[med-svn] [htslib] 02/02: Merge branch 'debian/unstable' of ssh://anonscm.debian.org/git/debian-med/htslib into debian/unstable

[Steffen Möller]

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

moeller pushed a commit to branch debian/unstable
in repository htslib.

commit 536682b04feffea28b9073db4f0b29d2bc4f3d46
Merge: cf5950e 1b39d8d
Author: Steffen Moeller <moeller at debian.org>
Date:   Mon Jan 23 00:46:04 2017 +0100

    Merge branch 'debian/unstable' of ssh://anonscm.debian.org/git/debian-med/htslib into debian/unstable

 .gitattributes                       |   8 +
 .gitignore                           |   2 +
 Makefile                             |  25 ++-
 NEWS                                 |  46 +++++
 bgzf.c                               | 337 ++++++++++++++++++++++++++++-------
 bgzip.c                              |  52 ++++--
 config.h.in                          |  11 ++
 configure.ac                         |   2 +
 cram/cram_codecs.c                   |  61 +++----
 cram/cram_codecs.h                   |   2 +-
 cram/cram_decode.c                   |  50 ++++--
 cram/cram_encode.c                   |  39 ++--
 cram/cram_external.c                 |   4 +-
 cram/cram_index.c                    |   2 +-
 cram/cram_io.c                       |  65 ++++++-
 cram/cram_samtools.c                 |   2 +-
 cram/cram_structs.h                  |   5 +
 cram/open_trace_file.c               |   2 +-
 cram/rANS_static.c                   |   8 +-
 cram/sam_header.c                    |   2 +-
 cram/thread_pool.c                   |  62 +------
 debian/README.source                 |  17 +-
 debian/changelog                     |  53 +++++-
 debian/compat                        |   2 +-
 debian/control                       |  12 +-
 debian/copyright                     |   4 +-
 debian/htslib-test.install           |   8 +-
 debian/libhts1.symbols               |   9 +-
 debian/patches/define_PATH_MAX.patch |  28 ++-
 debian/patches/literal_version.patch |  16 ++
 debian/patches/series                |   1 +
 debian/rules                         |   9 +-
 debian/tests/control                 |   3 +
 debian/tests/run-unit-test           |  19 ++
 debian/watch                         |   2 +-
 faidx.c                              |  77 ++++++--
 hfile.c                              |  23 ++-
 hfile_libcurl.c                      |   6 +-
 hts.c                                | 220 ++++++++++++-----------
 hts_internal.h                       |  23 ++-
 htsfile.1                            |   2 +-
 htsfile.c                            |   4 +-
 htslib/bgzf.h                        |  26 +--
 htslib/faidx.h                       |   2 +-
 htslib/hts.h                         |   8 +-
 htslib/sam.h                         |  20 +--
 htslib/vcf.h                         |   9 +-
 htslib_vars.mk                       |   6 +-
 kfunc.c                              |   2 +
 knetfile.c                           |   2 +
 kstring.c                            |   2 +
 plugin.c                             |  24 ++-
 sam.c                                | 105 ++++++-----
 tabix.1                              |   4 +-
 tabix.c                              |  44 +++--
 test/aux#aux_java.cram               | Bin 0 -> 3774 bytes
 test/ce#5b_java.cram                 | Bin 0 -> 6784 bytes
 test/fieldarith.c                    |   2 +
 test/formatcols.vcf                  |   6 +
 test/hfile.c                         |   2 +
 test/noroundtrip-out.vcf             |   9 +
 test/noroundtrip.vcf                 |   8 +
 test/sam.c                           |   7 +
 test/test-regidx.c                   |   2 +
 test/test-vcf-api.c                  |   2 +
 test/test-vcf-hdr-in.vcf             |   4 +-
 test/test-vcf-hdr.out                |   2 +-
 test/test-vcf-sweep.c                |   2 +
 test/test.pl                         | 104 ++++++++++-
 test/test_view.c                     |   8 +-
 test/test_view.pl                    |  93 ----------
 test/xx#large_aux_java.cram          | Bin 0 -> 22668 bytes
 test/xx#repeated.sam                 |   7 +
 vcf.c                                | 216 +++++++++++++++-------
 74 files changed, 1391 insertions(+), 662 deletions(-)

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