[med-svn] [rna-star] branch master updated (a721513 -> 8d0c4c4)
Andreas Tille
tille at debian.org
Thu May 19 16:16:38 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository rna-star.
from a721513 Fixed spacing errors found via `yamllint edam`
new 38c7b04 Use xz compression option in d/watch
new 834d1b2 Imported Upstream version 2.5.2a+dfsg
new 3da8d31 Merge tag 'upstream/2.5.2a+dfsg'
new 68533d5 New upstream version
new dc06f3d cme fix dpkg-control
new cc4e99e Update patches
new 8d0c4c4 Fix homepage
The 7 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:
.gitmodules | 3 -
CHANGES.md | 14 +
README.md | 2 +-
RELEASEnotes.md | 2 +-
debian/changelog | 9 +
debian/control | 13 +-
debian/patches/compilationstuff.patch | 31 -
debian/patches/donotuse_own_htslib.patch | 48 +-
debian/patches/mips_shm_noreserve.patch | 6 +-
debian/patches/series | 1 -
debian/rules | 3 -
debian/watch | 2 +-
source/BAMbinSortByCoordinate.cpp | 16 +-
source/BAMbinSortByCoordinate.h | 2 +-
source/BAMbinSortUnmapped.cpp | 8 +-
source/BAMbinSortUnmapped.h | 2 +-
source/BAMfunctions.cpp | 18 +-
source/BAMoutput.cpp | 54 +-
source/BAMoutput.h | 2 +-
source/ErrorWarning.cpp | 2 +-
source/Genome.cpp | 252 +-
source/Genome.h | 8 +-
source/Genome_insertSequences.cpp | 8 +-
source/InOutStreams.cpp | 20 +-
source/InOutStreams.h | 4 +-
source/IncludeDefine.h | 14 +-
source/Makefile | 2 +-
source/OutSJ.cpp | 16 +-
source/OutSJ.h | 26 +-
source/PackedArray.h | 6 +-
source/ParameterInfo.h | 34 +-
source/Parameters.cpp | 632 +--
source/Parameters.h | 150 +-
source/Parameters_openReadsFiles.cpp | 38 +-
source/Quantifications.cpp | 10 +-
source/Quantifications.h | 6 +-
source/ReadAlign.cpp | 62 +-
source/ReadAlign.h | 70 +-
source/ReadAlignChunk.cpp | 40 +-
source/ReadAlignChunk.h | 8 +-
source/ReadAlignChunk_mapChunk.cpp | 44 +-
source/ReadAlignChunk_processChunks.cpp | 70 +-
source/ReadAlign_alignBAM.cpp | 173 +-
source/ReadAlign_assignAlignToWindow.cpp | 44 +-
source/ReadAlign_chimericDetection.cpp | 108 +-
source/ReadAlign_createExtendWindowsWithAlign.cpp | 22 +-
source/ReadAlign_mapOneRead.cpp | 52 +-
source/ReadAlign_maxMappableLength2strands.cpp | 28 +-
source/ReadAlign_multMapSelect.cpp | 50 +-
source/ReadAlign_oneRead.cpp | 40 +-
source/ReadAlign_outputAlignments.cpp | 173 +-
source/ReadAlign_outputTranscriptCIGARp.cpp | 32 +-
source/ReadAlign_outputTranscriptSAM.cpp | 148 +-
source/ReadAlign_outputTranscriptSJ.cpp | 22 +-
source/ReadAlign_quantTranscriptome.cpp | 36 +-
source/ReadAlign_stitchPieces.cpp | 159 +-
source/ReadAlign_stitchWindowSeeds.cpp | 164 +-
source/ReadAlign_storeAligns.cpp | 46 +-
source/STAR.cpp | 194 +-
source/SequenceFuns.cpp | 38 +-
source/SequenceFuns.h | 2 +-
source/SharedMemory.cpp | 24 +-
source/SharedMemory.h | 6 +-
source/SjdbClass.h | 2 +-
source/Stats.cpp | 26 +-
source/Stats.h | 12 +-
source/SuffixArrayFuns.cpp | 162 +-
source/SuffixArrayFuns.h | 2 +-
source/ThreadControl.h | 8 +-
source/Transcript.cpp | 18 +-
source/Transcript.h | 34 +-
source/Transcript_alignScore.cpp | 8 +-
source/Transcriptome.cpp | 32 +-
source/Transcriptome.h | 6 +-
source/Transcriptome_geneCountsAddAlign.cpp | 26 +-
source/Transcriptome_quantAlign.cpp | 28 +-
source/VERSION | 2 +-
source/alignSmithWaterman.cpp | 76 +-
source/bamRemoveDuplicates.cpp | 54 +-
source/binarySearch2.cpp | 8 +-
source/blocksOverlap.cpp | 14 +-
source/extendAlign.cpp | 28 +-
source/funCompareUintAndSuffixes.cpp | 20 +-
source/funCompareUintAndSuffixes.h | 6 +-
source/funCompareUintAndSuffixesMemcmp.cpp | 33 +
source/funCompareUintAndSuffixesMemcmp.h | 10 +
source/genomeGenerate.cpp | 214 +-
source/genomeParametersWrite.cpp | 12 +-
source/genomeSAindex.cpp | 86 +-
source/genomeScanFastaFiles.cpp | 54 +-
source/insertSeqSA.cpp | 141 +-
source/loadGTF.cpp | 80 +-
source/mapThreadsSpawn.cpp | 8 +-
source/outputSJ.cpp | 26 +-
source/parametersDefault | 72 +-
source/parametersDefault.xxd | 4339 +++++++++++----------
source/readLoad.cpp | 66 +-
source/serviceFuns.cpp | 18 +-
source/signalFromBAM.cpp | 54 +-
source/sjSplitAlign.cpp | 2 +-
source/sjdbBuildIndex.cpp | 108 +-
source/sjdbInsertJunctions.cpp | 26 +-
source/sjdbLoadFromFiles.cpp | 6 +-
source/sjdbLoadFromStream.cpp | 2 +-
source/sjdbPrepare.cpp | 58 +-
source/sortSuffixesBucket.cpp | 100 +
source/sortSuffixesBucket.h | 3 +
source/stitchAlignToTranscript.cpp | 124 +-
source/stitchGapIndel.cpp | 28 +-
source/stitchWindowAligns.cpp | 140 +-
source/streamFuns.cpp | 16 +-
source/sysRemoveDir.cpp | 2 +-
112 files changed, 5068 insertions(+), 4651 deletions(-)
delete mode 100644 debian/patches/compilationstuff.patch
create mode 100644 source/funCompareUintAndSuffixesMemcmp.cpp
create mode 100644 source/funCompareUintAndSuffixesMemcmp.h
create mode 100644 source/sortSuffixesBucket.cpp
create mode 100644 source/sortSuffixesBucket.h
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