[med-svn] samtools branch debian/unstable updated (096bc41 -> 0de58f7)
Charles Plessy
plessy at moszumanska.debian.org
Tue Apr 26 11:43:29 UTC 2016
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch debian/unstable
in repository samtools.
from 096bc41 dch -r
new 493b1ca Merge version number bump and NEWS file from master
new 3c197df set a matrix.include for all os options
new befba2e Include <unistd.h> for isatty() [minor]
new de68be6 Happy New Year
new 664cc5f Fixed a known-failure (mpileup -d) issue; now passes.
new 74a3e0a Add #include <config.h> to all *.c source files [minor]
new 59ab663 Fix -O option for reads without OQ tag
new 03a6bc5 Improved documentation of mpileup -l vs -r.
new a5cdff6 Remove gcc build on OSX
new c613147 Tidied up the mpileup.[123].sam files to not use RNAME fields with no @SQ records.
new 23b91e8 Improved documentation of how mpileup -d/-L work.
new c152c47 Fix typo.
new 3d792ba Merge pull request #525 from samtools/mpileup_depth
new bf85440 Grammar fix.
new dae373b Ignore .exe extension; don't force core and ~ ignorance
new ac5b8e7 Use AC_SYS_LARGEFILE configure test instead of -D_FILE_OFFSET_BITS=64
new ce44eb3 Add check on hts_close to quickcheck
new 6e3ac27 Fixed bam_get_library() crash.
new 2dcdd62 Adds a usage note to `samtools quickcheck`
new d49c73b Reformat "Notes" in long -? usage output
new 3c8a69f Fix samtools merge -n usage doc [minor]
new f63a282 Recreate missing @SQ header from BAM binary header
new cd7e005 Fix indentation [minor]
new 3baa47b manpage: fix typo [minor]
new 09dda53 fastx: only show relevant usage options for fasta/fastq commands
new 3312225 Merge fasta usage message improvements (PR #555)
new 6994f30 Check sam_read1() return value correctly
new de96bfb Fix warnings from adding HTS_RESULT_USED to htslib prototypes.
new 0e260d9 Ensure fp is always closed in write_buffer.
new 24d3235 Use print_error_errno() where appropriate
new 1152881 Various tidying up and segfault fixes
new f6db782 Merge error checking improvements (PR #467)
new 72679e1 Fix \r\n thinko [minor]
new 9968e4c Make samtools sort notice when it clobbers other sorts
new 5f53e3c Propagate errno from sort worker threads
new b5047ab Removed a (harmless) perl warning from test harness.
new 8471a0d Add `@CO` headers only once when merging sort temp files
new 5839af6 Write sort's temporary files alongside the *output* file
new 897c002 Samtools release 1.3.1: bug fixes, notably sort temporary file fixes
new 0c961b2 Merge tag '1.3.1' into debian/unstable
new 0de58f7 New upstream release; no new copyright nor license notice.
The 41 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 | 5 +-
.travis.yml | 16 +-
Makefile | 122 ++++++-------
NEWS | 41 +++++
README | 6 +-
bam.c | 18 +-
bam.h | 9 +-
bam2bcf.c | 2 +
bam2bcf_indel.c | 2 +
bam2depth.c | 2 +
bam_addrprg.c | 2 +
bam_aux.c | 2 +
bam_cat.c | 93 +++++++---
bam_color.c | 2 +
bam_flags.c | 2 +
bam_import.c | 2 +
bam_index.c | 2 +
bam_lpileup.c | 2 +
bam_mate.c | 80 ++++++---
bam_md.c | 64 +++++--
bam_plbuf.c | 2 +
bam_plcmd.c | 6 +-
bam_quickcheck.c | 22 ++-
bam_reheader.c | 64 +++++--
bam_rmdup.c | 109 +++++++++---
bam_rmdupse.c | 64 +++++--
bam_sort.c | 267 ++++++++++++++++++++--------
bam_split.c | 88 +++++----
bam_stat.c | 2 +
bam_tview.c | 2 +
bam_tview_html.c | 2 +
bamshuf.c | 141 ++++++++++++---
bamtk.c | 6 +-
bedcov.c | 2 +
bedidx.c | 2 +
config.h.in | 11 ++
configure.ac | 2 +
cut_target.c | 2 +
debian/changelog | 6 +
debian/copyright | 4 +-
dict.c | 5 +-
errmod.c | 2 +
faidx.c | 6 +-
kprobaln.c | 2 +
misc/ace2sam.c | 2 +
misc/maq2sam.c | 2 +
misc/md5fa.c | 2 +
misc/md5sum-lite.c | 2 +
misc/wgsim.1 | 2 +-
misc/wgsim.c | 2 +
padding.c | 42 +++--
phase.c | 89 +++++++---
sam.c | 18 +-
sam_header.c | 2 +
sam_opts.c | 2 +
sam_view.c | 84 +++++----
sample.c | 2 +
samtools.1 | 54 ++++--
stats.c | 2 +
stats_isize.c | 2 +
test/dat/mpileup.1.sam | 42 ++---
test/dat/mpileup.2.sam | 8 +-
test/dat/mpileup.3.sam | 12 +-
test/dat/view.001.sam | 2 +-
test/merge/test_bam_translate.c | 2 +
test/merge/test_rtrans_build.c | 2 +
test/merge/test_trans_tbl_init.c | 16 +-
test/mpileup/mpileup.reg | 2 +-
test/quickcheck/5.quickcheck.truncated.cram | Bin 0 -> 11960 bytes
test/quickcheck/all.expected | 1 +
test/split/test_count_rg.c | 2 +
test/split/test_expand_format_string.c | 2 +
test/split/test_filter_header_rg.c | 2 +
test/split/test_parse_args.c | 2 +
test/test.c | 2 +
test/test.pl | 12 +-
test/tview/test_get_rg_sample.c | 2 +
test/vcf-miniview.c | 2 +
78 files changed, 1241 insertions(+), 474 deletions(-)
create mode 100644 test/quickcheck/5.quickcheck.truncated.cram
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