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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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