[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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