This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch debian in repository sga.
commit ce3049d13a17719aaf17ff68d820540eaabade7c Merge: 5a7f800 592d36b Author: Andreas Tille <[email protected]> Date: Thu Dec 31 13:18:37 2015 +0100 Merge tag 'upstream/0.10.14' into debian Upstream version 0.10.14 README.md | 2 +- src/.gitignore | 9 + src/Algorithm/ErrorCorrectProcess.cpp | 20 +- src/Algorithm/ErrorCorrectProcess.h | 3 + src/Algorithm/KmerOverlaps.cpp | 35 +- src/Algorithm/KmerOverlaps.h | 1 + src/Algorithm/QCProcess.cpp | 24 +- src/Algorithm/QCProcess.h | 2 + src/GraphDiff/DeBruijnHaplotypeBuilder.cpp | 145 ++++- src/GraphDiff/DeBruijnHaplotypeBuilder.h | 8 + src/GraphDiff/DindelRealignWindow.cpp | 293 ++++------ src/GraphDiff/DindelRealignWindow.h | 19 +- src/GraphDiff/DindelUtil.cpp | 175 +++--- src/GraphDiff/DindelUtil.h | 7 - src/GraphDiff/GraphCompare.cpp | 54 +- src/GraphDiff/GraphCompare.h | 4 - src/GraphDiff/HapgenUtil.cpp | 257 +++++++-- src/GraphDiff/HapgenUtil.h | 59 +- src/SGA/Makefile.am | 16 +- src/SGA/SGACommon.h | 3 +- src/SGA/correct.cpp | 43 +- src/SGA/filter.cpp | 16 +- src/SGA/fm-merge.cpp | 4 +- src/SGA/gen-ssa.cpp | 24 +- src/SGA/graph-concordance.cpp | 487 ++++++++++++++++ src/SGA/graph-concordance.h | 23 + src/SGA/graph-diff.cpp | 90 ++- src/SGA/index.cpp | 42 +- src/SGA/kmer-count.cpp | 291 ++++++++++ src/SGA/kmer-count.h | 8 + src/SGA/{overlap.cpp => overlap-long.cpp} | 260 +++++---- src/SGA/overlap-long.h | 26 + src/SGA/overlap.cpp | 19 +- src/SGA/preprocess.cpp | 40 +- src/SGA/preqc.cpp | 70 ++- src/SGA/rmdup.cpp | 2 +- src/SGA/sga.cpp | 53 +- src/SGA/somatic-variant-filters.cpp | 864 +++++++++++++++++++++++++++++ src/SGA/somatic-variant-filters.h | 23 + src/SQG/ASQG.cpp | 11 + src/SQG/ASQG.h | 7 + src/SuffixTools/BWTIndexSet.h | 3 +- src/SuffixTools/SparseGapArray.h | 2 +- src/Thirdparty/multiple_alignment.cpp | 82 +++ src/Thirdparty/multiple_alignment.h | 7 + src/Thirdparty/overlapper.cpp | 299 ++++++---- src/Thirdparty/overlapper.h | 33 +- src/Util/Makefile.am | 1 + src/Util/SGAStats.h | 2 +- src/Util/SeqReader.cpp | 8 +- src/Util/SeqReader.h | 2 +- src/Util/VCFUtil.cpp | 44 +- src/Util/VCFUtil.h | 10 +- src/Util/VariantIndex.cpp | 96 ++++ src/Util/VariantIndex.h | 59 ++ src/bin/sga-align | 5 +- src/bin/sga-astat.py | 8 +- src/bin/sga-preqc-report.py | 39 +- src/bin/sga-variant-filters.pl | 115 ---- src/configure.ac | 2 +- 60 files changed, 3422 insertions(+), 934 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sga.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
