[med-svn] [ngs-sdk] 02/05: Merge tag 'upstream/1.2.4'

Andreas Tille tille at debian.org
Mon Jun 6 10:55:55 UTC 2016


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

tille pushed a commit to branch master
in repository ngs-sdk.

commit b76f13cf84381bd213de0e88c687ba1761f6536b
Merge: 4b269c9 97eabb4
Author: Andreas Tille <tille at debian.org>
Date:   Mon Jun 6 12:41:33 2016 +0200

    Merge tag 'upstream/1.2.4'
    
    Upstream version 1.2.4

 .gitignore                                         |    9 +
 Makefile => CHANGES                                |   56 +-
 CHANGES.md                                         |   16 +
 Makefile                                           |    1 -
 configure                                          |    2 +-
 ngs-bam/setup/install.perl                         |    5 +-
 ngs-bam/setup/package.prl                          |    2 +-
 ngs-java/Makefile.java                             |   17 +-
 ngs-java/build.xml                                 |   30 +-
 ngs-java/examples/Makefile                         |   17 +-
 ngs-java/examples/examples/DumpReferenceFASTA.java |  132 +++
 ngs-java/examples/expected.txt                     |  531 +++++++++
 ngs-java/gov/nih/nlm/ncbi/ngs/DownloadManager.java |  143 +++
 ngs-java/gov/nih/nlm/ncbi/ngs/LMProperties.java    |  202 ++++
 .../gov/nih/nlm/ncbi/ngs/LibDependencies.java      |   12 +-
 ngs-java/gov/nih/nlm/ncbi/ngs/LibManager.java      | 1136 +++++++-------------
 ngs-java/gov/nih/nlm/ncbi/ngs/LibPathIterator.java |   32 +-
 .../gov/nih/nlm/ncbi/ngs/LibVersionChecker.java    |  206 ++++
 ngs-java/gov/nih/nlm/ncbi/ngs/Logger.java          |   21 +-
 ngs-java/gov/nih/nlm/ncbi/ngs/Manager.java         |   20 +-
 ngs-java/gov/nih/nlm/ncbi/ngs/NGS.java             |   12 +
 ngs-java/gov/nih/nlm/ncbi/ngs/Version.java         |   16 +-
 .../ngs/error/LibraryIncompatibleVersionError.java |   54 +-
 .../nih/nlm/ncbi/ngs/error/LibraryLoadError.java   |   80 ++
 .../nlm/ncbi/ngs/error/LibraryNotFoundError.java   |   26 +-
 .../ngs/error/cause/ConnectionProblemCause.java    |   27 +-
 .../ngs/error/cause/DownloadDisabledCause.java     |   27 +-
 .../ncbi/ngs/error/cause/InvalidLibraryCause.java  |   29 +-
 .../nlm/ncbi/ngs/error/cause/JvmErrorCause.java    |   29 +-
 .../nlm/ncbi/ngs/error/cause/LibraryLoadCause.java |   14 +-
 .../nlm/ncbi/ngs/error/cause/OutdatedJarCause.java |   16 +-
 .../ngs/error/cause/PrereleaseReqLibCause.java     |   27 +-
 .../ncbi/ngs/error/cause/UnsupportedArchCause.java |   28 +-
 ngs-java/ngs/ReadCollection.java                   |    2 +
 ngs-java/setup/package.prl                         |    2 +-
 ngs-python/build.xml                               |   19 +-
 ngs-python/examples/AlignSliceTest.py              |    3 +
 ngs-python/examples/AlignSliceTest26.py            |    3 +
 ngs-python/examples/AlignTest.py                   |    3 +
 ngs-python/examples/AlignTest26.py                 |    3 +
 .../{AlignTest.py => DumpReferenceFASTA.py}        |   76 +-
 ngs-python/examples/FragTest.py                    |    3 +
 ngs-python/examples/FragTest26.py                  |    3 +
 ngs-python/examples/PileupTest.py                  |    3 +
 ngs-python/examples/PileupTest26.py                |    3 +
 ngs-python/examples/RefTest.py                     |    3 +
 ngs-python/examples/RefTest26.py                   |    3 +
 ngs-python/ngs/Alignment.py                        |    2 +-
 ngs-python/ngs/LibManager.py                       |    2 +-
 ngs-python/ngs/Pileup.py                           |    2 +-
 ngs-python/ngs/PileupEvent.py                      |    4 +-
 ngs-python/ngs/ReadCollection.py                   |   14 +-
 ngs-python/ngs/Refcount.py                         |   27 +-
 ngs-python/ngs/Reference.py                        |    2 +-
 ngs-python/ngs/Statistics.py                       |    2 +-
 ngs-python/setup/package.prl                       |    2 +-
 ngs-sdk/dispatch/PackageItf.cpp                    |    7 +
 ngs-sdk/dispatch/version.h                         |    2 +-
 ngs-sdk/examples/DumpReferenceFASTA.cpp            |    5 +-
 ngs-sdk/examples/Makefile                          |  104 +-
 ngs-sdk/examples/expected.txt                      |  531 +++++++++
 ngs-sdk/language/c++/ReferenceSequence.cpp         |   12 +-
 ngs-sdk/language/python/Makefile                   |    1 -
 .../language/python/py_AlignmentIteratorItf.cpp    |   26 +-
 ngs-sdk/language/python/py_AlignmentItf.cpp        |  621 ++++++++++-
 ngs-sdk/language/python/py_ErrorMsg.cpp            |   27 -
 ngs-sdk/language/python/py_ErrorMsg.hpp            |  307 ------
 ngs-sdk/language/python/py_FragmentIteratorItf.cpp |   26 +-
 ngs-sdk/language/python/py_FragmentItf.cpp         |  135 ++-
 .../language/python/py_PileupEventIteratorItf.cpp  |   26 +-
 ngs-sdk/language/python/py_PileupEventItf.cpp      |  324 +++++-
 ngs-sdk/language/python/py_PileupIteratorItf.cpp   |   26 +-
 ngs-sdk/language/python/py_PileupItf.cpp           |  108 +-
 ngs-sdk/language/python/py_ReadCollectionItf.cpp   |  405 ++++++-
 .../language/python/py_ReadGroupIteratorItf.cpp    |   26 +-
 ngs-sdk/language/python/py_ReadGroupItf.cpp        |   54 +-
 ngs-sdk/language/python/py_ReadIteratorItf.cpp     |   26 +-
 ngs-sdk/language/python/py_ReadItf.cpp             |  216 +++-
 .../language/python/py_ReferenceIteratorItf.cpp    |   26 +-
 ngs-sdk/language/python/py_ReferenceItf.cpp        |  378 ++++++-
 .../language/python/py_ReferenceSequenceItf.cpp    |  135 ++-
 ngs-sdk/language/python/py_StatisticsItf.cpp       |  162 ++-
 ngs-sdk/language/python/py_StringItf.cpp           |   27 +-
 ngs-sdk/{ => ngs}/win/stdbool.h                    |    0
 ngs-sdk/setup/package.prl                          |    2 +-
 ngs-sdk/win/.gitignore                             |    1 -
 ngs-sdk/win/build.xml                              |   67 ++
 ngs-sdk/win/libadapter.files                       |   35 +
 ngs-sdk/win/libadapter.vcxproj                     |   64 --
 ngs-sdk/win/libdispatch.files                      |   54 +
 ngs-sdk/win/libdispatch.vcxproj                    |   84 --
 ngs-sdk/win/libngs-c++.files                       |   23 +
 ngs-sdk/win/libngs-c++.vcxproj                     |   53 -
 ngs-sdk/win/libtest_engine.files                   |   18 +
 ngs-sdk/win/libtest_engine.vcxproj                 |   42 -
 ngs-sdk/win/ngs-sdk.files                          |   79 ++
 ngs-sdk/win/ngs-sdk.vcxproj                        |  124 ---
 ngs-sdk/win/ngs-test.files                         |    6 +
 ngs-sdk/win/vs2010/.gitignore                      |    4 +
 .../libngs-adapt-c++-4ff9a6f5.ipch                 |  Bin 0 -> 524288 bytes
 ngs-sdk/win/{ => vs2010}/lib-project.props         |    7 +
 ngs-sdk/win/vs2010/libadapter.vcxproj              |   27 +
 .../win/{ => vs2010}/libadapter.vcxproj.filters    |    0
 ngs-sdk/win/vs2010/libdispatch.vcxproj             |   27 +
 .../win/{ => vs2010}/libdispatch.vcxproj.filters   |    0
 ngs-sdk/win/vs2010/libngs-c++.vcxproj              |   27 +
 .../win/{ => vs2010}/libngs-c++.vcxproj.filters    |    0
 ngs-sdk/win/vs2010/libtest_engine.vcxproj          |   26 +
 .../{ => vs2010}/libtest_engine.vcxproj.filters    |    0
 ngs-sdk/win/{ => vs2010}/ngs-common.props          |   21 +-
 ngs-sdk/win/{ => vs2010}/ngs-sdk.sln               |    0
 ngs-sdk/win/vs2010/ngs-sdk.vcxproj                 |   55 +
 ngs-sdk/win/{ => vs2010}/ngs-sdk.vcxproj.filters   |    0
 ngs-sdk/win/{ => vs2010}/ngs-test.vcxproj          |   52 +-
 ngs-sdk/win/{ => vs2010}/ngs-test.vcxproj.filters  |    0
 ngs-sdk/win/vs2013/.gitignore                      |    4 +
 ngs-sdk/win/{ => vs2013}/lib-project.props         |    7 +
 ngs-sdk/win/vs2013/libadapter.vcxproj              |    9 +
 .../win/{ => vs2013}/libadapter.vcxproj.filters    |  200 ++--
 ngs-sdk/win/vs2013/libdispatch.vcxproj             |    9 +
 .../win/{ => vs2013}/libdispatch.vcxproj.filters   |    0
 ngs-sdk/win/vs2013/libngs-c++.vcxproj              |    9 +
 .../win/{ => vs2013}/libngs-c++.vcxproj.filters    |    0
 ngs-sdk/win/vs2013/libtest_engine.vcxproj          |    8 +
 .../{ => vs2013}/libtest_engine.vcxproj.filters    |   98 +-
 ngs-sdk/win/{ => vs2013}/ngs-common.props          |   44 +-
 ngs-sdk/win/{ => vs2013}/ngs-sdk.sln               |  250 ++---
 ngs-sdk/win/vs2013/ngs-sdk.vcxproj                 |   37 +
 ngs-sdk/win/{ => vs2013}/ngs-sdk.vcxproj.filters   |  486 ++++-----
 ngs-sdk/win/{ => vs2013}/ngs-test.vcxproj          |   36 +-
 ngs-sdk/win/{ => vs2013}/ngs-test.vcxproj.filters  |   34 +-
 131 files changed, 6527 insertions(+), 2506 deletions(-)

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