[med-svn] [ngs-sdk] 02/03: Merge tag 'upstream/1.0.1'
Andreas Tille
tille at debian.org
Mon Feb 2 10:44:26 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 b492824c5cc94d0bb1e4a437f0ab1c6c7cd22037
Merge: 29d28b8 3387fab
Author: Andreas Tille <tille at debian.org>
Date: Mon Feb 2 11:43:30 2015 +0100
Merge tag 'upstream/1.0.1'
Upstream version 1.0.1
.gitignore | 5 +-
ngs-python/Makefile => Makefile | 39 +-
configure | 32 +-
ngs-bam/.gitignore | 2 +
{ngs-python => ngs-bam}/Makefile | 24 +-
ngs-bam/Makefile.libs | 112 ++
{ngs-sdk => ngs-bam}/Makefile.rules | 8 +-
ngs-bam/bam.cpp | 682 ++++++++++
ngs-bam/bam.hpp | 547 ++++++++
{ngs-python => ngs-bam}/configure | 6 +-
ngs-bam/ngs-bam.cpp | 632 ++++++++++
ngs-bam/ngs-bam/ngs-bam.hpp | 45 +
ngs-python/configure => ngs-bam/setup/install | 10 +-
ngs-bam/setup/install.perl | 1324 ++++++++++++++++++++
ngs-bam/setup/install.prl | 6 +
{ngs-java => ngs-bam/setup}/konfigure.perl | 782 ++++++++----
.../configure => ngs-bam/setup/ngs-bam/install | 12 +-
ngs-bam/setup/ngs-bam/linux/os.prl | 2 +
ngs-bam/setup/ngs-bam/mac/os.prl | 2 +
{ngs-java => ngs-bam/setup}/os-arch.perl | 4 +-
ngs-java/os-arch.pm => ngs-bam/setup/os-arch.prl | 6 +-
ngs-bam/setup/package.prl | 31 +
ngs-java/.gitignore | 9 +-
ngs-java/Makefile.java | 45 +-
ngs-java/Makefile.rules | 4 +-
ngs-java/configure | 6 +-
.../gov/nih/nlm/ncbi/ngs/HttpException.java | 27 +-
ngs-java/gov/nih/nlm/ncbi/ngs/HttpManager.java | 94 +-
ngs-java/gov/nih/nlm/ncbi/ngs/LibManager.java | 122 +-
ngs-java/gov/nih/nlm/ncbi/ngs/LibPathIterator.java | 95 +-
ngs-java/gov/nih/nlm/ncbi/ngs/Makefile | 37 +-
ngs-java/gov/nih/nlm/ncbi/ngs/Manager.java | 13 +-
ngs-java/ngs/Alignment.java | 9 +
ngs-java/ngs/Fragment.java | 4 +-
ngs-java/ngs/Read.java | 4 +-
ngs-java/ngs/ReadCollection.java | 5 +-
ngs-java/ngs/Reference.java | 4 +-
ngs-java/ngs/itf/AlignmentItf.java | 12 +
ngs-java/package.pm | 29 -
ngs-python/configure => ngs-java/setup/install | 10 +-
ngs-java/setup/install.perl | 1324 ++++++++++++++++++++
ngs-java/setup/install.prl | 4 +
{ngs-python => ngs-java/setup}/konfigure.perl | 782 ++++++++----
.../configure => ngs-java/setup/ngs-java/install | 12 +-
ngs-java/setup/ngs-java/linux/os.prl | 2 +
ngs-java/setup/ngs-java/mac/os.prl | 2 +
{ngs-python => ngs-java/setup}/os-arch.perl | 4 +-
ngs-sdk/os-arch.pm => ngs-java/setup/os-arch.prl | 6 +-
ngs-java/setup/package.prl | 17 +
ngs-java/win-configure.bat | 2 -
ngs-python/.gitignore | 9 +-
ngs-python/Makefile | 2 +-
ngs-python/Makefile.python | 17 +-
ngs-python/Makefile.rules | 4 +-
ngs-python/configure | 6 +-
ngs-python/examples/AlignSliceTest.py | 67 +
ngs-python/examples/AlignSliceTest26.py | 67 +
ngs-python/examples/AlignTest.py | 73 ++
ngs-python/examples/AlignTest26.py | 73 ++
ngs-python/examples/FragTest.py | 70 ++
ngs-python/examples/FragTest26.py | 70 ++
ngs-python/examples/RefTest.py | 62 +
ngs-python/examples/RefTest26.py | 63 +
ngs-python/ngs/Alignment.py | 47 +-
ngs-python/ngs/AlignmentIterator.py | 4 +-
ngs-python/ngs/Fragment.py | 30 +-
ngs-python/ngs/FragmentIterator.py | 4 +-
ngs-python/ngs/LibManager.py | 187 ++-
ngs-python/ngs/Pileup.py | 6 +-
ngs-python/ngs/PileupEvent.py | 6 +-
ngs-python/ngs/PileupEventIterator.py | 4 +-
ngs-python/ngs/PileupIterator.py | 4 +-
ngs-python/ngs/Read.py | 31 +-
ngs-python/ngs/ReadCollection.py | 107 +-
ngs-python/ngs/ReadGroup.py | 6 +-
ngs-python/ngs/ReadGroupIterator.py | 4 +-
ngs-python/ngs/ReadIterator.py | 4 +-
ngs-python/ngs/Refcount.py | 12 +-
ngs-python/ngs/Reference.py | 68 +-
ngs-python/ngs/ReferenceIterator.py | 4 +-
ngs-python/ngs/Statistics.py | 50 +-
ngs-python/ngs/String.py | 26 +-
ngs-python/ngs/__init__.py | 2 +-
ngs-python/setup.py | 8 +-
ngs-python/{configure => setup/install} | 10 +-
ngs-python/setup/install.perl | 1324 ++++++++++++++++++++
ngs-python/setup/install.prl | 4 +
{ngs-sdk => ngs-python/setup}/konfigure.perl | 782 ++++++++----
ngs-python/{configure => setup/ngs-python/install} | 12 +-
ngs-python/setup/ngs-python/linux/os.prl | 2 +
ngs-python/setup/ngs-python/mac/os.prl | 2 +
{ngs-sdk => ngs-python/setup}/os-arch.perl | 4 +-
ngs-python/{os-arch.pm => setup/os-arch.prl} | 6 +-
ngs-python/{package.pm => setup/package.prl} | 26 +-
ngs-python/win-configure.bat | 1 -
ngs-sdk/.gitignore | 13 +-
ngs-sdk/Makefile.install | 18 +-
ngs-sdk/Makefile.libs | 14 +-
ngs-sdk/Makefile.rules | 4 +-
ngs-sdk/adapter/AlignmentItf.cpp | 23 +-
ngs-sdk/adapter/Makefile | 2 +-
.../{ngs/defs.h => adapter/unix/fat86/atomic32.h} | 20 +-
ngs-sdk/configure | 6 +-
ngs-sdk/dispatch/AlignmentItf.cpp | 24 +
ngs-sdk/language/java/jni_AlignmentItf.cpp | 28 +
ngs-sdk/language/java/jni_AlignmentItf.h | 8 +
ngs-sdk/language/python/py_AlignmentItf.cpp | 1 +
ngs-sdk/language/python/py_AlignmentItf.h | 1 +
ngs-sdk/ngs/Alignment.hpp | 10 +-
ngs-sdk/ngs/AlignmentIterator.hpp | 2 +-
ngs-sdk/ngs/Fragment.hpp | 2 +-
ngs-sdk/ngs/FragmentIterator.hpp | 2 +-
ngs-sdk/ngs/Pileup.hpp | 2 +-
ngs-sdk/ngs/PileupEvent.hpp | 47 +-
ngs-sdk/ngs/PileupEventIterator.hpp | 2 +-
ngs-sdk/ngs/PileupIterator.hpp | 2 +-
ngs-sdk/ngs/Read.hpp | 2 +-
ngs-sdk/ngs/ReadCollection.hpp | 2 +-
ngs-sdk/ngs/ReadGroup.hpp | 2 +-
ngs-sdk/ngs/ReadGroupIterator.hpp | 2 +-
ngs-sdk/ngs/ReadIterator.hpp | 2 +-
ngs-sdk/ngs/Reference.hpp | 2 +-
ngs-sdk/ngs/ReferenceIterator.hpp | 2 +-
ngs-sdk/ngs/Statistics.hpp | 2 +-
ngs-sdk/ngs/StringRef.hpp | 8 +-
ngs-sdk/ngs/adapter/AlignmentItf.hpp | 2 +
ngs-sdk/ngs/itf/AlignmentItf.h | 4 +
ngs-sdk/ngs/itf/AlignmentItf.hpp | 4 +-
ngs-sdk/ngs/itf/ErrBlock.hpp | 2 +-
ngs-sdk/ngs/itf/ErrorMsg.hpp | 2 +-
ngs-sdk/ngs/itf/FragmentItf.hpp | 2 +-
ngs-sdk/ngs/itf/PileupEventItf.hpp | 2 +-
ngs-sdk/ngs/itf/PileupItf.hpp | 2 +-
ngs-sdk/ngs/itf/ReadCollectionItf.hpp | 2 +-
ngs-sdk/ngs/itf/ReadGroupItf.hpp | 2 +-
ngs-sdk/ngs/itf/ReadItf.hpp | 2 +-
ngs-sdk/ngs/itf/Refcount.hpp | 4 +-
ngs-sdk/ngs/itf/ReferenceItf.hpp | 2 +-
ngs-sdk/ngs/itf/StatisticsItf.hpp | 2 +-
ngs-sdk/ngs/itf/StringItf.hpp | 2 +-
ngs-sdk/ngs/itf/defs.h | 13 -
ngs-python/configure => ngs-sdk/setup/install | 10 +-
ngs-sdk/setup/install.perl | 1324 ++++++++++++++++++++
ngs-sdk/setup/install.prl | 6 +
{ngs-java => ngs-sdk/setup}/konfigure.perl | 782 ++++++++----
.../configure => ngs-sdk/setup/ngs-c++/install | 12 +-
ngs-sdk/setup/ngs-c++/install.prl | 5 +
ngs-sdk/setup/ngs-c++/linux/os.prl | 2 +
ngs-sdk/setup/ngs-c++/mac/os.prl | 2 +
.../setup/ngs-engine-dev/install | 12 +-
ngs-sdk/setup/ngs-engine-dev/install.prl | 5 +
ngs-sdk/setup/ngs-engine-dev/linux/os.prl | 2 +
ngs-sdk/setup/ngs-engine-dev/mac/os.prl | 2 +
{ngs-java => ngs-sdk/setup}/os-arch.perl | 4 +-
ngs-java/os-arch.pm => ngs-sdk/setup/os-arch.prl | 6 +-
ngs-sdk/{package.pm => setup/package.prl} | 3 +-
ngs-sdk/test/test_engine/AlignmentItf.hpp | 7 +-
ngs-sdk/test/test_engine/PileupEventItf.hpp | 2 +-
ngs-sdk/test/test_engine/PileupItf.hpp | 2 +-
ngs-sdk/test/test_engine/ReadCollectionItf.hpp | 2 +-
ngs-sdk/test/test_engine/ReadGroupItf.hpp | 2 +-
ngs-sdk/test/test_engine/ReadItf.hpp | 2 +-
ngs-sdk/test/test_engine/ReferenceItf.hpp | 2 +-
ngs-sdk/test/test_engine/StatisticsItf.hpp | 2 +-
ngs-sdk/test/test_engine/test_engine.cpp | 18 +-
ngs-sdk/test/test_engine/test_engine.hpp | 2 +-
ngs-sdk/win-configure.bat | 2 -
ngs-sdk/win/lib-project.props | 13 +
ngs-sdk/win/libadapter.vcxproj | 211 +---
ngs-sdk/win/libdispatch.vcxproj | 242 +---
ngs-sdk/win/libngs-c++.vcxproj | 189 +--
ngs-sdk/win/libngs.vcxproj | 187 ---
ngs-sdk/win/libngs.vcxproj.filters | 123 --
ngs-sdk/win/libtest_engine.vcxproj | 207 +--
ngs-sdk/win/ngs-common.props | 73 +-
ngs-sdk/win/ngs-sdk.vcxproj | 262 ++--
ngs-sdk/win/ngs-test.vcxproj | 202 +--
177 files changed, 11697 insertions(+), 2903 deletions(-)
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