[med-svn] samtools 01/02: Merge tag '1.3' into debian/unstable
Charles Plessy
plessy at moszumanska.debian.org
Thu Dec 24 05:00:40 UTC 2015
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch debian/unstable
in repository samtools.
commit 95c561dc652f4d762d562504f52935270d585ab2
Merge: 4a5274b ed3191b
Author: Charles Plessy <plessy at debian.org>
Date: Thu Dec 24 13:55:19 2015 +0900
Merge tag '1.3' into debian/unstable
Samtools release 1.3: many improvements, fixes, new commands
* The obsolete "samtools sort in.bam out.prefix" usage has been removed.
If you are still using -f, -o, or out.prefix, convert to use -T PREFIX
and/or -o FILE instead. (#295, #349, #356, #418, PR #441; see also
discussions in #171, #213.)
* The "bamshuf" command has been renamed to "collate" (hence the term
bamshuf no longer appears in the documentation, though it still works
on the command line for compatibility with existing scripts).
* The mpileup command now outputs the unseen allele in VCF/BCF as <*>
rather than X or <X> as previously, and now has AD, ADF, ADR, INFO/AD,
INFO/ADF, INFO/ADR --output-tags annotations that largely supersede
the existing DV, DP4, DPR annotations.
* The mpileup command now applies BAQ calculations at all base positions,
regardless of which -l or -r options are used (previously with -l it was
not applied to the first few tens of bases of each chromosome, leading
to different mpileup results with -l vs. -r; #79, #125, #286, #407).
* Samtools now has a configure script which checks your build environment
and facilitates choosing which HTSlib to build against. See INSTALL
for details.
* Samtools's Makefile now fully supports the standard convention of
allowing CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS to be overridden as needed.
Previously it listened to $(LDLIBS) instead; if you were overriding
that, you should now override LIBS rather than LDLIBS.
* A new addreplacerg command that adds or alters @RG headers and RG:Z
record tags has been added.
* The rmdup command no longer immediately aborts (previously it always
aborted with "bam_get_library() not yet implemented"), but remains
not recommended for most use (#159, #252, #291, #393).
* Merging files with millions of headers now completes in a reasonable
amount of time (#337, #373, #419, #453; thanks to Nathan Weeks,
Chris Smowton, Martin Pollard, Rob Davies).
* Samtools index's optional index output path argument works again (#199).
* Fixed calmd, targetcut, and potential mpileup segfaults when given broken
alignments with POS far beyond the end of their reference sequences.
* If you have source code using bam_md.c's bam_fillmd1_core(), bam_cap_mapQ(),
or bam_prob_realn_core() functions, note that these now take an additional
ref_len parameter. (The versions named without "_core" are unchanged.)
* The tview command's colour scheme has been altered to be more suitable
for users with colour blindness (#457).
* Samtools depad command now handles CIGAR N operators and accepts
CRAM files (#201, #404).
* Samtools stats now outputs separate "N" and "other" columns in the
ACGT content per cycle section (#376).
* Added -a option to samtools depth to show all locations, including
zero depth sites (#374).
* New samtools dict command, which creates a sequence dictionary
(as used by Picard) from a FASTA reference file.
* Samtools stats --target-regions option works again.
* Added legacy API sam.h functions sam_index_load() and samfetch() providing
bam_fetch()-style iteration over either BAM or CRAM files. (In general
we recommend recoding against the htslib API directly, but this addition
may help existing libbam-using programs to be CRAM-enabled easily.)
* Fixed legacy API's samopen() to write headers only with "wh" when writing
SAM files. Plain "w" suppresses headers for SAM file output, but this
was broken in 1.2.
* "samtools fixmate - -" works in pipelines again; with 1.0 to 1.2,
this failed with "[bam_mating] cannot determine output format".
* Restored previous "samtools calmd -u" behaviour of writing compression
level 0 BAM files. Samtools 1.0 to 1.2 incorrectly wrote raw non-BGZF
BAM files, which cannot be read by most other tools. (Samtools commands
other than calmd were unaffected by this bug.)
* Restored bam_nt16_nt4_table[] to legacy API header bam.h.
* Fixed bugs #269, #305, #320, #328, #346, #353, #365, #392, #410, #445,
#462, #475, and #495.
.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 +-
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 +-
196 files changed, 32880 insertions(+), 21832 deletions(-)
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