[med-svn] [sga] branch debian updated (5a7f800 -> 18b84c8)

[Andreas Tille]

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

tille pushed a change to branch debian
in repository sga.

      from  5a7f800   Follow request of ftpmaster to give a hint that some files can also be distributed under older versions of GPL
       new  592d36b   Imported Upstream version 0.10.14
       new  ce3049d   Merge tag 'upstream/0.10.14' into debian
       new  a61f106   New upstream version
       new  8b4dd85   Specify correct location of files in d/copyright
       new  18b84c8   Upload to unstable

The 5 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 +-
 debian/changelog                                   |   7 +
 debian/copyright                                   |  34 +-
 debian/patches/0002-no-rpath.patch                 |   8 +-
 debian/patches/0003-do-not-dist-unsup-script.patch |   4 +-
 .../patches/0004-Add-help-to-sga-bam2de.pl.patch   |  10 +-
 ...0005-Remove-extensions-on-scripts-we-ship.patch |   4 +-
 debian/patches/0006-remove-google-addsense.patch   |   6 +-
 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 +-
 67 files changed, 3428 insertions(+), 979 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

-- 
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