[med-svn] [htslib] branch debian/unstable updated (8210cf3 -> 15eac2b)

[Charles Plessy]

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plessy pushed a change to branch debian/unstable
in repository htslib.

      from  8210cf3   htslib (1.0-2) unstable; urgency=medium
      adds  1f1e3f6   Merge version number and soname bump from master
      adds  1903fd4   Set explicit REF_PATH to make tests self-contained
      adds  b6934ff   Force nul termination of the kstr holding the CRAM index so that sscanf doesn't attempt to check beyond the bounds of the string memory.
      adds  3fe4cf8   Ensure hand-made kstring is NUL-terminated
      adds  89e267a   Ensure items to be installed are built and up-to-date
      adds  546bfcb   vcf: Output "." not "nan" in scalar INFO fields
      adds  6af42b1   vcf: separate header lookup from field getter
      adds  410cf54   Merge pull request #127 from broadinstitute/broad_header_lookup
      adds  6c6c75b   Make hts_idx_push no longer return 0 after the first unmapped read. This fixes idxstats
      adds  ebbad4b   Merge pull request #124 from dpryan79/develop
      adds  830ea73   faidx API to access sequence stats
      adds  20558bc   bcf_get_info_values: Return correct INT8 and INT16 missing value
      adds  cf4eab0   Minor documentation update
      adds  575be14   Correct reference lines
      adds  3f30883   Removed the .gz, .Z, .sz etc suffix searching when looking for reference files.
      adds  d25c678   Remove the | from the default REF_PATH.
      adds  fa6011a   bgzf: Write plain gzip files if is_gzip set
      adds  dcefe5b   Don't install libhts.so.1 as a man page
      adds  5a0ee03   Release 1.1: various minor bug fixes
       new  1357fbd   Merge tag '1.1' into debian/unstable
       new  be365db   New upstream release, no new copyright nor license notice.
       new  87549cd   Updated symbols file.
       new  873ea9b   Removed orphan paragraph.
       new  49de2b9   Allow parallel build.
       new  7fe3bb5   Normalise source package control file (VCS-Browser, Pre-Depends).
       new  0e5e9e6   Conforms to Policy 3.9.6.
       new  15eac2b   htslib (1.1-1) unstable; urgency=medium

The 8 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               |  12 +++--
 README.md              |   4 +-
 bgzf.c                 |  33 +++++++++++-
 cram/cram_index.c      |   2 +
 cram/cram_io.c         |   2 +-
 cram/open_trace_file.c |  60 ++++++++++------------
 debian/changelog       |  11 ++++
 debian/control         |   9 ++--
 debian/copyright       |  28 +----------
 debian/libhts1.symbols |   7 ++-
 debian/rules           |   2 +-
 faidx.c                |  12 ++++-
 hts.c                  |   4 --
 htslib/faidx.h         |  15 ++++++
 htslib/khash_str2int.h |   6 ++-
 htslib/vcf.h           |  11 ++++
 tabix.1                |   2 +-
 vcf.c                  | 134 +++++++++++++++++++++++++++++++------------------
 18 files changed, 220 insertions(+), 134 deletions(-)

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