[med-svn] [subread] branch upstream updated (ea3f671 -> 32f5127)
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Wed Nov 11 18:07:02 UTC 2015
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a change to branch upstream
in repository subread.
from ea3f671 Imported Upstream version 1.4.6-p5+dfsg
new 32f5127 Imported Upstream version 1.5.0+dfsg
The 1 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:
doc/MDSplot.png | Bin 22947 -> 0 bytes
doc/SubreadUsersGuide.bib | 73 -
doc/SubreadUsersGuide.tex | 220 +-
doc/indel.png | Bin 108132 -> 0 bytes
doc/junction.png | Bin 172344 -> 0 bytes
doc/seed-and-vote.png | Bin 112767 -> 0 bytes
doc/voom_mean_variance.png | Bin 99213 -> 0 bytes
src/BACK-sambam-file.h | 56 -
src/HelperFunctions.c | 305 +-
src/HelperFunctions.h | 20 +-
src/Makefile.FreeBSD | 3 +-
src/Makefile.Linux | 14 +-
src/Makefile.MacOS | 17 +-
src/SNPCalling.c | 11 +-
src/SUBindel.c | 11 +-
src/SeekGZ.h | 10 +
src/core-bigtable.c | 488 +++
src/core-bigtable.h | 49 +
src/core-indel.c | 561 ++-
src/core-indel.h | 71 +-
src/core-interface-aligner.c | 275 +-
src/core-interface-subjunc.c | 326 +-
src/core-junction-V2.c | 2922 --------------
src/core-junction.c | 4140 +++++++++++++++-----
src/core-junction.h | 53 +-
src/core.c | 3216 ++++++++-------
src/core.h | 358 +-
src/coverage_calc.c | 25 +-
src/del4-mmap-test.c | 44 +
src/filterJunctionTable.c | 7 +-
src/fullscan.c | 35 +-
src/gene-algorithms.c | 36 +-
src/gene-algorithms.h | 6 +-
src/global-reassembly.c | 30 +-
src/hashtable.c | 15 +-
src/hashtable.h | 4 +-
src/index-builder.c | 83 +-
src/input-files.c | 3017 ++++++++++++--
src/input-files.h | 121 +-
src/makefile.version | 2 +-
src/propmapped.c | 18 +-
src/qualityScores.c | 33 +-
src/read-repair.c | 130 +
src/readSummary.c | 2770 +++++++------
src/removeDupReads.c | 23 +-
src/samMappedBases.c | 124 +
src/sambam-file.c | 55 +-
src/sambam-file.h | 3 +
src/seek-zlib.c | 338 ++
src/seek-zlib.h | 23 +
src/sorted-hashtable.c | 20 +-
src/subfilter.c | 48 +
src/subread.h | 87 +-
src/subtools.c | 9 +-
src/t.c | 4 +
src/test-seek-zlib.c | 101 +
src/test_qs.c | 106 +
src/zlib_test.c | 88 +
src/zpipe.c | 192 -
test/featureCounts/data/DEL4-1385690721.FC | 9 -
test/featureCounts/data/DEL4-1385690721.FC.summary | 9 -
test/featureCounts/data/corner-BINS.SAF | 7 +
test/featureCounts/data/corner-BINS.sam | 9 +
test/featureCounts/data/corner-JUNC.sam | 8 +-
test/featureCounts/data/test-chrname.sam | 604 +--
test/featureCounts/data/test-minimum-dup.ora | 9 +
...ce.ora.summary => test-minimum-dup.ora.summary} | 9 +-
test/featureCounts/featureCounts-test.sh | 2 +-
test/featureCounts/result/test-minimum.FC | 9 -
test/featureCounts/result/test-minimum.FC.summary | 12 -
test/featureCounts/test_all.sh | 6 -
test/featureCounts/test_corner_cases.sh | 2 +
test/subjunc/subjunc-test.sh | 4 +-
test/subread-align/subread-align-test.sh | 14 +-
test/subread-align/test-tmp.log | 36 +-
75 files changed, 12848 insertions(+), 8697 deletions(-)
delete mode 100644 doc/MDSplot.png
delete mode 100644 doc/SubreadUsersGuide.bib
delete mode 100644 doc/indel.png
delete mode 100644 doc/junction.png
delete mode 100644 doc/seed-and-vote.png
delete mode 100644 doc/voom_mean_variance.png
delete mode 100644 src/BACK-sambam-file.h
create mode 100644 src/SeekGZ.h
create mode 100644 src/core-bigtable.c
create mode 100644 src/core-bigtable.h
delete mode 100644 src/core-junction-V2.c
create mode 100644 src/del4-mmap-test.c
create mode 100644 src/read-repair.c
create mode 100644 src/samMappedBases.c
create mode 100644 src/seek-zlib.c
create mode 100644 src/seek-zlib.h
create mode 100644 src/subfilter.c
create mode 100644 src/t.c
create mode 100644 src/test-seek-zlib.c
create mode 100644 src/test_qs.c
create mode 100644 src/zlib_test.c
delete mode 100644 src/zpipe.c
delete mode 100644 test/featureCounts/data/DEL4-1385690721.FC
delete mode 100644 test/featureCounts/data/DEL4-1385690721.FC.summary
create mode 100644 test/featureCounts/data/corner-BINS.SAF
create mode 100644 test/featureCounts/data/corner-BINS.sam
create mode 100644 test/featureCounts/data/test-minimum-dup.ora
rename test/featureCounts/data/{test-minimum-5reduce.ora.summary => test-minimum-dup.ora.summary} (61%)
delete mode 100644 test/featureCounts/result/test-minimum.FC
delete mode 100644 test/featureCounts/result/test-minimum.FC.summary
delete mode 100644 test/featureCounts/test_all.sh
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