[med-svn] samtools branch develop updated (256e657 -> 85f1c53)

[Charles Plessy]

This is an automated email from the git hooks/post-receive script.

plessy pushed a change to branch develop
in repository samtools.

      from  256e657   Fix CRLF-style line termination
       new  d0ebd20   Free the outer struct last
       new  51467d0   Fix compilation with the Clang compiler.
       new  4ce9296   Fix type mismatches between types in sizeof() in malloc/calloc/realloc calls. This generates a warning in the clang analyzer, designed to catch incorrectly sized memory allocations.
       new  92a1cb3   Merge branch master of git://github.com/leecbaker/samtools
       new  bb313d1   mpileup: Allow up to five alleles (N,A,C,G,T)
       new  399b283   New "flags" command plus moved filtering from htslib/pileup to BAM reading callbacks
       new  c1e1fa1   On behalf of Peter Chines, test that filter mask replaces (not just adds to) default mask
       new  5d5458f   mpileup: Disabled CDF version of MWU annotations and made it optional at compile time
       new  b140662   Use floor(x+0.5) instead of C99's round()
       new  ab349a2   Fixed GCC section so that read cycle column begins with 1 instead of 0.
       new  da69b48   Merge pull request #95 from wtsi-hgi/develop
       new  6007ab1   Rearrange (so tags can see main_depth()) [minor]
       new  4a18e5f   Remove incorrect parameter check
       new  af54972   Merge branch 'develop' into calling
       new  58a95a6   Merge branch 'calling' into develop
       new  9a39e01   plot-bamstats: Skip generation of empty GCD graphs
       new  eabd608   Adds tests for usage message for samtools and all subcommands
       new  6f27dcd   Modifies test.pl so that it exits with non-zero status if any tests fail.
       new  f11d48b   Fail when tests fail
       new  9e78230   stats: Fix of mismmatch-per-cycle calculation in presence of hard-clipped reads
       new  d141b26   Usage message tweaks to satisfy test/test.pl's test_usage()
       new  d09cf94   Moved khash_utils.h into htslib
       new  c56835b   Updated the khash_utils.h dependency
       new  85f1c53   stats: realloc buffers in MPC calculation if necessary, unclipped length can be bigger seq_len

The 24 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                |   3 +
 Makefile               |   5 +-
 bam2bcf.c              |  50 +--
 bam2bcf.h              |   2 +-
 bam2bcf_indel.c        |   2 +-
 bam2depth.c            |  30 +-
 bam_flags.c            |  43 +++
 bam_index.c            |   4 +-
 bam_lpileup.c          |   2 +-
 bam_md.c               |   2 +-
 bam_plcmd.c            |  95 ++---
 bam_sort.c             |   4 +-
 bamshuf.c              |   6 +-
 bamtk.c                |   5 +-
 bedcov.c               |  19 +-
 cut_target.c           |  27 +-
 errmod.c               |   1 -
 faidx.c                |   2 +-
 khash_utils.h          |  81 ----
 kprobaln.c             |   4 +-
 misc/plot-bamstats     |   2 +-
 phase.c                |  29 +-
 sam_header.c           |   2 +-
 sample.c               |   2 +-
 samtools.h             |   9 +
 stats.c                |  38 +-
 test/dat/mpileup.out.2 | 976 ++++++++++++++++++++++++-------------------------
 test/dat/mpileup.out.3 |  11 +
 test/test.pl           |  94 ++++-
 29 files changed, 841 insertions(+), 709 deletions(-)
 create mode 100644 bam_flags.c
 delete mode 100644 khash_utils.h
 create mode 100644 test/dat/mpileup.out.3

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/samtools.git