[med-svn] [mach-haplotyper] 07/09: Update upstream source from tag 'upstream/1.0.18'

[Andreas Tille]

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tille pushed a commit to branch master
in repository mach-haplotyper.

commit 1dc1a40b91d4c6319568bb37905d69910b8a5a93
Merge: 8b159e6 367f8ea
Author: Andreas Tille <tille at debian.org>
Date:   Sun Dec 10 17:48:03 2017 +0100

    Update upstream source from tag 'upstream/1.0.18'
    
    Update to upstream version '1.0.18'
    with Debian dir f7a2d6cbba4668955c9e95f5554fd4a2e14d9065

 Makefile                        |  175 +++
 libsrc/BasicHash.cpp            |  164 +++
 libsrc/BasicHash.h              |   85 ++
 libsrc/Constant.h               |   61 +
 libsrc/Error.cpp                |   69 +
 libsrc/Error.h                  |   35 +
 libsrc/FortranFormat.cpp        |  373 ++++++
 libsrc/FortranFormat.h          |  100 ++
 libsrc/GenotypeLists.cpp        |  486 +++++++
 libsrc/GenotypeLists.h          |   61 +
 libsrc/Hash.cpp                 |  130 ++
 libsrc/Hash.h                   |   27 +
 libsrc/InputFile.cpp            |   63 +
 libsrc/InputFile.h              |  158 +++
 libsrc/IntArray.cpp             |  389 ++++++
 libsrc/IntArray.h               |  153 +++
 libsrc/Kinship.cpp              |   92 ++
 libsrc/Kinship.h                |   43 +
 libsrc/KinshipX.cpp             |   63 +
 libsrc/KinshipX.h               |   41 +
 libsrc/LongArray.cpp            |  148 +++
 libsrc/LongArray.h              |   78 ++
 libsrc/LongHash.cpp             |   20 +
 libsrc/LongHash.h               |  247 ++++
 libsrc/LongInt.h                |  204 +++
 libsrc/LongLongCounter.cpp      |   60 +
 libsrc/LongLongCounter.h        |   36 +
 libsrc/MapFunction.cpp          |   44 +
 libsrc/MapFunction.h            |   25 +
 libsrc/MathConstant.h           |   52 +
 libsrc/MathMatrix.cpp           |  711 ++++++++++
 libsrc/MathMatrix.h             |  194 +++
 libsrc/MathStats.cpp            |  494 +++++++
 libsrc/MathStats.h              |   77 ++
 libsrc/MathVector.cpp           |  652 +++++++++
 libsrc/MathVector.h             |  207 +++
 libsrc/MemoryAllocators.cpp     |  260 ++++
 libsrc/MemoryAllocators.h       |  103 ++
 libsrc/MemoryInfo.cpp           |   38 +
 libsrc/MemoryInfo.h             |   26 +
 libsrc/MiniDeflate.cpp          |  349 +++++
 libsrc/MiniDeflate.h            |  103 ++
 libsrc/Parameters.cpp           |  735 +++++++++++
 libsrc/Parameters.h             |  292 +++++
 libsrc/Pedigree.cpp             |  916 +++++++++++++
 libsrc/Pedigree.h               |  155 +++
 libsrc/PedigreeAlleleFreq.cpp   |  260 ++++
 libsrc/PedigreeAlleleFreq.h     |   36 +
 libsrc/PedigreeAlleles.h        |  143 ++
 libsrc/PedigreeDescription.cpp  |  826 ++++++++++++
 libsrc/PedigreeDescription.h    |   82 ++
 libsrc/PedigreeFamily.cpp       |  294 +++++
 libsrc/PedigreeFamily.h         |   63 +
 libsrc/PedigreeGlobals.cpp      |  856 ++++++++++++
 libsrc/PedigreeGlobals.h        |  175 +++
 libsrc/PedigreeLoader.cpp       |  605 +++++++++
 libsrc/PedigreePerson.cpp       |  234 ++++
 libsrc/PedigreePerson.h         |  133 ++
 libsrc/PedigreeTrim.cpp         |  188 +++
 libsrc/PedigreeTwin.cpp         |  182 +++
 libsrc/QuickIndex.cpp           |  232 ++++
 libsrc/QuickIndex.h             |   52 +
 libsrc/Random.cpp               |  407 ++++++
 libsrc/Random.h                 |  133 ++
 libsrc/Sort.cpp                 |  369 ++++++
 libsrc/Sort.h                   |   36 +
 libsrc/StringArray.cpp          |  325 +++++
 libsrc/StringArray.h            |  118 ++
 libsrc/StringBasics.cpp         | 1255 ++++++++++++++++++
 libsrc/StringBasics.h           |  274 ++++
 libsrc/StringHash.cpp           |  647 +++++++++
 libsrc/StringHash.h             |  276 ++++
 libsrc/StringMap.cpp            |  541 ++++++++
 libsrc/StringMap.h              |  122 ++
 libsrc/TraitTransformations.cpp |  121 ++
 libsrc/TraitTransformations.h   |   30 +
 mach1/AssociationAnalysis.cpp   |  201 +++
 mach1/AssociationAnalysis.h     |   38 +
 mach1/CostCalculator.cpp        |  136 ++
 mach1/CostCalculator.h          |   45 +
 mach1/DosageCalculator.cpp      |  347 +++++
 mach1/DosageCalculator.h        |   71 +
 mach1/ErrorRate.cpp             |   65 +
 mach1/ErrorRate.h               |   40 +
 mach1/HaplotypeKey.cpp          |  305 +++++
 mach1/HaplotypeKey.h            |   98 ++
 mach1/HaplotypeLoader.cpp       |  882 +++++++++++++
 mach1/HaplotypeLoader.h         |   80 ++
 mach1/Haplotyper.cpp            | 2755 +++++++++++++++++++++++++++++++++++++++
 mach1/Haplotyper.h              |  323 +++++
 mach1/Main.cpp                  |  635 +++++++++
 mach1/Manners.cpp               |   81 ++
 mach1/Manners.h                 |   36 +
 mach1/MergeHaplotypes.cpp       |  205 +++
 mach1/MergeHaplotypes.h         |   56 +
 mach1/OutputHandlers.cpp        |  364 ++++++
 mach1/OutputHandlers.h          |   56 +
 thunder/Main.cpp                |  470 +++++++
 thunder/ShotgunHaplotyper.cpp   |  250 ++++
 thunder/ShotgunHaplotyper.h     |   44 +
 thunder/ShotgunManners.cpp      |   68 +
 thunder/ShotgunManners.h        |   36 +
 102 files changed, 25696 insertions(+)

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