[med-svn] [sga] branch master updated (3cae268 -> 592d36b)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository sga.

      from  3cae268   Imported Upstream version 0.10.13
       new  592d36b   Imported Upstream version 0.10.14

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:
 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 ++++++++++++
 .../{haplotype-filter.h => graph-concordance.h}    |  12 +-
 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 +++++++++++++++++++++
 ...aplotype-filter.h => somatic-variant-filters.h} |  12 +-
 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, 3388 insertions(+), 946 deletions(-)
 create mode 100644 src/SGA/graph-concordance.cpp
 copy src/SGA/{haplotype-filter.h => graph-concordance.h} (55%)
 create mode 100644 src/SGA/kmer-count.cpp
 create mode 100644 src/SGA/kmer-count.h
 copy src/SGA/{overlap.cpp => overlap-long.cpp} (65%)
 create mode 100644 src/SGA/overlap-long.h
 create mode 100644 src/SGA/somatic-variant-filters.cpp
 copy src/SGA/{haplotype-filter.h => somatic-variant-filters.h} (54%)
 create mode 100644 src/Util/VariantIndex.cpp
 create mode 100644 src/Util/VariantIndex.h
 delete mode 100755 src/bin/sga-variant-filters.pl

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sga.git