[med-svn] samtools branch master updated (ed3191b -> 897c002)
Charles Plessy
plessy at moszumanska.debian.org
Tue Apr 26 11:45:18 UTC 2016
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch master
in repository samtools.
from ed3191b Samtools release 1.3: many improvements, bug fixes, and new commands
adds 493b1ca Merge version number bump and NEWS file from master
adds 3c197df set a matrix.include for all os options
adds befba2e Include <unistd.h> for isatty() [minor]
adds de68be6 Happy New Year
adds 664cc5f Fixed a known-failure (mpileup -d) issue; now passes.
adds 74a3e0a Add #include <config.h> to all *.c source files [minor]
adds 59ab663 Fix -O option for reads without OQ tag
adds 03a6bc5 Improved documentation of mpileup -l vs -r.
adds a5cdff6 Remove gcc build on OSX
adds c613147 Tidied up the mpileup.[123].sam files to not use RNAME fields with no @SQ records.
adds 23b91e8 Improved documentation of how mpileup -d/-L work.
adds c152c47 Fix typo.
adds 3d792ba Merge pull request #525 from samtools/mpileup_depth
adds bf85440 Grammar fix.
adds dae373b Ignore .exe extension; don't force core and ~ ignorance
adds ac5b8e7 Use AC_SYS_LARGEFILE configure test instead of -D_FILE_OFFSET_BITS=64
adds ce44eb3 Add check on hts_close to quickcheck
adds 6e3ac27 Fixed bam_get_library() crash.
adds 2dcdd62 Adds a usage note to `samtools quickcheck`
adds d49c73b Reformat "Notes" in long -? usage output
adds 3c8a69f Fix samtools merge -n usage doc [minor]
adds f63a282 Recreate missing @SQ header from BAM binary header
adds cd7e005 Fix indentation [minor]
adds 3baa47b manpage: fix typo [minor]
adds 09dda53 fastx: only show relevant usage options for fasta/fastq commands
adds 3312225 Merge fasta usage message improvements (PR #555)
adds 6994f30 Check sam_read1() return value correctly
adds de96bfb Fix warnings from adding HTS_RESULT_USED to htslib prototypes.
adds 0e260d9 Ensure fp is always closed in write_buffer.
adds 24d3235 Use print_error_errno() where appropriate
adds 1152881 Various tidying up and segfault fixes
adds f6db782 Merge error checking improvements (PR #467)
adds 72679e1 Fix \r\n thinko [minor]
adds 9968e4c Make samtools sort notice when it clobbers other sorts
adds 5f53e3c Propagate errno from sort worker threads
adds b5047ab Removed a (harmless) perl warning from test harness.
adds 8471a0d Add `@CO` headers only once when merging sort temp files
adds 5839af6 Write sort's temporary files alongside the *output* file
adds 897c002 Samtools release 1.3.1: bug fixes, notably sort temporary file fixes
No new revisions were added by this update.
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 +
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 +
76 files changed, 1233 insertions(+), 472 deletions(-)
create mode 100644 test/quickcheck/5.quickcheck.truncated.cram
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