[med-svn] [subread] 02/04: Merge tag 'upstream/1.5.0-p1+dfsg'
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Tue Jan 5 15:29:25 UTC 2016
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malex-guest pushed a commit to branch master
in repository subread.
commit f05ffca422b375ae2148fcc19f149dec7d625aff
Merge: c478725 5acf640
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Tue Jan 5 15:47:09 2016 +0100
Merge tag 'upstream/1.5.0-p1+dfsg'
Upstream version 1.5.0-p1+dfsg
doc/SubreadUsersGuide.tex | 77 +-
src/HelperFunctions.c | 17 +-
src/HelperFunctions.h | 4 +-
src/Makefile.FreeBSD | 11 +-
src/Makefile.Linux | 9 +
src/Makefile.MacOS | 10 +
src/SNPCalling.c | 10 +-
src/SUBindel.c | 2 +-
src/SeekGZ.h | 10 -
src/build-sam-index.c | 5 +-
src/core-indel.c | 27 +-
src/core-interface-aligner.c | 45 +-
src/core-interface-subjunc.c | 61 +-
src/core-junction.c | 68 +-
src/core-junction.h | 2 +-
src/core.c | 178 +-
src/core.h | 5 +
src/coverage_calc.c | 32 +-
src/fullscan.c | 4 +-
src/gene-algorithms.c | 14 +-
src/gene-algorithms.h | 4 +-
src/gene-value-index.c | 7 +-
src/gene-value-index.h | 2 +-
src/index-builder.c | 64 +-
src/input-files.c | 541 ++-
src/input-files.h | 14 +-
src/makefile.version | 2 +-
src/mergeVCF.c | 2 +-
src/read-repair.c | 29 +-
src/readSummary.c | 443 +-
src/sambam-file.c | 45 +-
src/sambam-file.h | 4 +-
src/seek-zlib.c | 32 +-
src/sorted-hashtable.c | 48 +-
src/sorted-hashtable.h | 3 +-
src/subread.h | 10 +-
src/t.c | 4 -
test/featureCounts/data/across_genes.gtf | 8 +
test/featureCounts/data/across_genes_r1.bam | Bin 0 -> 231 bytes
test/featureCounts/data/across_genes_r1.bam.ora | 8 +
test/featureCounts/data/across_genes_r1.sam | 4 +
test/featureCounts/data/across_genes_r1.sam.ora | 8 +
test/featureCounts/data/across_genes_r2.bam | Bin 0 -> 226 bytes
test/featureCounts/data/across_genes_r2.bam.ora | 8 +
test/featureCounts/data/across_genes_r2.sam | 4 +
test/featureCounts/data/across_genes_r2.sam.ora | 8 +
test/featureCounts/data/across_intron.gtf | 3 +
test/featureCounts/data/across_intron_r1.bam | Bin 0 -> 245 bytes
test/featureCounts/data/across_intron_r1.bam.ora | 3 +
test/featureCounts/data/across_intron_r1.sam | 5 +
test/featureCounts/data/across_intron_r1.sam.ora | 3 +
test/featureCounts/data/across_intron_r2.bam | Bin 0 -> 245 bytes
test/featureCounts/data/across_intron_r2.bam.ora | 3 +
test/featureCounts/data/across_intron_r2.sam | 5 +
test/featureCounts/data/across_intron_r2.sam.ora | 3 +
test/featureCounts/data/compare.sh | 15 +-
test/featureCounts/data/corner-BothEnds.ora | 8 +
test/featureCounts/data/corner-CHIMERIC.ora | 10 -
test/featureCounts/data/corner-CHIMERIC.sam | 27 -
test/featureCounts/data/corner-Chimeric.ora | 8 +
test/featureCounts/data/corner-DoNotSort.ora | 8 +
test/featureCounts/data/corner-Extend3.ora | 8 +
test/featureCounts/data/corner-Extend5.ora | 8 +
test/featureCounts/data/corner-Fraction.ora | 8 +
test/featureCounts/data/corner-IgnoreDup.ora | 8 +
test/featureCounts/data/corner-Jcounts-FA.ora | 8 +
.../data/corner-Jcounts-FA.ora.jcounts | 277 ++
test/featureCounts/data/corner-Jcounts.ora | 8 +
test/featureCounts/data/corner-Jcounts.ora.jcounts | 277 ++
test/featureCounts/data/corner-LargestOverlap.ora | 8 +
test/featureCounts/data/corner-MaxOPs.ora | 8 +
test/featureCounts/data/corner-MinMAPQ.ora | 8 +
test/featureCounts/data/corner-MinOverlap.ora | 8 +
test/featureCounts/data/corner-MultiMapping.ora | 8 +
test/featureCounts/data/corner-PEdist.ora | 8 +
test/featureCounts/data/corner-Read2Pos3.ora | 8 +
test/featureCounts/data/corner-Read2Pos5.ora | 8 +
test/featureCounts/data/intron_between.bam | Bin 0 -> 221 bytes
test/featureCounts/data/intron_between.bam.ora | 2 +
test/featureCounts/data/intron_between.gtf | 2 +
test/featureCounts/data/intron_between.sam | 4 +
test/featureCounts/data/intron_between.sam.ora | 2 +
.../featureCounts/data/intron_between_nointron.bam | Bin 0 -> 206 bytes
.../data/intron_between_nointron.bam.ora | 2 +
.../featureCounts/data/intron_between_nointron.sam | 4 +
.../data/intron_between_nointron.sam.ora | 2 +
test/featureCounts/data/test-dup.sam | 1003 ++++
test/featureCounts/data/test-junc.sam | 5000 ++++++++++++++++++++
test/featureCounts/featureCounts-test.sh | 2 +-
test/featureCounts/test_commonusage.sh | 62 +
test/featureCounts/test_corner_cases.sh | 24 +
test/featureCounts/test_featurelevel.sh | 11 +
92 files changed, 8258 insertions(+), 522 deletions(-)
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