[med-svn] [subread] branch master updated (c478725 -> 31219a9)
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Tue Jan 5 15:29:24 UTC 2016
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a change to branch master
in repository subread.
from c478725 d/changelog: update and upload to unstable
new 5acf640 Imported Upstream version 1.5.0-p1+dfsg
new f05ffca Merge tag 'upstream/1.5.0-p1+dfsg'
new ab3327c d/changelog: new upstream version d/patches: refresh and remove applied patches d/filter.pl: drop $_ as it is the default anyway
new 31219a9 d/changelog: upload to unstable
The 4 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:
debian/changelog | 7 +
debian/filter.pl | 24 +-
debian/patches/fix_repair_usage.patch | 13 -
debian/patches/series | 1 -
debian/patches/syntax_err.patch | 2 +-
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 +
.../data/{test-minimum.sam => test-dup.sam} | 600 +--
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 +
97 files changed, 7575 insertions(+), 849 deletions(-)
delete mode 100644 debian/patches/fix_repair_usage.patch
delete mode 100644 src/SeekGZ.h
delete mode 100644 src/t.c
create mode 100644 test/featureCounts/data/across_genes.gtf
create mode 100644 test/featureCounts/data/across_genes_r1.bam
create mode 100644 test/featureCounts/data/across_genes_r1.bam.ora
create mode 100644 test/featureCounts/data/across_genes_r1.sam
create mode 100644 test/featureCounts/data/across_genes_r1.sam.ora
create mode 100644 test/featureCounts/data/across_genes_r2.bam
create mode 100644 test/featureCounts/data/across_genes_r2.bam.ora
create mode 100644 test/featureCounts/data/across_genes_r2.sam
create mode 100644 test/featureCounts/data/across_genes_r2.sam.ora
create mode 100644 test/featureCounts/data/across_intron.gtf
create mode 100644 test/featureCounts/data/across_intron_r1.bam
create mode 100644 test/featureCounts/data/across_intron_r1.bam.ora
create mode 100644 test/featureCounts/data/across_intron_r1.sam
create mode 100644 test/featureCounts/data/across_intron_r1.sam.ora
create mode 100644 test/featureCounts/data/across_intron_r2.bam
create mode 100644 test/featureCounts/data/across_intron_r2.bam.ora
create mode 100644 test/featureCounts/data/across_intron_r2.sam
create mode 100644 test/featureCounts/data/across_intron_r2.sam.ora
create mode 100644 test/featureCounts/data/corner-BothEnds.ora
delete mode 100644 test/featureCounts/data/corner-CHIMERIC.ora
delete mode 100644 test/featureCounts/data/corner-CHIMERIC.sam
create mode 100644 test/featureCounts/data/corner-Chimeric.ora
create mode 100644 test/featureCounts/data/corner-DoNotSort.ora
create mode 100644 test/featureCounts/data/corner-Extend3.ora
create mode 100644 test/featureCounts/data/corner-Extend5.ora
create mode 100644 test/featureCounts/data/corner-Fraction.ora
create mode 100644 test/featureCounts/data/corner-IgnoreDup.ora
create mode 100644 test/featureCounts/data/corner-Jcounts-FA.ora
create mode 100644 test/featureCounts/data/corner-Jcounts-FA.ora.jcounts
create mode 100644 test/featureCounts/data/corner-Jcounts.ora
create mode 100644 test/featureCounts/data/corner-Jcounts.ora.jcounts
create mode 100644 test/featureCounts/data/corner-LargestOverlap.ora
create mode 100644 test/featureCounts/data/corner-MaxOPs.ora
create mode 100644 test/featureCounts/data/corner-MinMAPQ.ora
create mode 100644 test/featureCounts/data/corner-MinOverlap.ora
create mode 100644 test/featureCounts/data/corner-MultiMapping.ora
create mode 100644 test/featureCounts/data/corner-PEdist.ora
create mode 100644 test/featureCounts/data/corner-Read2Pos3.ora
create mode 100644 test/featureCounts/data/corner-Read2Pos5.ora
create mode 100644 test/featureCounts/data/intron_between.bam
create mode 100644 test/featureCounts/data/intron_between.bam.ora
create mode 100644 test/featureCounts/data/intron_between.gtf
create mode 100644 test/featureCounts/data/intron_between.sam
create mode 100644 test/featureCounts/data/intron_between.sam.ora
create mode 100644 test/featureCounts/data/intron_between_nointron.bam
create mode 100644 test/featureCounts/data/intron_between_nointron.bam.ora
create mode 100644 test/featureCounts/data/intron_between_nointron.sam
create mode 100644 test/featureCounts/data/intron_between_nointron.sam.ora
copy test/featureCounts/data/{test-minimum.sam => test-dup.sam} (77%)
create mode 100644 test/featureCounts/data/test-junc.sam
create mode 100644 test/featureCounts/test_commonusage.sh
create mode 100644 test/featureCounts/test_featurelevel.sh
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