[med-svn] [rna-star] branch master updated (886ad43 -> 289dd10)
Andreas Tille
tille at debian.org
Thu Dec 31 11:54:07 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository rna-star.
from 886ad43 Packaging moved from svn to git
new 86f7372 Imported Upstream version 2.5.0a+dfsg
new 9114a96 Merge tag 'upstream/2.5.0a+dfsg'
new 0e2f079 New upstream version + adapted patches
new 421ecd8 Adapt to new doc names
new 58c7395 Fix patch
new 289dd10 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:
.travis.yml | 7 +
CHANGES | 259 ---
CHANGES.md | 330 +++
LICENSE | 2 +-
Makefile | 24 +
README | 41 -
README.md | 128 ++
RELEASEnotes => RELEASEnotes.md | 24 +-
STAR-Fusion-0.1.1/LICENSE | 28 -
STAR-Fusion-0.1.1/README.md | 103 -
STAR-Fusion-0.1.1/STAR-Fusion | 755 -------
STAR-Fusion-0.1.1/lib/SAM_entry.pm | 544 -----
STAR-Fusion-0.1.1/lib/SAM_reader.pm | 109 -
STAR-Fusion-0.1.1/notes | 1 -
STAR-Fusion-0.1.1/test/Chimeric.out.junction.gz | Bin 237561 -> 0 bytes
STAR-Fusion-0.1.1/test/Chimeric.out.sam.gz | Bin 507939 -> 0 bytes
STAR-Fusion-0.1.1/test/cleanMe.sh | 4 -
STAR-Fusion-0.1.1/test/runMe.sh | 4 -
debian/changelog | 5 +-
debian/docs | 3 +-
debian/patches/compilationstuff.patch | 48 +-
debian/patches/donotuse_own_htslib.patch | 55 +-
debian/patches/mips_shm_noreserve.patch | 2 +-
doc/STARmanual.pdf | Bin 242969 -> 249630 bytes
extras/doc-latex/STARmanual.tex | 32 +-
extras/doc-latex/parametersDefault.tex | 56 +-
extras/doc-latex/texlive.profile | 33 +
extras/doc-latex/texlive_install.sh | 49 +
...awk => sjFromSAMcollapseUandM_inclOverlaps.awk} | 11 +-
source/Genome.cpp | 37 +-
source/Genome.h | 4 +
source/Genome_insertSequences.cpp | 33 +
source/GlobalVariables.cpp | 5 +-
source/IncludeDefine.h | 9 +-
source/Makefile | 126 +-
source/Parameters.cpp | 159 +-
source/Parameters.h | 44 +-
source/ReadAlign.cpp | 6 +-
source/ReadAlign.h | 10 +-
source/ReadAlignChunk.cpp | 2 +-
source/ReadAlignChunk_processChunks.cpp | 4 +-
source/ReadAlign_alignBAM.cpp | 2 +-
source/ReadAlign_chimericDetection.cpp | 7 +-
source/ReadAlign_multMapSelect.cpp | 72 +-
source/ReadAlign_outputAlignments.cpp | 32 +-
source/ReadAlign_outputTranscriptSAM.cpp | 2 +-
source/ReadAlign_stitchWindowSeeds.cpp | 12 +-
source/STAR.cpp | 47 +-
{extras/doc-latex => source}/STARmanual.tex | 2 +-
source/SuffixArrayFuns.cpp | 200 ++
source/SuffixArrayFuns.h | 4 +-
source/Transcriptome.cpp | 14 +-
source/VERSION | 2 +-
source/bam_cat.c | 3 +
source/bam_cat.h | 8 +
source/extendAlign.cpp | 20 +-
source/extendAlign.h | 3 +-
source/funCompareUintAndSuffixes.cpp | 40 +
source/funCompareUintAndSuffixes.h | 7 +
source/genomeGenerate.cpp | 344 +--
source/genomeParametersWrite.cpp | 3 +-
source/genomeSAindex.cpp | 265 +++
source/genomeSAindex.h | 10 +
source/genomeScanFastaFiles.cpp | 100 +
source/genomeScanFastaFiles.h | 9 +
source/insertSeqSA.cpp | 280 +++
source/insertSeqSA.h | 10 +
source/loadGTF.cpp | 22 +-
source/parametersDefault | 44 +-
source/parametersDefault.xxd | 2305 ++++++++++++++++++++
source/readLoad.cpp | 10 +-
source/serviceFuns.cpp | 2 +
source/sjSplitAlign.cpp | 3 +
source/sjdbBuildIndex.cpp | 157 +-
source/sjdbInsertJunctions.cpp | 26 +-
source/stitchAlignToTranscript.cpp | 11 +-
source/stitchGapIndel.cpp | 3 +
source/stitchWindowAligns.cpp | 37 +-
source/streamFuns.cpp | 14 +-
source/streamFuns.h | 6 +-
80 files changed, 4768 insertions(+), 2466 deletions(-)
create mode 100644 .travis.yml
delete mode 100644 CHANGES
create mode 100644 CHANGES.md
create mode 100644 Makefile
delete mode 100644 README
create mode 100644 README.md
rename RELEASEnotes => RELEASEnotes.md (75%)
delete mode 100644 STAR-Fusion-0.1.1/LICENSE
delete mode 100644 STAR-Fusion-0.1.1/README.md
delete mode 100755 STAR-Fusion-0.1.1/STAR-Fusion
delete mode 100644 STAR-Fusion-0.1.1/lib/SAM_entry.pm
delete mode 100644 STAR-Fusion-0.1.1/lib/SAM_reader.pm
delete mode 100644 STAR-Fusion-0.1.1/notes
delete mode 100644 STAR-Fusion-0.1.1/test/Chimeric.out.junction.gz
delete mode 100644 STAR-Fusion-0.1.1/test/Chimeric.out.sam.gz
delete mode 100755 STAR-Fusion-0.1.1/test/cleanMe.sh
delete mode 100755 STAR-Fusion-0.1.1/test/runMe.sh
create mode 100644 extras/doc-latex/texlive.profile
create mode 100755 extras/doc-latex/texlive_install.sh
copy extras/scripts/{sjFromSAMcollapseUandM.awk => sjFromSAMcollapseUandM_inclOverlaps.awk} (83%)
create mode 100644 source/Genome_insertSequences.cpp
copy {extras/doc-latex => source}/STARmanual.tex (99%)
create mode 100644 source/bam_cat.h
create mode 100644 source/funCompareUintAndSuffixes.cpp
create mode 100644 source/funCompareUintAndSuffixes.h
create mode 100644 source/genomeSAindex.cpp
create mode 100644 source/genomeSAindex.h
create mode 100644 source/genomeScanFastaFiles.cpp
create mode 100644 source/genomeScanFastaFiles.h
create mode 100644 source/insertSeqSA.cpp
create mode 100644 source/insertSeqSA.h
create mode 100644 source/parametersDefault.xxd
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/rna-star.git
More information about the debian-med-commit
mailing list