[med-svn] [fastqc] branch master updated (6383c2b -> d476cc0)

[Andreas Tille]

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tille pushed a change to branch master
in repository fastqc.

      from  6383c2b   Crafted EDAM annotation for FASTQC
       new  cdadf23   Add compression method to watch file
       new  c00d2b4   Imported Upstream version 0.11.5+dfsg
       new  93d800f   Merge tag 'upstream/0.11.5+dfsg'
       new  c5af05d   New upstream version
       new  3c67afd   Adapt patches
       new  d476cc0   cme fix dpkg-control; upload to unstable

The 6 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 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                                   |   10 +-
 debian/control                                     |    4 +-
 debian/patches/adapt_to_htslib.patch               |   54 +-
 debian/patches/fix-help-call.patch                 |   16 +-
 debian/patches/set_configuration_path.patch        |  103 +-
 debian/rules                                       |    4 -
 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 +-
 74 files changed, 10361 insertions(+), 10339 deletions(-)

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