[med-svn] [htslib] 01/02: Merge branch 'debian/unstable' into debian/jessie-backports

[Charles Plessy]

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

plessy pushed a commit to branch debian/jessie-backports
in repository htslib.

commit b8ab89e2f8ee688c9374ab12db593657bea0b66e
Merge: c047803 c8c5494
Author: Charles Plessy <plessy at debian.org>
Date:   Sun May 8 21:28:10 2016 +0900

    Merge branch 'debian/unstable' into debian/jessie-backports
    
    Conflicts:
    	debian/changelog

 .gitattributes                       |   8 +
 .gitignore                           |   2 +
 Makefile                             |  25 ++-
 NEWS                                 |  35 ++++
 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                       |  61 ++++++-
 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                 |  14 +-
 debian/changelog                     |  24 +++
 debian/control                       |   7 +-
 debian/copyright                     |   4 +-
 debian/libhts1.symbols               |   9 +-
 debian/patches/literal_version.patch |  16 ++
 debian/patches/series                |   1 +
 debian/rules                         |   4 +
 debian/upstream/tabix.edam           |  16 ++
 faidx.c                              |  77 ++++++--
 hfile.c                              |  17 +-
 hfile_libcurl.c                      |   6 +-
 hts.c                                | 211 +++++++++++-----------
 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 +
 sam.c                                | 102 ++++++-----
 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 +++++++++++++++-------
 67 files changed, 1271 insertions(+), 635 deletions(-)

diff --cc debian/changelog
index de7f842,2aff3f3..d593271
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,27 +1,33 @@@
+ htslib (1.3.1-1) unstable; urgency=medium
+ 
+   36bf59a Merge tag '1.3.1' into debian/unstable
+   559f8b4 Remove add_largefile.patch, applied upstream.
+   7163afb Update symbols file. Missing _vcf_parse_format at Base and fai_read at Base.
+   c2c1df3 Build-depend on libcurl4-gnutls-dev and libssl-dev.
+   3b219b8 Enable libcurl.
+   9101580 Conforms to the Policy version 3.9.8.
+ 
+  -- Charles Plessy <plessy at debian.org>  Mon, 25 Apr 2016 22:28:11 +0900
+ 
+ htslib (1.3-2) unstable; urgency=medium
+ 
+   * Team upload
+ 
+   [ Steffen Moeller and Jon Ison ]
+   * Introduction of EDAM annotation
+ 
+   [ Sascha Steinbiss ]
+   * Include upstream patch for large file support
+   * Run configure as part of the build
+ 
+  -- Sascha Steinbiss <sascha at steinbiss.name>  Mon, 08 Feb 2016 16:46:35 +0000
+ 
 +htslib (1.3-1~bpo8+1) jessie-backports; urgency=medium
 +
 +  * Rebuild for jessie-backports.
 +
 + -- Charles Plessy <plessy at debian.org>  Mon, 08 Feb 2016 12:42:45 +0900
 +
  htslib (1.3-1) unstable; urgency=medium
  
    * Team upload

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/htslib.git