[med-svn] samtools branch debian/unstable updated (1f661b2 -> d12ab1e)
Charles Plessy
plessy at moszumanska.debian.org
Wed Sep 24 23:24:46 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch debian/unstable
in repository samtools.
from 1f661b2 Current changelog.
adds 2192dda Merge version number bump from master branch
adds e3d4eee fix DPR annotation
adds a0254ac No need to initialise array anyway
adds c8e1a2b stats: Compute checksum for names/seqs/quals
adds 6099d57 Merge stats checksums
adds f5288ca Replace bcftools+bcf_filter.sh with new vcf-miniview
adds d0e4a6c Insulate test case from $GREP_OPTIONS
adds 9579135 Update expected output with symbolic "<X>" alleles
adds a7e257d Update QS values in expected output, and don't truncate them
adds 258b4e6 Modified the mpileup tests to have local copies of appropriate reference sequences. All other tests already had this (but accidentally escaped in some circumstances).
adds eeb4b22 Merge minimal MD5 reference area for mpileup tests
new f62826f Clean after fix in e3d4eee
new 57e71e7 Fix fixmates for supplementary reads
new a9d452c fixes #271
new 904f1f5 fixes #272
new f4b6333 Merge #! fixes to misc/ scripts
new faf4dd6 Formatting fixes for better grinding into HTML
new 7d678aa Recanonicalise test/test.pl whitespace -- USE -b/-w TO DIFF/BLAME
new bc00bde mpileup: conform to VCFv4.2 spec, version string should be quoted
new 1f8267d Recanonicalise padding.c whitespace -- USE -b/-w TO DIFF/BLAME
new 7b5a9ea Reduce use of abort, remove assert(fp), pass one string to fprintf not multicall
new 20817a8 Merge abort/assert reduction (PR #290)
new a4ca344 Fixmates ct fix
new f2b42d4 Merge fixmate ct improvements (PR #292)
new 8c908df Remove view -Q qual_scale option
new b67461f Free the kstring allocated in bam_fillmd1_core in all cases
new ef00bd8 Describe compression level settings
new 7fe3838 Use hash table to merge reference sequence headers
new 68ca977 Release 1.1: bug fixes
new c448d48 Merge tag '1.1' into debian/unstable
new db22ee9 Merge version number bump from master branch
new b7c4b4d Ensure usage tests have a terminal on stdin
new d12ab1e Merge branch 'develop' into debian/unstable
The 22 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.gitignore | 1 +
Makefile | 20 +-
NEWS | 15 +
bam.c | 1 -
bam.h | 2 +-
bam2bcf.c | 11 +-
bam2bcf.h | 2 +
bam_mate.c | 43 +-
bam_md.c | 9 +-
bam_plbuf.c | 1 -
bam_plcmd.c | 34 +-
bam_sort.c | 31 +-
bam_split.c | 1 -
bam_stat.c | 20 +-
bam_tview.c | 17 +-
bamshuf.c | 36 +-
bamtk.c | 1 -
misc/blast2sam.pl | 2 +-
misc/bowtie2sam.pl | 2 +-
misc/interpolate_sam.pl | 3 +-
misc/novo2sam.pl | 6 +-
misc/psl2sam.pl | 2 +-
misc/sam2vcf.pl | 2 +-
misc/samtools.pl | 2 +-
misc/seq_cache_populate.pl | 2 +-
misc/soap2sam.pl | 2 +-
misc/varfilter.py | 2 +-
misc/wgsim_eval.pl | 2 +-
misc/zoom2sam.pl | 2 +-
padding.c | 16 +-
sam_view.c | 18 +-
samtools.1 | 73 +-
stats.c | 26 +
test/dat/mpileup.out.2 | 2 +-
test/dat/mpileup.out.4 | 527 ++
test/fixmate/2_isize_overflow.sam.expected | 6 +-
test/fixmate/3_reverse_read_pp_lt.sam.expected | 2 +-
test/fixmate/4_reverse_read_pp_equal.sam.expected | 2 +-
.../{4_reverse_read_pp_equal.sam => 5_ct.sam} | 0
...ead_pp_equal.sam.expected => 5_ct.sam.expected} | 0
...read_pp_equal.sam.expected => 6_ct_replace.sam} | 4 +-
...qual.sam.expected => 6_ct_replace.sam.expected} | 0
test/mpileup/bcf_filter.sh | 29 -
test/mpileup/expected/48.out | 8206 ++++++++++----------
test/mpileup/expected/49.out | 8206 ++++++++++----------
test/mpileup/expected/50.out | 8206 ++++++++++----------
test/mpileup/expected/51.out | 8206 ++++++++++----------
test/mpileup/expected/53.out | 2 +-
test/mpileup/expected/54.out | 2 +-
test/mpileup/expected/55.out | 2 +-
test/mpileup/expected/56.out | 2 +-
test/mpileup/expected/57.out | 2 +-
test/mpileup/expected/58.out | 2 +-
test/mpileup/expected/59.out | 2 +-
test/mpileup/expected/61.out | 2 +-
test/mpileup/expected/63.out | 2 +-
test/mpileup/expected/65.out | 2 +-
test/mpileup/expected/67.out | 2 +-
test/mpileup/expected/70.out | 2 +-
test/mpileup/expected/71.out | 2 +-
test/mpileup/expected/73.out | 2 +-
test/mpileup/expected/75.out | 2 +-
test/mpileup/md5/02099b2aad2cfe707759353724fb40ae | 1 +
test/mpileup/md5/0d4dfc45807d6a11439e858605cb364d | 1 +
test/mpileup/md5/351f64d4f4f9ddd45b35336ad97aa6de | 1 +
test/mpileup/md5/6ec590eb82c361a61e6baabce20109bc | 1 +
test/mpileup/md5/6f60cdf4c739651ae72d53e2e94825c1 | 1 +
test/mpileup/md5/73d180d5cb3860a2713927b6812eab0e | 1 +
test/mpileup/mpileup.reg | 60 +-
test/mpileup/regression.sh | 12 +-
test/stat/1.stats.expected | 3 +
test/stat/2.stats.expected | 3 +
test/stat/3.stats.expected | 3 +
test/stat/4.stats.expected | 3 +
test/stat/5.stats.expected | 3 +
test/stat/6.stats.expected | 3 +
test/test.pl | 1484 ++--
test/vcf-miniview.c | 115 +
78 files changed, 18135 insertions(+), 17393 deletions(-)
create mode 100644 test/dat/mpileup.out.4
copy test/fixmate/{4_reverse_read_pp_equal.sam => 5_ct.sam} (100%)
copy test/fixmate/{4_reverse_read_pp_equal.sam.expected => 5_ct.sam.expected} (100%)
copy test/fixmate/{4_reverse_read_pp_equal.sam.expected => 6_ct_replace.sam} (95%)
copy test/fixmate/{4_reverse_read_pp_equal.sam.expected => 6_ct_replace.sam.expected} (100%)
delete mode 100755 test/mpileup/bcf_filter.sh
create mode 100644 test/mpileup/md5/02099b2aad2cfe707759353724fb40ae
create mode 100644 test/mpileup/md5/0d4dfc45807d6a11439e858605cb364d
create mode 100644 test/mpileup/md5/351f64d4f4f9ddd45b35336ad97aa6de
create mode 100644 test/mpileup/md5/6ec590eb82c361a61e6baabce20109bc
create mode 100644 test/mpileup/md5/6f60cdf4c739651ae72d53e2e94825c1
create mode 100644 test/mpileup/md5/73d180d5cb3860a2713927b6812eab0e
create mode 100644 test/vcf-miniview.c
--
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