[med-svn] [subread] branch master updated (7b55f96 -> c478725)
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Wed Nov 11 18:06:58 UTC 2015
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a change to branch master
in repository subread.
from 7b55f96 d/changelog: upload to unstable
new 32f5127 Imported Upstream version 1.5.0+dfsg
new 7504147 Merge tag 'upstream/1.5.0+dfsg'
new e00d918 d/changelog: imported new upstream version
new f134ef5 d/patches: remove and refresh
new d657499 d/tests/subread-tests: update tests with parameters introduced in the new version
new aa0d319 debian/rules: do not build the documentation this time, as the upstream didn't provide all sources
new 266d293 d/subread.install: remove globalReassembly and subtools, add repair d/rules: generate man page for repair d/patches/fix_repair_usage.patch: s/removeDup/repair/g d/patches/syntax_err.patch: s/requried/required/ d/patches/fix_syntax.patch: removed d/subread.docs: do not install pdf file d/doc-base: removed due to removal of pdf d/control: remove texlive-latex-extra from build-depends d/copyright: remove stanza for non-existing file
new c478725 d/changelog: update and upload to unstable
The 8 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 | 8 +
debian/control | 2 +-
debian/copyright | 7 -
debian/doc-base | 12 -
debian/patches/arch_specific_flags.patch | 2 +-
debian/patches/fix_repair_usage.patch | 13 +
debian/patches/fix_syntax.patch | 13 -
debian/patches/series | 3 +-
debian/patches/syntax_err.patch | 13 +
debian/rules | 6 +-
debian/subread.docs | 1 -
debian/subread.install | 3 +-
debian/tests/subread-tests | 18 +-
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 +-
88 files changed, 12897 insertions(+), 8749 deletions(-)
delete mode 100644 debian/doc-base
create mode 100644 debian/patches/fix_repair_usage.patch
delete mode 100644 debian/patches/fix_syntax.patch
create mode 100644 debian/patches/syntax_err.patch
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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