[med-svn] [subread] 01/02: Merge tag 'debian/1.5.1+dfsg-4' into debian/jessie-backports

[Andreas Tille]

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tille pushed a commit to branch debian/jessie-backports
in repository subread.

commit 619673380d8744f4561c92faa1fd31e1b42065a8
Merge: 791782a b750d4a
Author: Andreas Tille <tille at debian.org>
Date:   Sun Jun 25 09:47:04 2017 +0200

    Merge tag 'debian/1.5.1+dfsg-4' into debian/jessie-backports

 annotation/hg38_RefSeq_exon.txt               | 261753 +++++++++++++++++++++++
 debian/README.source                          |      6 -
 debian/changelog                              |     45 +
 debian/compat                                 |      2 +-
 debian/control                                |      2 +-
 debian/copyright                              |      2 +-
 debian/patches/arch_specific_flags.patch      |      6 +-
 debian/patches/fix_ftbfs_kfreebsd.patch       |      4 +-
 debian/patches/series                         |      1 -
 debian/patches/syntax_err.patch               |     13 -
 debian/rules                                  |     15 +-
 debian/watch                                  |      4 +-
 doc/SubreadUsersGuide.tex                     |    143 +-
 src/Makefile                                  |      2 +-
 src/Makefile.FreeBSD                          |      2 +-
 src/Makefile.Linux                            |      2 +-
 src/Makefile.MacOS                            |      2 +-
 src/SNPCalling.c                              |      8 +-
 src/core-indel.c                              |     38 +-
 src/core-interface-aligner.c                  |      5 +
 src/core-interface-subjunc.c                  |      6 +
 src/core-junction.c                           |      2 +-
 src/core.c                                    |     86 +-
 src/core.h                                    |      5 +-
 src/gene-value-index.c                        |      5 +-
 src/input-files.c                             |     54 +-
 src/input-files.h                             |      2 +
 src/interval_merge.c                          |     24 +-
 src/makefile.version                          |      2 +-
 src/readSummary.c                             |   1166 +-
 test/featureCounts/data/corner-MinOverlap.ora |      8 +-
 test/featureCounts/data/corner-fractions.SAF  |      5 +
 test/featureCounts/data/corner-fractions.ora  |      3 +
 test/featureCounts/data/corner-fractions.sam  |      7 +
 test/featureCounts/data/test-fracOverlap.ora  |      4 +
 test/featureCounts/data/test-fracOverlap.sam  |      4 +
 test/featureCounts/test_corner_cases.sh       |      8 +-
 37 files changed, 262940 insertions(+), 506 deletions(-)

diff --cc debian/changelog
index b844f6a,f907ec7..8ce18fd
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,48 +1,54 @@@
+ subread (1.5.1+dfsg-4) unstable; urgency=medium
+ 
+   * Fix watch file
+   * debhelper 10
+   * remove outdated information from README.source
+ 
+  -- Andreas Tille <tille at debian.org>  Fri, 02 Dec 2016 08:22:05 +0100
+ 
+ subread (1.5.1+dfsg-3) unstable; urgency=medium
+ 
+   * Pass triplet-prefixed CC to make
+ 
+  -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Mon, 05 Sep 2016 14:59:37 +0200
+ 
+ subread (1.5.1+dfsg-2) unstable; urgency=medium
+ 
+   * Team upload.
+   * Make build reproducible.
+     - Add compiler flags to ensure use of -fdebug-prefix-map.
+ 
+  -- Sascha Steinbiss <satta at debian.org>  Sun, 04 Sep 2016 15:16:33 +0000
+ 
+ subread (1.5.1+dfsg-1) unstable; urgency=medium
+ 
+   * Imported Upstream version 1.5.1+dfsg
+   * Fix copyright Format: s/http/https/
+   * Refresh and remove applied patches
+ 
+  -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Sun, 28 Aug 2016 08:43:33 +0200
+ 
+ subread (1.5.0-p3+dfsg-3) unstable; urgency=medium
+ 
+   * Team upload.
+   * Further address reproducibility by forcing mode on tarball contents.
+ 
+  -- Sascha Steinbiss <satta at debian.org>  Thu, 21 Jul 2016 13:23:14 +0000
+ 
+ subread (1.5.0-p3+dfsg-2) unstable; urgency=medium
+ 
+   * Team upload.
+   * Make build reproducible by ensuring umask and mtime of
+     archive contents are deterministic.
+ 
+  -- Sascha Steinbiss <satta at debian.org>  Mon, 18 Jul 2016 07:46:12 +0000
+ 
 +subread (1.5.0-p3+dfsg-1~bpo8+1) jessie-backports; urgency=medium
 +
 +  * Rebuild for jessie-backports.
 +
 + -- Andreas Tille <tille at debian.org>  Mon, 20 Jun 2016 09:45:35 +0200
 +
  subread (1.5.0-p3+dfsg-1) unstable; urgency=medium
  
    * Drop get-orig-source target, update d/watch to repack and use compression xz

-- 
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