[med-svn] [ngs-sdk] branch upstream updated (b17318c -> 3387fab)
Andreas Tille
tille at debian.org
Mon Feb 2 10:44:27 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository ngs-sdk.
from b17318c Imported Upstream version 1.0.0
new 3387fab Imported Upstream version 1.0.1
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.gitignore | 5 +-
ngs-sdk/language/Makefile => Makefile | 29 +-
configure | 32 +-
ngs-bam/.gitignore | 2 +
{ngs-sdk => ngs-bam}/Makefile | 21 +-
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-sdk/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 +-
.../ngs/{FileCreator.java => HttpException.java} | 16 +-
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-java/{os-arch.pm => 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 +-
.../ErrorMsg.hpp => adapter/unix/fat86/atomic32.h} | 13 +-
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/defs.h | 43 -
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-sdk/{os-arch.pm => 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 +--
178 files changed, 11684 insertions(+), 2928 deletions(-)
copy ngs-sdk/language/Makefile => Makefile (82%)
create mode 100644 ngs-bam/.gitignore
copy {ngs-sdk => ngs-bam}/Makefile (85%)
create mode 100644 ngs-bam/Makefile.libs
copy {ngs-sdk => ngs-bam}/Makefile.rules (90%)
create mode 100644 ngs-bam/bam.cpp
create mode 100644 ngs-bam/bam.hpp
copy {ngs-python => ngs-bam}/configure (93%)
create mode 100644 ngs-bam/ngs-bam.cpp
create mode 100644 ngs-bam/ngs-bam/ngs-bam.hpp
copy ngs-python/configure => ngs-bam/setup/install (83%)
create mode 100644 ngs-bam/setup/install.perl
create mode 100644 ngs-bam/setup/install.prl
copy {ngs-java => ngs-bam/setup}/konfigure.perl (60%)
copy ngs-python/configure => ngs-bam/setup/ngs-bam/install (82%)
create mode 100644 ngs-bam/setup/ngs-bam/linux/os.prl
create mode 100644 ngs-bam/setup/ngs-bam/mac/os.prl
copy {ngs-java => ngs-bam/setup}/os-arch.perl (80%)
copy ngs-sdk/os-arch.pm => ngs-bam/setup/os-arch.prl (95%)
create mode 100644 ngs-bam/setup/package.prl
copy ngs-java/gov/nih/nlm/ncbi/ngs/{FileCreator.java => HttpException.java} (80%)
delete mode 100644 ngs-java/package.pm
copy ngs-python/configure => ngs-java/setup/install (83%)
create mode 100644 ngs-java/setup/install.perl
create mode 100644 ngs-java/setup/install.prl
rename {ngs-python => ngs-java/setup}/konfigure.perl (60%)
copy ngs-python/configure => ngs-java/setup/ngs-java/install (82%)
create mode 100644 ngs-java/setup/ngs-java/linux/os.prl
create mode 100644 ngs-java/setup/ngs-java/mac/os.prl
rename {ngs-python => ngs-java/setup}/os-arch.perl (80%)
rename ngs-java/{os-arch.pm => setup/os-arch.prl} (95%)
create mode 100644 ngs-java/setup/package.prl
delete mode 100644 ngs-java/win-configure.bat
create mode 100644 ngs-python/examples/AlignSliceTest.py
create mode 100644 ngs-python/examples/AlignSliceTest26.py
create mode 100644 ngs-python/examples/AlignTest.py
create mode 100644 ngs-python/examples/AlignTest26.py
create mode 100644 ngs-python/examples/FragTest.py
create mode 100644 ngs-python/examples/FragTest26.py
create mode 100644 ngs-python/examples/RefTest.py
create mode 100644 ngs-python/examples/RefTest26.py
copy ngs-python/{configure => setup/install} (83%)
create mode 100644 ngs-python/setup/install.perl
create mode 100644 ngs-python/setup/install.prl
rename {ngs-sdk => ngs-python/setup}/konfigure.perl (60%)
copy ngs-python/{configure => setup/ngs-python/install} (82%)
create mode 100644 ngs-python/setup/ngs-python/linux/os.prl
create mode 100644 ngs-python/setup/ngs-python/mac/os.prl
rename {ngs-sdk => ngs-python/setup}/os-arch.perl (80%)
rename ngs-python/{os-arch.pm => setup/os-arch.prl} (95%)
rename ngs-python/{package.pm => setup/package.prl} (67%)
delete mode 100644 ngs-python/win-configure.bat
copy ngs-sdk/{ngs/ErrorMsg.hpp => adapter/unix/fat86/atomic32.h} (88%)
delete mode 100644 ngs-sdk/ngs/defs.h
copy ngs-python/configure => ngs-sdk/setup/install (83%)
create mode 100644 ngs-sdk/setup/install.perl
create mode 100644 ngs-sdk/setup/install.prl
rename {ngs-java => ngs-sdk/setup}/konfigure.perl (60%)
copy ngs-python/configure => ngs-sdk/setup/ngs-c++/install (82%)
create mode 100644 ngs-sdk/setup/ngs-c++/install.prl
create mode 100644 ngs-sdk/setup/ngs-c++/linux/os.prl
create mode 100644 ngs-sdk/setup/ngs-c++/mac/os.prl
copy ngs-python/configure => ngs-sdk/setup/ngs-engine-dev/install (82%)
create mode 100644 ngs-sdk/setup/ngs-engine-dev/install.prl
create mode 100644 ngs-sdk/setup/ngs-engine-dev/linux/os.prl
create mode 100644 ngs-sdk/setup/ngs-engine-dev/mac/os.prl
rename {ngs-java => ngs-sdk/setup}/os-arch.perl (80%)
rename ngs-sdk/{os-arch.pm => setup/os-arch.prl} (95%)
rename ngs-sdk/{package.pm => setup/package.prl} (86%)
delete mode 100644 ngs-sdk/win-configure.bat
create mode 100644 ngs-sdk/win/lib-project.props
delete mode 100644 ngs-sdk/win/libngs.vcxproj
delete mode 100644 ngs-sdk/win/libngs.vcxproj.filters
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