[med-svn] [htslib] branch master updated (30646ba -> 9b683f1)

[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  30646ba   Upload to unstable after verifying that bcftools does not need these htslib*.mk fragments
       new  29f0445   Start using default Debian Med repository layout
       new  a7cd55f   New upstream version 1.5
       new  05e80df   Update upstream source from tag 'upstream/1.5'
       new  a2ccfa8   Switch to default Debian Med repository layout
       new  0b1efff   New upstream version 1.6
       new  57b2527   Update upstream source from tag 'upstream/1.6'
       new  0876f84   New upstream version
       new  86a38d1   Remove debian/patches/literal_version.patch since upstream stops running make to get the version number
       new  02927ed   Refresh patches
       new  ca55c40   Update symbols file
       new  9b683f1   Upload to experimental

The 11 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:
 .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 +-
 debian/README.source                        |  37 ---
 debian/changelog                            |  10 +
 debian/gbp.conf                             |  10 -
 debian/libhts2.symbols                      |   9 +-
 debian/patches/877670.patch                 |   4 +-
 debian/patches/htslib-add-cram_to_bam.patch |   2 +-
 debian/patches/literal_version.patch        |  16 -
 debian/patches/series                       |   1 -
 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 +-
 htslib/vcf_sweep.h => hts_os.c              |  42 ++-
 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/{vcf_sweep.h => hts_os.h}            |  47 +--
 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 ++
 75 files changed, 1691 insertions(+), 683 deletions(-)
 create mode 100644 .appveyor.yml
 delete mode 100644 debian/README.source
 delete mode 100644 debian/patches/literal_version.patch
 copy htslib/vcf_sweep.h => hts_os.c (61%)
 copy htslib/{vcf_sweep.h => hts_os.h} (53%)
 create mode 100644 test/test-bcf-translate.c
 create mode 100644 test/test-bcf-translate.out
 create mode 100755 version.sh
 create mode 100644 win/rand.c
 create mode 100644 win/rand.h

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