[med-svn] [htslib] 06/11: Update upstream source from tag 'upstream/1.6'

[Andreas Tille]

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tille pushed a commit to branch master
in repository htslib.

commit 57b25277979c5ca6b38863d0f51e5222832a50b2
Merge: a2ccfa8 0b1efff
Author: Andreas Tille <tille at debian.org>
Date:   Mon Dec 11 14:18:17 2017 +0100

    Update upstream source from tag 'upstream/1.6'
    
    Update to upstream version '1.6'
    with Debian dir c44c4d262d49c67ceb10a485df8636b06c710141

 .appveyor.yml               |  43 +++++
 INSTALL                     |   6 +
 Makefile                    |  66 ++++---
 NEWS                        |  37 +++-
 bcf_sr_sort.c               |  38 ++--
 bcf_sr_sort.h               |   6 +-
 bgzf.c                      |  15 ++
 bgzip.c                     |  18 +-
 configure.ac                |  24 ++-
 cram/cram_codecs.c          |  75 ++++----
 cram/cram_decode.c          |  70 ++++---
 cram/cram_encode.c          |  62 +++----
 cram/cram_external.c        |   3 +-
 cram/cram_index.c           |   6 +-
 cram/cram_io.c              | 107 ++++++-----
 cram/cram_stats.c           |  10 +-
 cram/cram_structs.h         |   3 +-
 cram/mFILE.c                |   3 +-
 cram/mFILE.h                |   5 +
 cram/os.h                   |  24 +--
 cram/sam_header.c           |   6 +-
 errmod.c                    |   2 +
 hfile.c                     |  27 ++-
 hfile_internal.h            |   9 +-
 hfile_libcurl.c             | 433 ++++++++++++++++++++++++++++++++++++--------
 hfile_s3.c                  | 191 ++++++++++++-------
 hts.c                       | 121 ++++++++-----
 hts_internal.h              |   2 +-
 hts_os.c                    |  40 ++++
 htsfile.1                   |   2 +-
 htslib/bgzf.h               |   4 +
 htslib/hfile.h              |   4 +
 htslib/hts.h                |   5 +-
 htslib/hts_defs.h           |  18 ++
 htslib/hts_endian.h         |   6 +-
 htslib/hts_os.h             |  59 ++++++
 htslib/knetfile.h           |   2 +-
 htslib/ksort.h              |   8 +-
 htslib/regidx.h             |  10 +-
 htslib/sam.h                |   6 +-
 htslib/vcfutils.h           |   4 +-
 knetfile.c                  |   4 +-
 kstring.c                   |   2 +-
 multipart.c                 |  31 +++-
 realn.c                     |   2 +-
 regidx.c                    |  24 +--
 sam.c                       |  27 ++-
 synced_bcf_reader.c         |   4 +-
 tabix.1                     |   2 +-
 tabix.c                     |   4 +-
 test/compare_sam.pl         |   2 +
 test/hfile.c                |   4 +-
 test/sam.c                  |   2 +-
 test/tabix/test-tabix.sh    |   7 +-
 test/test-bcf-sr.c          |  12 +-
 test/test-bcf-sr.pl         |   6 +-
 test/test-bcf-translate.c   | 192 ++++++++++++++++++++
 test/test-bcf-translate.out |  18 ++
 test/test-regidx.c          |   8 +-
 test/test.pl                |  92 +++++++---
 test/test_bgzf.c            |  19 +-
 test/test_view.c            |  55 ++++--
 vcf.c                       |  43 +++--
 vcfutils.c                  |   2 +-
 version.sh                  |  31 ++++
 win/rand.c                  |  98 ++++++++++
 win/rand.h                  |  24 +++
 67 files changed, 1726 insertions(+), 569 deletions(-)

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