[med-svn] [sga] 02/05: Merge tag 'upstream/0.10.14' into debian

[Andreas Tille]

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tille pushed a commit to branch debian
in repository sga.

commit ce3049d13a17719aaf17ff68d820540eaabade7c
Merge: 5a7f800 592d36b
Author: Andreas Tille <tille at debian.org>
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(-)

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