[med-svn] [htslib] branch master updated (87141ea -> 406c7d0)

[Andreas Tille]

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

tille pushed a change to branch master
in repository htslib.

      from  87141ea   Release 1.3: plugins, libcurl, CRAM v3.0, many bug fixes
       new  c72ae90   Merge version number bump and NEWS file from master
       new  ae4c86a   Avoid POSIX Issue 7-specific errno value [minor]
       new  0382edf   Use getopt.h's descriptive constants in long options array
       new  70bfd53   Happy New Year
       new  df4a80e   Free all in-flight pileups in bam_plp_destroy()
       new  a6e4883   Ignore .exe and .dSYM extensions
       new  4c0c448   Clarify misleading code formatting [minor]
       new  92654ef   Fixed crash in CRAM generation with cigar ops > 2^27 in size.
       new  c789bed   Force detached read-pairs if they span references.
       new  f1327a7   Add AC_SYS_LARGEFILE test so 32-bit systems can access 2GiB+ files
       new  72cb247   allow spaces in vcf header lines
       new  3fac82b   remove code duplication from thread_pool.c
       new  406c7d0   Squash a duplicated conditional into a single one.

The 13 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            |  2 ++
 Makefile              | 20 ++++++++---------
 bgzip.c               | 32 +++++++++++++++-----------
 config.h.in           | 11 +++++++++
 configure.ac          |  2 ++
 cram/cram_encode.c    | 11 +++++----
 cram/thread_pool.c    | 62 +++------------------------------------------------
 hfile_libcurl.c       |  4 ----
 htsfile.c             |  4 ++--
 kfunc.c               |  2 ++
 knetfile.c            |  2 ++
 kstring.c             |  2 ++
 sam.c                 | 55 +++++++++++++++++++++++----------------------
 tabix.c               | 44 ++++++++++++++++++++----------------
 test/fieldarith.c     |  2 ++
 test/hfile.c          |  2 ++
 test/sam.c            |  2 ++
 test/test-regidx.c    |  2 ++
 test/test-vcf-api.c   |  2 ++
 test/test-vcf-sweep.c |  2 ++
 test/test_view.c      |  2 ++
 vcf.c                 | 16 +++++++++----
 22 files changed, 141 insertions(+), 142 deletions(-)

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