.c | 88 +-
bam_tview.h | 6 +-
bam_tview_curses.c | 112 +-
bam_tview_html.c | 10 +-
bamshuf.c | 112 +-
bamtk.c | 107 +-
bedcov.c | 31 +-
config.h.in | 39 +
config.mk.in | 52 +
configure.ac | 101 +
cut_target.c | 70 +-
debian/NEWS | 9 +
debian/ax_with_htslib.m4 | 140 +
debian/changelog | 29 +
debian/control | 15 +-
debian/copyright | 22 +-
debian/mans/ace2sam.1 | 24 +
debian/mans/samtools.pl.1 | 19 +
debian/mans/wgsim.1 | 44 +
debian/patches/fix_segfault_with_small_ref.patch | 54 -
debian/patches/i386-build.patch | 48 -
debian/patches/literal_version.patch | 16 +
debian/patches/mayhem.patch | 69 +
debian/patches/series | 6 +-
debian/patches/spelling.patch | 15 +
debian/rules | 21 +-
debian/samtools.install | 1 +
debian/samtools.lintian-overrides | 4 +
debian/source/options | 1 +
dict.c | 151 +
errmod.c | 4 +-
examples/00README.txt | 2 +-
install-sh | 501 ++
misc/md5.c | 298 -
misc/md5.h | 57 -
misc/md5fa.c | 47 +-
misc/md5sum-lite.c | 61 +
misc/plot-bamstats | 25 +-
misc/wgsim.1 | 55 +
misc/wgsim.c | 143 +-
misc/wgsim_eval.pl | 376 +-
padding.c | 287 +-
phase.c | 44 +-
sam.c | 29 +-
sam.h | 26 +-
sam_opts.c | 153 +
sam_opts.h | 99 +
sam_view.c | 795 +-
samtools.1 | 1458 +++-
samtools.h | 12 +-
stats.c | 1075 +--
test/addrprg/1_fixup.sam | 30 +
test/addrprg/1_fixup.sam.expected | 30 +
test/addrprg/1_fixup.sam.expected.err | 0
test/addrprg/2_fixup_orphan.sam | 30 +
test/addrprg/2_fixup_orphan.sam.expected | 30 +
test/addrprg/2_fixup_orphan.sam.expected.err | 0
test/addrprg/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 +
test/addrprg/4_fixup_norg.sam.expected.err | 0
test/bam2fq/1.1.fq.expected | 72 +
test/bam2fq/1.2.fq.expected | 72 +
test/bam2fq/1.stdout.expected | 0
test/bam2fq/2.1.fq.expected | 72 +
test/bam2fq/2.2.fq.expected | 72 +
test/bam2fq/2.s.fq.expected | 0
test/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 +
test/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 +
test/bam2fq/4.stdout.expected | 0
test/dat/.gitignore | 2 +
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/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 | 2 +-
test/dat/mpileup.2.sam | 2 +-
test/dat/mpileup.3.sam | 2 +-
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 +
test/merge/.gitignore | 1 -
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/test_bam_translate.c | 35 +-
test/merge/test_pretty_header.c | 87 -
test/merge/test_trans_tbl_init.c | 415 +-
test/mpileup/.gitignore | 1 +
test/mpileup/depth.reg | 39 +
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/16.out | 182 +-
test/mpileup/expected/19.out | 182 +-
test/mpileup/expected/20.out | 12 +-
test/mpileup/expected/21.out | 182 +-
test/mpileup/expected/22.out | 182 +-
test/mpileup/expected/23.out | 4 +-
test/mpileup/expected/24.out | 4 +-
test/mpileup/expected/25.out | 4 +-
test/mpileup/expected/33.out | 4 +-
test/mpileup/expected/34.out | 4 +-
test/mpileup/expected/4.out | 56 +-
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/76.out | 182 +-
test/mpileup/expected/77.out | 182 +-
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/d4_12.out | 60 +
test/mpileup/expected/d4_12b.out | 17 +
test/mpileup/expected/d4_12r.out | 12 +
test/mpileup/mpileup.reg | 6 +-
test/mpileup/regression.sh | 18 +-
test/mpileup/xx#depth1.sam | 6 +
test/mpileup/xx#depth2.sam | 6 +
test/mpileup/xx.bed | 2 +
test/mpileup/xx.bed2 | 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
test/quickcheck/all.expected | 2 +
.../1_view1.sam.expected} | 77 +-
test/reheader/1_view1.sam.expected.err | 0
.../2_view1.sam.expected} | 61 +-
test/reheader/2_view1.sam.expected.err | 0
.../3_view1.sam.expected} | 57 +-
test/reheader/3_view1.sam.expected.err | 0
test/reheader/hdr.sam | 28 +
test/split/test_count_rg.c | 9 +-
test/split/test_expand_format_string.c | 13 +-
test/split/test_filter_header_rg.c | 15 +-
test/split/test_parse_args.c | 32 +-
test/stat/1.stats.expected | 72 +-
test/stat/{5.stats.expected => 10.stats.expected} | 250 +-
test/stat/10_map_cigar.sam | 8 +
...ed => 10_map_cigar.sam_s1_a_1.expected.bamstat} | 72 +-
...ed => 10_map_cigar.sam_s1_b_1.expected.bamstat} | 72 +-
...ted => 1_map_cigar.sam_s1_a_1.expected.bamstat} | 72 +-
test/stat/2.stats.expected | 72 +-
test/stat/3.stats.expected | 2 +-
test/stat/4.stats.expected | 72 +-
test/stat/5.stats.expected | 72 +-
test/stat/6.stats.expected | 72 +-
test/stat/{5.stats.expected => 7.stats.expected} | 83 +-
test/stat/7_supp.sam | 6 +
test/stat/{6.stats.expected => 8.stats.expected} | 76 +-
test/stat/8_secondary.sam | 6 +
test/stat/{1.stats.expected => 9.stats.expected} | 72 +-
test/test.pl | 270 +-
214 files changed, 33277 insertions(+), 21972 deletions(-)
diff --cc debian/changelog
index de378b8,da9eccf..8204f4b
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,10 -1,32 +1,39 @@@
+ samtools (1.3-1) unstable; urgency=medium
+
+ [ Charles Plessy ]
+ 95c561d Merge tag '1.3' into debian/unstable
+
+ [ Sascha Steinbiss ]
+ * Team upload
+ * Adapt to new build system
+ * Use secure Vcs-Git
+ * Patch autoconf not to use make to extract version
+ * Clean up d/copyright
+ * Fix spelling
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Fri, 05 Feb 2016 08:32:40 +0000
+
+ samtools (1.2-4) unstable; urgency=medium
+
+ * Team upload
+ * Fix synopsis
+ * Fix Vcs-Browser
+ * Add lintian-override to document that the language extensions are used
+ internally
+ * Fix spelling
+ * Fix Mayhem issues caused by unlimited reads of gz input
+ Closes: #716199, #716197
+ * Provide some more manpages
+
+ -- Andreas Tille <tille at debian.org> Mon, 21 Dec 2015 13:49:05 +0100
+
+samtools (1.2-3~bpo8+1) jessie-backports; urgency=medium
+
+ * Team upload.
+ * Rebuild for jessie-backports.
+
+ -- Afif Elghraoui <afif at ghraoui.name> Sun, 04 Oct 2015 18:22:30 -0700
+
samtools (1.2-3) unstable; urgency=medium
* Team upload.
--
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