[med-svn] samtools branch debian/unstable updated (32563cc -> ae32134)

[Andreas Tille]

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

tille pushed a change to branch debian/unstable
in repository samtools.

      from  32563cc   Rebuild against properly named libhts which had a soname change
      adds  a230f81   Merge version number bump and NEWS file from master
       new  f5120be   Add "-b <bam.fofn>" flag to samtools cat.
       new  ea2cbba   Document the "-b bam-list" option to samtools cat.
       new  ea171c4   Remove two tiny memory leaks in samtools merge.
       new  692e058   Cram lossy names (#543)
       new  54a91c1   Implemented tab completion
       new  fd02fc5   Dynamically generate options
       new  2485345   Cleaned up subcommand name retrieval
       new  193eecb   Changed '==' to '-eq'
       new  0bfa8d4   Captialised variables for consistency
       new  2389a31   Fixed slight bug in default behaviour
       new  86dddab   Merge pull request #560 from george-hall-wtsi/tab_completion
       new  a22f979   Update bam_tview_curses.c
       new  90b995f   Merge pull request to enable large vertical movement in tview (#257)
       new  8c20354   Option -G to exclude based on a set of bits.
       new  b1b6717   Improved wording of usage and updated man page.
       new  8b779df   Another change to view/bam2fq filtering wording.
       new  1129520   Improvements for C99/XOPEN compliance.
       new  6485200   Switch to -lpthread instead of -pthread for linking.
       new  6d612fe   Added option to produce fastq files from BC or other tags
       new  d7b0234   Output CRAM as temporary sort format iff there are more than 64k cigar ops.
       new  0aa9fab   Bam2fq comment improvements (no code changed).
       new  f13cf4a   NEWS update.
       new  8f8600a   Release 1.4.1: summary
       new  2ba4095   Merge tag '1.4.1' into debian/unstable
       new  dd7a117   New upstream version
       new  ae32134   Close bug, upload to unstable

The 26 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:
 Makefile                                         |  21 +-
 NEWS                                             |  27 +-
 README                                           |   6 +-
 bam.h                                            |   2 +-
 bam2bcf_indel.c                                  |  14 +-
 bam_cat.c                                        |  60 +++-
 bam_plcmd.c                                      |   1 +
 bam_reheader.c                                   |   4 +-
 bam_sort.c                                       |  55 +--
 bam_tview_curses.c                               |   2 +
 debian/changelog                                 |   7 +
 misc/samtools_tab_completion                     |  77 ++++
 misc/wgsim.1                                     |   2 +-
 sam.h                                            |   2 +-
 sam_view.c                                       | 433 ++++++++++++++++++-----
 samtools.1                                       | 119 ++++++-
 stats.c                                          |   2 +-
 test/bam2fq/{4.1.fq.expected => 5.1.fq.expected} |  34 +-
 test/bam2fq/{4.2.fq.expected => 5.2.fq.expected} |  34 +-
 test/bam2fq/{4.s.fq.expected => 5.s.fq.expected} |   4 +-
 test/bam2fq/bc.fq.expected                       |  12 +
 test/bam2fq/bc_split.fq.expected                 |  12 +
 test/dat/{bam2fq.003.sam => bam2fq.004.sam}      |   2 +-
 test/dat/{bam2fq.003.sam => bam2fq.005.sam}      |   8 +-
 test/test.pl                                     |   5 +-
 25 files changed, 751 insertions(+), 194 deletions(-)
 create mode 100644 misc/samtools_tab_completion
 copy test/bam2fq/{4.1.fq.expected => 5.1.fq.expected} (58%)
 copy test/bam2fq/{4.2.fq.expected => 5.2.fq.expected} (58%)
 copy test/bam2fq/{4.s.fq.expected => 5.s.fq.expected} (58%)
 create mode 100644 test/bam2fq/bc.fq.expected
 create mode 100644 test/bam2fq/bc_split.fq.expected
 copy test/dat/{bam2fq.003.sam => bam2fq.004.sam} (98%)
 copy test/dat/{bam2fq.003.sam => bam2fq.005.sam} (89%)

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