[med-svn] [ngs-sdk] 02/03: Merge tag 'upstream/1.2.3'
Andreas Tille
tille at debian.org
Tue Dec 29 20:35:03 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository ngs-sdk.
commit 9c9130f41c323378315ab9c5e22f47ef5c95c13b
Merge: 738c9ed e66c5d5
Author: Andreas Tille <tille at debian.org>
Date: Tue Dec 29 12:47:31 2015 +0100
Merge tag 'upstream/1.2.3'
Upstream version 1.2.3
.gitignore | 4 +
LICENSE | 66 +
Makefile | 10 +-
README.md | 8 +-
ngs-bam/Makefile.rules | 2 +-
ngs-bam/bam.cpp | 52 +-
ngs-bam/bam.hpp | 25 +-
{ngs-sdk => ngs-bam}/examples/AlignTest.cpp | 62 +-
{ngs-sdk => ngs-bam}/examples/Makefile | 69 +-
{ngs-sdk => ngs-bam}/examples/Makefile.config | 27 +
ngs-bam/examples/README.md | 6 +
ngs-bam/ngs-bam.cpp | 30 +-
ngs-bam/setup/install.perl | 9 +-
ngs-bam/setup/install.prl | 12 +-
ngs-bam/setup/konfigure.perl | 431 +-
ngs-bam/setup/os-arch.prl | 6 +-
ngs-bam/setup/package.prl | 17 +-
ngs-java/Makefile | 4 +-
ngs-java/Makefile.java | 70 +-
ngs-java/Makefile.rules | 6 +-
ngs-java/build.xml | 107 +
ngs-java/examples/Makefile | 66 +-
ngs-java/examples/examples/PileupTest.java | 148 +
ngs-java/examples/examples/ReadGroupTest.java | 78 +
ngs-java/examples/examples/SparkKMer.java | 137 +
ngs-java/examples/expected.txt | 115 +
ngs-java/gov/nih/nlm/ncbi/ngs/FileCreator.java | 2 +
ngs-java/gov/nih/nlm/ncbi/ngs/HttpException.java | 2 +-
ngs-java/gov/nih/nlm/ncbi/ngs/HttpManager.java | 47 +-
ngs-java/gov/nih/nlm/ncbi/ngs/LibManager.java | 1087 +-
ngs-java/gov/nih/nlm/ncbi/ngs/LibPathIterator.java | 49 +-
ngs-java/gov/nih/nlm/ncbi/ngs/Logger.java | 50 +-
ngs-java/gov/nih/nlm/ncbi/ngs/Manager.java | 100 +-
ngs-java/gov/nih/nlm/ncbi/ngs/NGS.java | 97 +
ngs-java/gov/nih/nlm/ncbi/ngs/TestyTheBear.java | 383 -
ngs-java/gov/nih/nlm/ncbi/ngs/Version.java | 313 +
ngs-java/ngs/Alignment.java | 42 +-
ngs-java/ngs/ErrorMsg.java | 2 +-
ngs-java/ngs/Fragment.java | 29 +
.../ngs/{PileupEventIterator.java => Package.java} | 24 +-
ngs-java/ngs/Pileup.java | 16 +-
ngs-java/ngs/PileupEvent.java | 96 +-
ngs-java/ngs/PileupEventIterator.java | 8 +
ngs-java/ngs/Read.java | 28 +
ngs-java/ngs/ReadCollection.java | 22 +
ngs-java/ngs/ReadGroup.java | 2 +
ngs-java/ngs/Reference.java | 79 +-
.../ngs/{Reference.java => ReferenceSequence.java} | 95 +-
ngs-java/ngs/itf/AlignmentItf.java | 14 +
ngs-java/ngs/itf/FragmentItf.java | 16 +
ngs-java/ngs/itf/PileupEventIteratorItf.java | 12 +
ngs-java/ngs/itf/PileupEventItf.java | 65 +-
ngs-java/ngs/itf/PileupItf.java | 212 +-
ngs-java/ngs/itf/ReadCollectionItf.java | 18 +
ngs-java/ngs/itf/ReadItf.java | 24 +
ngs-java/ngs/itf/ReferenceItf.java | 91 +-
ngs-java/ngs/itf/ReferenceSequenceItf.java | 152 +
ngs-java/setup/install.perl | 9 +-
ngs-java/setup/konfigure.perl | 431 +-
ngs-java/setup/os-arch.prl | 6 +-
ngs-java/setup/package.prl | 8 +-
ngs-python/Makefile | 2 +-
ngs-python/Makefile.python | 21 +-
ngs-python/build.xml | 78 +
ngs-python/examples/AlignTest.py | 3 +-
ngs-python/examples/AlignTest26.py | 3 +-
ngs-python/examples/FragTest.py | 5 +-
ngs-python/examples/FragTest26.py | 5 +-
{ngs-java => ngs-python}/examples/Makefile | 70 +-
ngs-python/examples/PileupTest.py | 109 +
ngs-python/examples/PileupTest26.py | 109 +
ngs-python/examples/expected.txt | 115 +
ngs-python/ngs/Alignment.py | 26 +-
ngs-python/ngs/Fragment.py | 10 +-
ngs-python/ngs/LibChecker.py | 70 +
ngs-python/ngs/LibManager.py | 176 +-
.../ngs/{PileupEventIterator.py => Package.py} | 32 +-
ngs-python/ngs/Pileup.py | 17 +-
ngs-python/ngs/PileupEvent.py | 71 +-
ngs-python/ngs/PileupEventIterator.py | 10 +-
ngs-python/ngs/Read.py | 16 +-
ngs-python/ngs/ReadCollection.py | 32 +-
ngs-python/ngs/ReadGroupIterator.py | 2 +-
ngs-python/ngs/Reference.py | 51 +-
ngs-python/ngs/ReferenceSequence.py | 104 +
ngs-python/ngs/String.py | 12 +-
ngs-python/ngs/__init__.py | 78 +-
ngs-python/setup/install.perl | 9 +-
ngs-python/setup/konfigure.perl | 431 +-
ngs-python/setup/os-arch.prl | 6 +-
ngs-python/setup/package.prl | 8 +-
ngs-sdk/Makefile | 7 +-
ngs-sdk/Makefile.install | 26 +-
ngs-sdk/Makefile.libs | 6 +-
ngs-sdk/Makefile.rules | 6 +-
ngs-sdk/adapter/AlignmentItf.cpp | 20 +-
ngs-sdk/adapter/Makefile | 40 +-
ngs-sdk/adapter/PileupEventItf.cpp | 92 +-
ngs-sdk/adapter/PileupItf.cpp | 11 +-
ngs-sdk/adapter/ReferenceItf.cpp | 43 +-
.../{PileupItf.cpp => ReferenceSequenceItf.cpp} | 65 +-
ngs-sdk/adapter/unix/i386/atomic32.h | 104 -
ngs-sdk/adapter/unix/x86_64/atomic32.h | 101 -
ngs-sdk/dispatch/AlignmentItf.cpp | 24 +
ngs-sdk/dispatch/FragmentItf.cpp | 48 +
ngs-sdk/dispatch/Makefile | 33 +-
.../PileupIterator.hpp => dispatch/PackageItf.cpp} | 25 +-
ngs-sdk/dispatch/PileupEventItf.cpp | 104 +-
ngs-sdk/dispatch/PileupItf.cpp | 12 +-
ngs-sdk/dispatch/ReadCollectionItf.cpp | 75 +-
ngs-sdk/dispatch/ReadItf.cpp | 24 +
ngs-sdk/dispatch/ReferenceItf.cpp | 189 +-
.../{PileupItf.cpp => ReferenceSequenceItf.cpp} | 87 +-
ngs-sdk/dispatch/version.h | 1 +
ngs-sdk/examples/.gitignore | 6 +-
ngs-sdk/examples/AlignSliceTest.cpp | 38 +-
ngs-sdk/examples/AlignTest.cpp | 50 +-
.../{FragTest.cpp => DumpReferenceFASTA.cpp} | 79 +-
.../examples/{FragTest.cpp => FastqTableDump.cpp} | 24 +-
ngs-sdk/examples/FragTest.cpp | 50 +-
ngs-sdk/examples/Makefile | 117 +-
ngs-sdk/examples/Makefile.config | 4 +-
ngs-sdk/examples/PileupTest.cpp | 171 +
.../examples/{AlignSliceTest.cpp => RefTest.cpp} | 51 +-
ngs-sdk/examples/expected.txt | 27878 +++++++++++++++++++
ngs-sdk/language/c++/Makefile | 33 +-
ngs-sdk/language/c++/Pileup.cpp | 12 +-
.../c++/{Pileup.cpp => ReferenceSequence.cpp} | 16 +-
ngs-sdk/language/java/Makefile | 2 +
ngs-sdk/language/java/jni_AlignmentIteratorItf.cpp | 2 +-
ngs-sdk/language/java/jni_AlignmentItf.cpp | 28 +
ngs-sdk/language/java/jni_AlignmentItf.h | 8 +
ngs-sdk/language/java/jni_FragmentItf.cpp | 56 +
ngs-sdk/language/java/jni_FragmentItf.h | 16 +
..._PileupEventIteratorItf.cpp => jni_Package.cpp} | 31 +-
ngs-sdk/language/java/jni_Package.h | 21 +
.../language/java/jni_PileupEventIteratorItf.cpp | 26 +
ngs-sdk/language/java/jni_PileupEventIteratorItf.h | 8 +
ngs-sdk/language/java/jni_PileupEventItf.cpp | 126 +-
ngs-sdk/language/java/jni_PileupEventItf.h | 36 +-
ngs-sdk/language/java/jni_PileupItf.cpp | 429 +-
ngs-sdk/language/java/jni_PileupItf.h | 118 +-
ngs-sdk/language/java/jni_ReadCollectionItf.cpp | 44 +
ngs-sdk/language/java/jni_ReadCollectionItf.h | 16 +
ngs-sdk/language/java/jni_ReadGroupItf.cpp | 36 +
ngs-sdk/language/java/jni_ReadItf.cpp | 85 +
ngs-sdk/language/java/jni_ReadItf.h | 24 +
ngs-sdk/language/java/jni_ReferenceItf.cpp | 117 +-
ngs-sdk/language/java/jni_ReferenceItf.h | 40 +-
..._PileupItf.cpp => jni_ReferenceSequenceItf.cpp} | 88 +-
ngs-sdk/language/java/jni_ReferenceSequenceItf.h | 54 +
ngs-sdk/language/java/jni_String.cpp | 2 +-
ngs-sdk/language/java/jni_md.h | 27 +-
ngs-sdk/language/python/Makefile | 2 +
ngs-sdk/language/python/py_AlignmentIteratorItf.h | 2 +-
ngs-sdk/language/python/py_AlignmentItf.h | 52 +-
ngs-sdk/language/python/py_ErrorMsg.hpp | 43 +-
ngs-sdk/language/python/py_FragmentIteratorItf.h | 2 +-
ngs-sdk/language/python/py_FragmentItf.cpp | 2 +
ngs-sdk/language/python/py_FragmentItf.h | 8 +-
.../language/python/py_PackageItf.cpp | 45 +-
.../{py_ReadIteratorItf.h => py_PackageItf.h} | 8 +-
.../language/python/py_PileupEventIteratorItf.cpp | 25 +
.../language/python/py_PileupEventIteratorItf.h | 3 +-
ngs-sdk/language/python/py_PileupEventItf.cpp | 6 +-
ngs-sdk/language/python/py_PileupEventItf.h | 26 +-
ngs-sdk/language/python/py_PileupIteratorItf.h | 2 +-
ngs-sdk/language/python/py_PileupItf.cpp | 2 +-
ngs-sdk/language/python/py_PileupItf.h | 8 +-
ngs-sdk/language/python/py_ReadCollectionItf.cpp | 2 +
ngs-sdk/language/python/py_ReadCollectionItf.h | 28 +-
ngs-sdk/language/python/py_ReadGroupIteratorItf.h | 2 +-
ngs-sdk/language/python/py_ReadGroupItf.h | 8 +-
ngs-sdk/language/python/py_ReadIteratorItf.h | 2 +-
ngs-sdk/language/python/py_ReadItf.cpp | 15 +-
ngs-sdk/language/python/py_ReadItf.h | 23 +-
ngs-sdk/language/python/py_Refcount.h | 6 +-
ngs-sdk/language/python/py_ReferenceIteratorItf.h | 2 +-
ngs-sdk/language/python/py_ReferenceItf.cpp | 21 +-
ngs-sdk/language/python/py_ReferenceItf.h | 25 +-
...FragmentItf.cpp => py_ReferenceSequenceItf.cpp} | 12 +-
...ventIteratorItf.h => py_ReferenceSequenceItf.h} | 12 +-
ngs-sdk/language/python/py_StatisticsItf.h | 12 +-
ngs-sdk/language/python/py_StringItf.h | 6 +-
ngs-sdk/language/python/py_ngs_defs.h | 5 +
ngs-sdk/ngs/Alignment.hpp | 32 +-
ngs-sdk/ngs/Fragment.hpp | 14 +
ngs-sdk/ngs/{itf/PileupItf.hpp => Package.hpp} | 53 +-
ngs-sdk/ngs/Pileup.hpp | 18 +-
ngs-sdk/ngs/PileupEvent.hpp | 135 +-
ngs-sdk/ngs/PileupEventIterator.hpp | 8 +
ngs-sdk/ngs/PileupIterator.hpp | 1 +
ngs-sdk/ngs/Read.hpp | 11 +-
ngs-sdk/ngs/ReadCollection.hpp | 12 +
ngs-sdk/ngs/Reference.hpp | 41 +
.../ngs/{Fragment.hpp => ReferenceSequence.hpp} | 83 +-
ngs-sdk/ngs/StringRef.hpp | 2 +-
ngs-sdk/ngs/adapter/AlignmentItf.hpp | 2 +
ngs-sdk/ngs/adapter/PileupEventItf.hpp | 17 +-
ngs-sdk/ngs/adapter/PileupItf.hpp | 22 +-
ngs-sdk/ngs/adapter/ReadCollectionItf.hpp | 4 +
ngs-sdk/ngs/adapter/ReferenceItf.hpp | 9 +
.../{PileupItf.hpp => ReferenceSequenceItf.hpp} | 42 +-
ngs-sdk/ngs/adapter/defs.h | 11 +-
ngs-sdk/ngs/inl/Alignment.hpp | 12 +-
ngs-sdk/ngs/inl/AlignmentIterator.hpp | 2 +-
ngs-sdk/ngs/inl/Fragment.hpp | 12 +-
ngs-sdk/ngs/inl/FragmentIterator.hpp | 2 +-
.../ngs/inl/{PileupIterator.hpp => Package.hpp} | 22 +-
ngs-sdk/ngs/inl/Pileup.hpp | 10 +-
ngs-sdk/ngs/inl/PileupEvent.hpp | 26 +-
ngs-sdk/ngs/inl/PileupEventIterator.hpp | 7 +-
ngs-sdk/ngs/inl/PileupIterator.hpp | 9 +-
ngs-sdk/ngs/inl/Read.hpp | 5 +
ngs-sdk/ngs/inl/ReadCollection.hpp | 10 +
ngs-sdk/ngs/inl/ReadIterator.hpp | 2 +-
ngs-sdk/ngs/inl/Reference.hpp | 31 +-
ngs-sdk/ngs/inl/ReferenceIterator.hpp | 2 +-
.../inl/{Fragment.hpp => ReferenceSequence.hpp} | 46 +-
ngs-sdk/ngs/inl/StringRef.hpp | 2 +-
ngs-sdk/ngs/itf/AlignmentItf.h | 3 +
ngs-sdk/ngs/itf/AlignmentItf.hpp | 2 +
ngs-sdk/ngs/itf/FragmentItf.h | 5 +
ngs-sdk/ngs/itf/FragmentItf.hpp | 4 +
.../FragmentIterator.hpp => itf/PackageItf.hpp} | 33 +-
ngs-sdk/ngs/itf/PileupEventItf.h | 8 +-
ngs-sdk/ngs/itf/PileupEventItf.hpp | 13 +-
ngs-sdk/ngs/itf/PileupItf.h | 2 +-
ngs-sdk/ngs/itf/PileupItf.hpp | 3 +-
ngs-sdk/ngs/itf/ReadCollectionItf.h | 5 +
ngs-sdk/ngs/itf/ReadCollectionItf.hpp | 4 +
ngs-sdk/ngs/itf/ReadItf.h | 3 +
ngs-sdk/ngs/itf/ReadItf.hpp | 2 +
ngs-sdk/ngs/itf/ReferenceItf.h | 24 +
ngs-sdk/ngs/itf/ReferenceItf.hpp | 12 +-
.../itf/{PileupItf.h => ReferenceSequenceItf.h} | 32 +-
.../{FragmentItf.hpp => ReferenceSequenceItf.hpp} | 29 +-
.../py_ngs_defs.h => ngs/unix/fat86/atomic32.h} | 18 +-
ngs-sdk/ngs/unix/i386/atomic32.h | 366 +
ngs-sdk/ngs/unix/x86_64/atomic32.h | 365 +
ngs-sdk/{ => ngs}/win/atomic32.h | 8 +-
ngs-sdk/setup/install.perl | 9 +-
ngs-sdk/setup/install.prl | 1 +
ngs-sdk/setup/konfigure.perl | 431 +-
ngs-sdk/setup/os-arch.prl | 6 +-
ngs-sdk/setup/package.prl | 4 +-
ngs-sdk/test/ngs-test/main.cpp | 51 +-
ngs-sdk/test/test_engine/AlignmentItf.hpp | 5 +
ngs-sdk/test/test_engine/Makefile | 2 +-
ngs-sdk/test/test_engine/PileupEventItf.hpp | 30 +-
ngs-sdk/test/test_engine/PileupItf.hpp | 103 +-
ngs-sdk/test/test_engine/ReadCollectionItf.hpp | 10 +
ngs-sdk/test/test_engine/ReferenceItf.hpp | 15 +
.../{PileupItf.hpp => ReferenceSequenceItf.hpp} | 62 +-
ngs-sdk/test/test_engine/test_engine.cpp | 2 -
ngs-sdk/win/libadapter.vcxproj | 2 +
ngs-sdk/win/libadapter.vcxproj.filters | 6 +
ngs-sdk/win/libdispatch.vcxproj | 5 +
ngs-sdk/win/libdispatch.vcxproj.filters | 15 +
ngs-sdk/win/libngs-c++.vcxproj | 1 +
ngs-sdk/win/libngs-c++.vcxproj.filters | 3 +
ngs-sdk/win/libtest_engine.vcxproj | 58 +-
ngs-sdk/win/libtest_engine.vcxproj.filters | 3 +
ngs-sdk/win/ngs-common.props | 6 +-
ngs-sdk/win/ngs-sdk.sln | 248 +-
ngs-sdk/win/ngs-sdk.vcxproj | 231 +-
ngs-sdk/win/ngs-sdk.vcxproj.filters | 348 +-
ngs-sdk/win/ngs-test.vcxproj | 93 +-
268 files changed, 38368 insertions(+), 3448 deletions(-)
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