[med-svn] [fastqc] 01/02: Merge branch 'master' into debian/jessie-backports
Andreas Tille
tille at debian.org
Thu Sep 1 18:19:46 UTC 2016
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 a0e68ba144518f258c8713db4ab9e1fbadeecfce
Merge: 3a8dedd d476cc0
Author: Andreas Tille <tille at debian.org>
Date: Tue Apr 5 11:49:57 2016 +0200
Merge branch 'master' into debian/jessie-backports
Configuration/adapter_list.txt | 49 +-
Configuration/contaminant_list.txt | 364 ++---
Configuration/limits.txt | 166 +-
Help/3 Analysis Modules/8 Duplicate Sequences.html | 4 +-
INSTALL.txt | 278 ++--
LICENSE.txt | 1348 ++++++++--------
README.txt | 88 +-
RELEASE_NOTES.txt | 1688 ++++++++++----------
Templates/header_template.html | 372 ++---
debian/changelog | 27 +
debian/control | 10 +-
debian/patches/Makefile.patch | 27 -
debian/patches/adapt_to_htslib.patch | 35 +
debian/patches/build_xml.patch | 2 +-
debian/patches/fastqc.patch | 2 +-
debian/patches/fix-help-call.patch | 16 +-
debian/patches/series | 2 +-
debian/patches/set_configuration_path.patch | 103 +-
debian/rules | 4 -
debian/upstream/edam | 13 +
debian/watch | 2 +-
run_fastqc.bat | 2 +-
.../babraham/FastQC/Analysis/AnalysisListener.java | 62 +-
uk/ac/babraham/FastQC/Analysis/AnalysisRunner.java | 230 +--
uk/ac/babraham/FastQC/Analysis/OfflineRunner.java | 382 ++---
uk/ac/babraham/FastQC/Dialogs/AboutDialog.java | 142 +-
.../babraham/FastQC/Dialogs/FastQCTitlePanel.java | 294 ++--
uk/ac/babraham/FastQC/Dialogs/WelcomePanel.java | 122 +-
uk/ac/babraham/FastQC/FastQCApplication.java | 676 ++++----
uk/ac/babraham/FastQC/FastQCMenuBar.java | 298 ++--
.../babraham/FastQC/FileFilters/BAMFileFilter.java | 72 +-
.../FastQC/FileFilters/CasavaFastQFileFilter.java | 78 +-
.../FastQC/FileFilters/FastQFileFilter.java | 72 +-
.../FastQC/FileFilters/GobyFileFilter.java | 72 +-
.../FastQC/FileFilters/MappedBAMFileFilter.java | 72 +-
.../FastQC/FileFilters/SequenceFileFilter.java | 110 +-
uk/ac/babraham/FastQC/Graphs/BaseGroup.java | 442 ++---
uk/ac/babraham/FastQC/Graphs/LineGraph.java | 470 +++---
uk/ac/babraham/FastQC/Graphs/QualityBoxPlot.java | 420 ++---
uk/ac/babraham/FastQC/Graphs/TileGraph.java | 300 ++--
uk/ac/babraham/FastQC/Help/HelpSearchPanel.java | 320 ++--
uk/ac/babraham/FastQC/Modules/AdapterContent.java | 772 ++++-----
.../babraham/FastQC/Modules/DuplicationLevel.java | 528 +++---
uk/ac/babraham/FastQC/Modules/GCModel/GCModel.java | 164 +-
.../FastQC/Modules/GCModel/GCModelValue.java | 80 +-
uk/ac/babraham/FastQC/Modules/KmerContent.java | 1160 +++++++-------
uk/ac/babraham/FastQC/Modules/ModuleConfig.java | 308 ++--
uk/ac/babraham/FastQC/Modules/ModuleFactory.java | 92 +-
uk/ac/babraham/FastQC/Modules/NContent.java | 330 ++--
.../FastQC/Modules/PerBaseQualityScores.java | 528 +++---
.../FastQC/Modules/PerBaseSequenceContent.java | 446 +++---
.../FastQC/Modules/PerSequenceGCContent.java | 532 +++---
.../FastQC/Modules/PerSequenceQualityScores.java | 332 ++--
.../FastQC/Modules/PerTileQualityScores.java | 718 ++++-----
uk/ac/babraham/FastQC/Modules/QCModule.java | 118 +-
.../FastQC/Modules/SequenceLengthDistribution.java | 480 +++---
uk/ac/babraham/FastQC/Report/stylesheet.txt | 110 +-
uk/ac/babraham/FastQC/Results/ResultsPanel.java | 324 ++--
uk/ac/babraham/FastQC/Sequence/BAMFile.java | 440 ++---
.../FastQC/Sequence/Contaminant/Contaminant.java | 308 ++--
.../Sequence/Contaminant/ContaminantHit.java | 128 +-
.../Sequence/Contaminant/ContaminentFinder.java | 226 +--
uk/ac/babraham/FastQC/Sequence/Fast5File.java | 178 +--
uk/ac/babraham/FastQC/Sequence/FastQFile.java | 700 ++++----
.../Sequence/QualityEncoding/PhredEncoding.java | 188 +--
uk/ac/babraham/FastQC/Sequence/Sequence.java | 152 +-
.../babraham/FastQC/Sequence/SequenceFactory.java | 226 +--
uk/ac/babraham/FastQC/Sequence/SequenceFile.java | 66 +-
.../FastQC/Sequence/SequenceFileGroup.java | 186 +--
.../FastQC/Sequence/SequenceFormatException.java | 56 +-
.../FastQC/Statistics/NormalDistribution.java | 98 +-
.../FastQC/Statistics/PearsonCorrelation.java | 210 +--
.../babraham/FastQC/Utilities/CasavaBasename.java | 270 ++--
.../FastQC/Utilities/HotColdColourGradient.java | 310 ++--
.../Utilities/MultiMemberGZIPInputStream.java | 222 +--
.../FastQC/Utilities/NameFormatException.java | 52 +-
.../FastQC/Utilities/NanoporeBasename.java | 198 +--
uk/ac/babraham/FastQC/Utilities/QualityCount.java | 190 +--
uk/ac/babraham/FastQC/Utilities/RGB.java | 88 +-
79 files changed, 10406 insertions(+), 10344 deletions(-)
diff --cc debian/changelog
index c634759,f20cee3..d29a151
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,30 +1,36 @@@
+ fastqc (0.11.5+dfsg-1) unstable; urgency=medium
+
+ [ Steffen Moeller ]
+ * Contribued EDAM ontology description to
+ debian/upstream/edam
+
+ [ Andreas Tille ]
+ * New upstream version
+ * Add compression method to watch file
+ * cme fix dpkg-control
+
+ -- Andreas Tille <tille at debian.org> Sun, 20 Mar 2016 14:30:17 +0100
+
+ fastqc (0.11.4+dfsg-3) unstable; urgency=medium
+
+ * Build-Depends: libhtsjdk-java | libsam-java and try to enable
+ htsjdk.jar in Build system
+
+ -- Andreas Tille <tille at debian.org> Thu, 14 Jan 2016 13:50:56 +0100
+
+ fastqc (0.11.4+dfsg-2) unstable; urgency=medium
+
+ * Add explicit Depends: default-jre | java7-runtime
+ Closes: #784057
+
+ -- Andreas Tille <tille at debian.org> Sun, 20 Dec 2015 20:01:08 +0100
+
+fastqc (0.11.4+dfsg-1~bpo8+1) jessie-backports; urgency=medium
+
+ * Rebuild for jessie-backports.
+
+ -- Andreas Tille <tille at debian.org> Tue, 15 Dec 2015 11:50:33 +0100
+
fastqc (0.11.4+dfsg-1) unstable; urgency=medium
* New upstream version
--
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