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

[Andreas Tille]

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

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

commit 5b4efb17e5aacefa04f7e0881a94575673823409
Merge: 01cde9f 166eb42
Author: Andreas Tille <tille at debian.org>
Date:   Fri Jun 9 22:50:06 2017 +0200

    Merge branch 'master' into debian/jessie-backports

 debian/changelog                  |  54 ++++
 debian/compat                     |   2 +-
 debian/control                    |  10 +-
 debian/docs                       |   1 -
 debian/fastqc.examples            |   1 +
 debian/install                    |   3 +-
 debian/patches/drop-fast5.patch   | 160 ++++++++++++
 debian/patches/fastqc.patch       |  11 +-
 debian/patches/htsjdk-api.patch   |  49 ++++
 debian/patches/series             |   2 +
 debian/rules                      |   3 +
 debian/source/include-binaries    |   1 +
 debian/tests.fastqc/example.fastq | 501 ++++++++++++++++++++++++++++++++++++++
 debian/tests.fastqc/toy.bam       | Bin 0 -> 478 bytes
 debian/tests.fastqc/toy.sam       |  14 ++
 debian/tests/control              |   3 +
 debian/tests/run-unit-test        |  31 +++
 debian/upstream/metadata          |   3 +
 debian/watch                      |   2 +-
 19 files changed, 837 insertions(+), 14 deletions(-)

diff --cc debian/changelog
index ccc2d18,304e196..eb3d4d8
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,57 +1,63 @@@
+ fastqc (0.11.5+dfsg-6) unstable; urgency=medium
+ 
+   * Team upload.
+   * Avoid use of SAMFileReader to fix FTBFS.
+     Closes: #846708
+   * Add autopkgtest cases and accompanying test data
+     for SAM/BAM input files.
+   * Make sure jar dependencies are found. Before fixing this,
+     htsjdk classes were not found at runtime. This problem only
+     surfaced with BAM/SAM inputs, which were not tested so far.
+ 
+  -- Sascha Steinbiss <satta at debian.org>  Thu, 08 Dec 2016 15:40:00 +0000
+ 
+ fastqc (0.11.5+dfsg-5) unstable; urgency=medium
+ 
+   [ Gilles Filippini ]
+   * New patch drop-fast5.patch to temporarily drop support for fast5
+     file format. This way we can drop the build-dependency on
+     libsis-jhdf5-java which doesn't support HDF5 1.10 yet (#842815).
+     fast5 files can easily be converted to fastq using poretools.
+     Closes: #844760
+ 
+   [ Andreas Tille ]
+   * debhelper 10
+   * d/watch: version=4
+ 
+  -- Andreas Tille <tille at debian.org>  Tue, 22 Nov 2016 14:43:31 +0100
+ 
+ fastqc (0.11.5+dfsg-4) unstable; urgency=low
+ 
+   * Team upload.
+   * Fix autopkgtest: add depend to unzip.
+   * Install upstream changelog using dh_installchangelogs.
+ 
+  -- Dylan Aïssi <bob.dybian at gmail.com>  Thu, 01 Sep 2016 23:05:15 +0200
+ 
+ fastqc (0.11.5+dfsg-3) unstable; urgency=medium
+ 
+   * Team upload.
+  
+   [ Canberk Koç ] 
+   * Autopkgtest added
+ 
+   [ Andreas Tille ]
+   * cme fix dpkg-control
+ 
+  -- Canberk Koç <canberkkoc at gmail.com>  Thu, 28 Jul 2016 02:04:17 +0300
+ 
+ fastqc (0.11.5+dfsg-2) unstable; urgency=medium
+ 
+   * Reintroduced omitted Configuration directory
+ 
+  -- Steffen Moeller <moeller at debian.org>  Wed, 06 Apr 2016 03:14:58 +0200
+ 
 +fastqc (0.11.5+dfsg-1~bpo8+1) jessie-backports; urgency=medium
 +
 +  * Rebuild for jessie-backports.
 +
 + -- Andreas Tille <tille at debian.org>  Tue, 05 Apr 2016 11:50:14 +0200
 +
  fastqc (0.11.5+dfsg-1) unstable; urgency=medium
  
    [ Steffen Moeller ]

-- 
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