[med-svn] [fastqc] branch debian/jessie-backports updated (3a8dedd -> 01cde9f)
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 change to branch debian/jessie-backports
in repository fastqc.
from 3a8dedd Rebuild for jessie-backports.
adds 7563daf Add explicit Depends: default-jre | java7-runtime
adds bc56edf Build-Depends: libhtsjdk-java | libsam-java and try to enable htsjdk.jar in Build system
adds 0c1f051 Remove deactivated patch
adds fbc845a Path to samtools changed when switching from libsam-java to libhtsjdk-java
adds 86c199c It seems there is no chance to keep libsam-java usable (for instance for backports)
adds 88a8397 Let ${java:Depends} do its automatically dependency generating job
adds cdad899 fix htsjdk import
adds 31c1e2e upload release using htsjdk
adds 6383c2b Crafted EDAM annotation for FASTQC
adds cdadf23 Add compression method to watch file
adds c00d2b4 Imported Upstream version 0.11.5+dfsg
adds 93d800f Merge tag 'upstream/0.11.5+dfsg'
adds c5af05d New upstream version
adds 3c67afd Adapt patches
adds d476cc0 cme fix dpkg-control; upload to unstable
new a0e68ba Merge branch 'master' into debian/jessie-backports
new 01cde9f Rebuild for jessie-backports
The 2 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 | 33 +
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, 10412 insertions(+), 10344 deletions(-)
delete mode 100644 debian/patches/Makefile.patch
create mode 100644 debian/patches/adapt_to_htslib.patch
create mode 100644 debian/upstream/edam
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fastqc.git
More information about the debian-med-commit
mailing list