[med-svn] [ngs-sdk] branch upstream updated (e66c5d5 -> 97eabb4)
Andreas Tille
tille at debian.org
Mon Jun 6 10:55:56 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository ngs-sdk.
from e66c5d5 Imported Upstream version 1.2.3
new 97eabb4 Imported Upstream version 1.2.4
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 | 9 +
configure => CHANGES | 40 +-
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 ++++
.../ngs/{FileCreator.java => LibDependencies.java} | 14 +-
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 +-
.../error/LibraryIncompatibleVersionError.java} | 61 +-
.../nih/nlm/ncbi/ngs/error/LibraryLoadError.java | 80 ++
.../LibraryNotFoundError.java} | 12 +-
.../cause/ConnectionProblemCause.java} | 16 +-
.../cause/DownloadDisabledCause.java} | 16 +-
.../cause/InvalidLibraryCause.java} | 15 +-
.../cause/JvmErrorCause.java} | 17 +-
.../cause/LibraryLoadCause.java} | 12 +-
.../cause/OutdatedJarCause.java} | 16 +-
.../cause/PrereleaseReqLibCause.java} | 16 +-
.../cause/UnsupportedArchCause.java} | 17 +-
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, 6506 insertions(+), 2434 deletions(-)
copy configure => CHANGES (52%)
mode change 100755 => 100644
create mode 100644 CHANGES.md
create mode 100644 ngs-java/examples/examples/DumpReferenceFASTA.java
create mode 100644 ngs-java/gov/nih/nlm/ncbi/ngs/DownloadManager.java
create mode 100644 ngs-java/gov/nih/nlm/ncbi/ngs/LMProperties.java
copy ngs-java/gov/nih/nlm/ncbi/ngs/{FileCreator.java => LibDependencies.java} (84%)
create mode 100644 ngs-java/gov/nih/nlm/ncbi/ngs/LibVersionChecker.java
copy ngs-java/{ngs/itf/Refcount.java => gov/nih/nlm/ncbi/ngs/error/LibraryIncompatibleVersionError.java} (57%)
create mode 100644 ngs-java/gov/nih/nlm/ncbi/ngs/error/LibraryLoadError.java
copy ngs-java/gov/nih/nlm/ncbi/ngs/{FileCreator.java => error/LibraryNotFoundError.java} (81%)
copy ngs-java/gov/nih/nlm/ncbi/ngs/{FileCreator.java => error/cause/ConnectionProblemCause.java} (72%)
copy ngs-java/gov/nih/nlm/ncbi/ngs/{FileCreator.java => error/cause/DownloadDisabledCause.java} (75%)
copy ngs-java/gov/nih/nlm/ncbi/ngs/{FileCreator.java => error/cause/InvalidLibraryCause.java} (77%)
copy ngs-java/gov/nih/nlm/ncbi/ngs/{FileCreator.java => error/cause/JvmErrorCause.java} (81%)
copy ngs-java/gov/nih/nlm/ncbi/ngs/{FileCreator.java => error/cause/LibraryLoadCause.java} (84%)
copy ngs-java/gov/nih/nlm/ncbi/ngs/{FileCreator.java => error/cause/OutdatedJarCause.java} (77%)
copy ngs-java/gov/nih/nlm/ncbi/ngs/{FileCreator.java => error/cause/PrereleaseReqLibCause.java} (75%)
copy ngs-java/gov/nih/nlm/ncbi/ngs/{FileCreator.java => error/cause/UnsupportedArchCause.java} (73%)
copy ngs-python/examples/{AlignTest.py => DumpReferenceFASTA.py} (53%)
delete mode 100644 ngs-sdk/language/python/py_ErrorMsg.cpp
rename ngs-sdk/{ => ngs}/win/stdbool.h (100%)
delete mode 100644 ngs-sdk/win/.gitignore
create mode 100644 ngs-sdk/win/build.xml
create mode 100644 ngs-sdk/win/libadapter.files
delete mode 100644 ngs-sdk/win/libadapter.vcxproj
create mode 100644 ngs-sdk/win/libdispatch.files
delete mode 100644 ngs-sdk/win/libdispatch.vcxproj
create mode 100644 ngs-sdk/win/libngs-c++.files
delete mode 100644 ngs-sdk/win/libngs-c++.vcxproj
create mode 100644 ngs-sdk/win/libtest_engine.files
delete mode 100644 ngs-sdk/win/libtest_engine.vcxproj
create mode 100644 ngs-sdk/win/ngs-sdk.files
delete mode 100644 ngs-sdk/win/ngs-sdk.vcxproj
create mode 100644 ngs-sdk/win/ngs-test.files
create mode 100644 ngs-sdk/win/vs2010/.gitignore
create mode 100644 ngs-sdk/win/vs2010/ipch/libadapter-2137bad9/libngs-adapt-c++-4ff9a6f5.ipch
copy ngs-sdk/win/{ => vs2010}/lib-project.props (57%)
create mode 100644 ngs-sdk/win/vs2010/libadapter.vcxproj
copy ngs-sdk/win/{ => vs2010}/libadapter.vcxproj.filters (100%)
create mode 100644 ngs-sdk/win/vs2010/libdispatch.vcxproj
copy ngs-sdk/win/{ => vs2010}/libdispatch.vcxproj.filters (100%)
create mode 100644 ngs-sdk/win/vs2010/libngs-c++.vcxproj
copy ngs-sdk/win/{ => vs2010}/libngs-c++.vcxproj.filters (100%)
create mode 100644 ngs-sdk/win/vs2010/libtest_engine.vcxproj
copy ngs-sdk/win/{ => vs2010}/libtest_engine.vcxproj.filters (100%)
copy ngs-sdk/win/{ => vs2010}/ngs-common.props (84%)
copy ngs-sdk/win/{ => vs2010}/ngs-sdk.sln (100%)
create mode 100644 ngs-sdk/win/vs2010/ngs-sdk.vcxproj
copy ngs-sdk/win/{ => vs2010}/ngs-sdk.vcxproj.filters (100%)
copy ngs-sdk/win/{ => vs2010}/ngs-test.vcxproj (59%)
copy ngs-sdk/win/{ => vs2010}/ngs-test.vcxproj.filters (100%)
create mode 100644 ngs-sdk/win/vs2013/.gitignore
rename ngs-sdk/win/{ => vs2013}/lib-project.props (57%)
create mode 100644 ngs-sdk/win/vs2013/libadapter.vcxproj
rename ngs-sdk/win/{ => vs2013}/libadapter.vcxproj.filters (97%)
create mode 100644 ngs-sdk/win/vs2013/libdispatch.vcxproj
rename ngs-sdk/win/{ => vs2013}/libdispatch.vcxproj.filters (100%)
create mode 100644 ngs-sdk/win/vs2013/libngs-c++.vcxproj
rename ngs-sdk/win/{ => vs2013}/libngs-c++.vcxproj.filters (100%)
create mode 100644 ngs-sdk/win/vs2013/libtest_engine.vcxproj
rename ngs-sdk/win/{ => vs2013}/libtest_engine.vcxproj.filters (96%)
rename ngs-sdk/win/{ => vs2013}/ngs-common.props (68%)
rename ngs-sdk/win/{ => vs2013}/ngs-sdk.sln (98%)
create mode 100644 ngs-sdk/win/vs2013/ngs-sdk.vcxproj
rename ngs-sdk/win/{ => vs2013}/ngs-sdk.vcxproj.filters (97%)
rename ngs-sdk/win/{ => vs2013}/ngs-test.vcxproj (59%)
rename ngs-sdk/win/{ => vs2013}/ngs-test.vcxproj.filters (96%)
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