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satta pushed a change to branch master
in repository rna-star.
from 2a4afac Updated references
new 4d28022 New upstream version 2.5.4a+dfsg
new 41dd973 Update upstream source from tag 'upstream/2.5.4a+dfsg'
new 9d575e2 new upstream version
The 3 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:
CHANGES.md | 18 +
README.md | 14 +-
debian/changelog | 8 +-
doc/STARmanual.pdf | Bin 264875 -> 266190
bytes
extras/doc-latex/convertParDefToLatexTable.awk | 5 +-
.../convertParDefToLatexTable.optOptTable.awk | 46 -
.../convertParDefToLatexTable.optTable.awk | 54 -
extras/doc-latex/parametersDefault.tex | 52 +-
extras/doc-latex/texlive.profile | 33 -
extras/doc-latex/texlive_install.sh | 49 -
extras/scripts/calcInsertCoverage.awk | 47 +
extras/scripts/extractSJfromGTF.sh | 10 +
extras/scripts/mergeLogFinal.awk | 34 +
extras/scripts/mergeSuperContig.awk | 71 +
extras/scripts/sjCollapseSamples.awk | 25 +
extras/scripts/sjMotif.m | 45 +
extras/scripts/tagXSstrandedData.awk | 18 +-
extras/scripts/transcriptTypes.awk | 36 +
extras/scripts/transfragsFromBedGraph.awk | 26 +
source/Chain.cpp | 2 +-
source/Genome.cpp | 6 +-
source/IncludeDefine.h | 4 +-
source/Makefile | 6 +-
source/Parameters.cpp | 46 +-
source/Parameters.h | 25 +-
source/Parameters_openReadsFiles.cpp | 31 +-
source/Parameters_readSAMheader.cpp | 37 +
source/ReadAlign.cpp | 1 +
source/ReadAlign.h | 5 +-
source/ReadAlignChunk_processChunks.cpp | 82 +-
source/ReadAlign_CIGAR.cpp | 62 +
source/ReadAlign_alignBAM.cpp | 110 +-
source/ReadAlign_calcCIGAR.cpp | 58 +
source/ReadAlign_chimericDetection.cpp | 9 +-
source/ReadAlign_oneRead.cpp | 4 +-
source/ReadAlign_outputAlignments.cpp | 2 +
source/ReadAlign_outputTranscriptSAM.cpp | 61 +-
source/ReadAlign_stitchWindowSeeds.cpp | 32 +-
source/STAR.cpp | 2 +
source/SequenceFuns.cpp | 43 +
source/SequenceFuns.h | 1 +
source/VERSION | 2 +-
source/genomeGenerate.cpp | 42 +
source/parametersDefault | 52 +-
source/parametersDefault.xxd | 4625 ++++++++++----------
source/readLoad.cpp | 17 +-
source/readLoad.h | 2 +-
source/sjdbPrepare.cpp | 2 +-
source/stitchAlignToTranscript.cpp | 4 +-
source/stitchWindowAligns.cpp | 32 +-
50 files changed, 3369 insertions(+), 2629 deletions(-)
delete mode 100644 extras/doc-latex/convertParDefToLatexTable.optOptTable.awk
delete mode 100644 extras/doc-latex/convertParDefToLatexTable.optTable.awk
delete mode 100644 extras/doc-latex/texlive.profile
delete mode 100755 extras/doc-latex/texlive_install.sh
create mode 100644 extras/scripts/calcInsertCoverage.awk
create mode 100755 extras/scripts/extractSJfromGTF.sh
create mode 100644 extras/scripts/mergeLogFinal.awk
create mode 100644 extras/scripts/mergeSuperContig.awk
create mode 100644 extras/scripts/sjCollapseSamples.awk
create mode 100644 extras/scripts/sjMotif.m
create mode 100644 extras/scripts/transcriptTypes.awk
create mode 100644 extras/scripts/transfragsFromBedGraph.awk
create mode 100644 source/Parameters_readSAMheader.cpp
create mode 100644 source/ReadAlign_CIGAR.cpp
create mode 100644 source/ReadAlign_calcCIGAR.cpp
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