[med-svn] samtools branch debian/unstable updated (6ce5671 -> c789e05)
Charles Plessy
plessy at moszumanska.debian.org
Mon Jun 15 13:03:49 UTC 2015
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch debian/unstable
in repository samtools.
from 6ce5671 Make autopkg test depend on tabix.
adds 281bf0a Recanonicalise regression.sh whitespace -- USE -b/-w TO DIFF/BLAME
adds 9c4099f Set output file threading only if there is an output file
adds 29395a5 Fixed a buffer overflow when dealing with cigar strings ending with a deletion.
adds 089ecbe Improved fix to mpileup. The previous one just skipped bases where we have no quality. This still includes them in the pileup, but with 0 qual instead.
adds 418fc0c Also fix buffer overrun on data where the sequence is "*".
adds 2fac99b Fixed up test data, now that it correctly outputs "n" instead.
adds 056ae75 Merge pull request #306 from jkbonfield/mpileup-fix
adds 59c56f0 Man page formatting fixes
adds 5ac61a2 Write failure messages to stderr
adds 6f1c154 Maintain HEAP_EMPTY invariant when an input is empty
adds d2e8d7a Avoid using htsFile is_foo bits directly
adds 4580150 Reflect changes in htslib API
adds 01465e8 Fix typo in 'samtools flagstats' output
adds 6c17071 Added a test for specifying the reference via samtools -T. This appeared to work in our previous tests, but did not due to the code sneakily reverting to the @SQ UR: field instead.
adds c02491f Merge origin/develop, prefering avoiding using htsFile internals
adds 4a2320a Avoid "my" variable redeclaration [minor]
adds a25229a Prevent warnings when compiling on a 32-bit host [minor]
adds dc1f438 stats: Calculate mismatches per cycle for unclipped length
adds 6b249e2 Merge branch 'develop' of github.com:samtools/samtools into develop
adds c61d8d1 Merge origin/develop into develop
adds bca67a9 Convert bam2bcf_indel.c to use the htslib API directly
adds 9e3bbcf Update comment documentation for bam_mate
adds 19c9f67 Remove unused kaln.c, kaln.h global aligner
adds 29b0367 Replace cryptic 'minQLen' with real description
adds 8dd3761 Use bam_init1/bam_destroy1 instead of creating/destroying by hand
adds 3fdca5b Make samtools merge work with SAM input files
adds 5d6a1e3 Avoid crashing on unopenable files [minor]
adds 7f47a7c Parse mpileup -r region against the right file's headers
adds f3f3d6d Large chromosome test case now passes
adds c06f698 Add a few comments to pileup and errmod code, move some existing ones to slightly better positions.
adds 311926c Fix typo.
adds 5c49bf9 Fixed samtools flagstat to use the samFile (htsFile) API instead of bamFile. This means it can now work on sam, bam and cram formats instead of only bam.
adds 2a40f2e Switch from hts_close to sam_close, for consistency (they're the same thing underneath).
adds 2bcfffd Added various hts_set_opt calls to set the CRAM_OPT_REQUIRED_FIELDS and CRAM_OPT_DECODE_MD options to avoid doing unnecessary decoding work.
adds a513827 Merge pull request #299 from jkbonfield/cram3
adds 581e707 bamtk.c requires only hts_version(), not <bam.h>
adds 446aae0 Happy New Year
adds e2ce81d Added checks to sam_hdr_write() return value.
adds c5df8be Added 'insert size' to the head of the IS section
adds 0cc7b47 Merge pull request #342 from nathanhaigh/develop
adds 8f50332 Documentation: Updated REF_CACHE location details.
adds 255f97d Release 1.2: various bug fixes
new a5f28a0 Merge tag '1.2' into debian/unstable
new 71af052 New upstream release ; no new copyright notice nor license term.
new 712a216 Corrected syntax.
new 23e44a4 Removed fix_coverage_cap.patch, obsoleted by -d option.
new 1091aab Refreshed fuzzy patches.
new c542e84 Build-depend on libhts-dev 1.2.
new c789e05 Current changelog.
The 7 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:
INSTALL | 2 +-
Makefile | 13 +-
NEWS | 16 +
README | 23 ++
bam.h | 2 +-
bam2bcf_indel.c | 40 +-
bam2depth.c | 16 +-
bam_mate.c | 3 +-
bam_md.c | 1 -
bam_plcmd.c | 63 ++-
bam_sort.c | 61 +--
bam_stat.c | 40 +-
bamtk.c | 6 +-
debian/changelog | 6 +-
debian/control | 4 +-
debian/copyright | 4 +-
debian/patches/dynamic-build.patch | 8 +-
debian/patches/fix_coverage_cap.patch | 13 -
debian/patches/fix_segfault_with_small_ref.patch | 16 +-
debian/patches/series | 2 +-
errmod.c | 7 +-
kaln.c | 486 -----------------------
kaln.h | 67 ----
misc/ace2sam.c | 2 +-
misc/plot-bamstats | 2 +-
misc/seq_cache_populate.pl | 5 +
padding.c | 2 +-
sam.c | 8 +-
sam.h | 3 +-
sam_view.c | 27 +-
samtools.1 | 36 +-
stats.c | 21 +-
test/merge/test_rtrans_build.c | 4 +-
test/merge/test_trans_tbl_init.c | 2 +-
test/mpileup/expected/9.out | 20 +-
test/mpileup/regression.sh | 125 +++---
test/stat/1.stats.expected | 2 +-
test/stat/2.stats.expected | 2 +-
test/stat/3.stats.expected | 2 +-
test/stat/4.stats.expected | 2 +-
test/stat/5.stats.expected | 2 +-
test/stat/6.stats.expected | 2 +-
test/test.pl | 41 +-
43 files changed, 415 insertions(+), 794 deletions(-)
delete mode 100644 debian/patches/fix_coverage_cap.patch
delete mode 100644 kaln.c
delete mode 100644 kaln.h
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