[med-svn] [fastqc] 03/06: Merge tag 'upstream/0.11.5+dfsg'

[Andreas Tille]

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tille pushed a commit to branch master
in repository fastqc.

commit 93d800f7e636a5ac270e93606b57c508c386f40a
Merge: cdadf23 c00d2b4
Author: Andreas Tille <tille at debian.org>
Date:   Sun Mar 20 14:08:19 2016 +0100

    Merge tag 'upstream/0.11.5+dfsg'
    
    Upstream version 0.11.5+dfsg

 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 ++---
 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 +-
 67 files changed, 10263 insertions(+), 10244 deletions(-)

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