[med-svn] [bitseq] 12/14: Update upstream source from tag 'upstream/0.7.5+dfsg'

[Andreas Tille]

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tille pushed a commit to branch master
in repository bitseq.

commit 743efef1a768b8af6f2c90c6239d00fa965421b8
Merge: 1462b12 ebcd5e8
Author: Andreas Tille <tille at debian.org>
Date:   Sat Dec 2 09:45:57 2017 +0100

    Update upstream source from tag 'upstream/0.7.5+dfsg'
    
    Update to upstream version '0.7.5+dfsg'
    with Debian dir 1aae05a45ce499652f21624437d6fb92b955e9fa

 ArgumentParser.cpp          |  308 ++++++++++++
 ArgumentParser.h            |  110 +++++
 CollapsedSampler.cpp        |   95 ++++
 CollapsedSampler.h          |   16 +
 FileHeader.cpp              |  117 +++++
 FileHeader.h                |   45 ++
 GibbsParameters.cpp         |  110 +++++
 GibbsParameters.h           |   45 ++
 GibbsSampler.cpp            |   97 ++++
 GibbsSampler.h              |   17 +
 Makefile                    |  129 +++++
 MyTimer.cpp                 |   60 +++
 MyTimer.h                   |   28 ++
 PosteriorSamples.cpp        |  299 ++++++++++++
 PosteriorSamples.h          |   66 +++
 README.md                   |   34 ++
 ReadDistribution.cpp        | 1126 +++++++++++++++++++++++++++++++++++++++++++
 ReadDistribution.h          |  134 +++++
 Sampler.cpp                 |  220 +++++++++
 Sampler.h                   |   99 ++++
 SimpleSparse.cpp            |   97 ++++
 SimpleSparse.h              |   27 ++
 TagAlignments.cpp           |  132 +++++
 TagAlignments.h             |   44 ++
 TranscriptExpression.cpp    |   87 ++++
 TranscriptExpression.h      |   38 ++
 TranscriptInfo.cpp          |  258 ++++++++++
 TranscriptInfo.h            |   75 +++
 TranscriptSequence.cpp      |  197 ++++++++
 TranscriptSequence.h        |   82 ++++
 VariationalBayes.cpp        |  384 +++++++++++++++
 VariationalBayes.h          |   45 ++
 _release_Makefile           |  122 +++++
 asa103/LICENSE.txt          |  165 +++++++
 asa103/asa103.hpp           |   96 ++++
 biocUpdate.sh               |   24 +
 changeList                  |   86 ++++
 checkTR.py                  |   76 +++
 common.cpp                  |   22 +
 common.h                    |   41 ++
 convertSamples.cpp          |  197 ++++++++
 estimateDE.cpp              |  326 +++++++++++++
 estimateExpression.cpp      |  597 +++++++++++++++++++++++
 estimateHyperPar.cpp        |  369 ++++++++++++++
 estimateVBExpression.cpp    |  238 +++++++++
 extractSamples.cpp          |  126 +++++
 extractTranscriptInfo.py    |   91 ++++
 getCounts.py                |   78 +++
 getFoldChange.cpp           |  112 +++++
 getGeneExpression.cpp       |  120 +++++
 getPPLR.cpp                 |  152 ++++++
 getVariance.cpp             |  167 +++++++
 getWithinGeneExpression.cpp |  248 ++++++++++
 lowess.cpp                  |  511 ++++++++++++++++++++
 lowess.h                    |   30 ++
 misc.cpp                    |  240 +++++++++
 misc.h                      |   84 ++++
 parameters1.txt             |   32 ++
 parseAlignment.cpp          |  612 +++++++++++++++++++++++
 parseAlignment.py           |  482 ++++++++++++++++++
 releaseDo.sh                |   52 ++
 releaseList                 |   55 +++
 tagAlignment.h              |   37 ++
 transposeFiles.cpp          |  146 ++++++
 transposeFiles.h            |    4 +
 transposeLargeFile.cpp      |   22 +
 66 files changed, 10381 insertions(+)

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