[med-svn] [htslib] branch develop updated (7994a4b -> c8ec7cb)

[Charles Plessy]

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plessy pushed a change to branch develop
in repository htslib.

      from  7994a4b   Merge branch 'bcftools+calling' into develop
      adds  1b2bc6e   Added decoding checks for the most obvious of sam parsing failures.
      adds  3f3758d   Removed old comment from earlier code.
      adds  3e18c41   Merge branch 'develop' of https://github.com/samtools/htslib into develop
      adds  bef7597   Further fixing of auxiliary tag decoding.
      adds  1344221   Added the ability to do samtools index on a CRAM file.
      adds  bc53b5d   Merge cram_index_build() from github.com/jkbonfield/htslib
      adds  923191c   l_qname is unsigned, so is always >= 0
      adds  bb71572   Ensure r is clearly always initialised [minor]
      adds  4e4501c   Use $(LDFLAGS) & $(LDLIBS) when linking shared objects
      adds  d6e1ad0   Use the exact type in malloc(N * sizeof(TYPE*)) etc
      adds  13b445b   Fix pointer arithmetic [minor]
      adds  06eeee1   Add HTS_NORETURN and annotate fail() as such
       new  6f5473a   Merge branch 'develop' into bcftools+calling
       new  715f5db   bcf_remove_alleles: Assume diploid genotypes if the ploidy cannot be determined, better to proceed than crash.
       new  18a5382   vcf: Update rlen on BCF output, this is important in BCF indexing, rlen is used as it is. Todo: also END should be checked with symbolic alleles
       new  c8ec7cb   Merge branch 'bcftools+calling' into develop

The 4 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          |    4 +-
 cram/cram_index.c |   85 +++++++++++++++++++++++++++++++++++++++
 cram/cram_index.h |   12 ++++++
 faidx.c           |    2 +-
 hts.c             |   14 +++----
 sam.c             |  114 +++++++++++++++++++++++++++++++++++++++++------------
 tbx.c             |    2 +-
 test/hfile.c      |   10 ++++-
 test/test_view.c  |   24 +++++++++--
 vcf.c             |    6 ++-
 vcfutils.c        |   22 +++++------
 11 files changed, 242 insertions(+), 53 deletions(-)

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