[med-svn] [ngs-sdk] 01/01: Merge tag 'debian/1.2.4-2' into debian/jessie-backports
Andreas Tille
tille at debian.org
Tue Jul 12 13:32:14 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch debian/jessie-backports
in repository ngs-sdk.
commit b16068223b941a5a29b348dfaf6c459a5974a92c
Merge: f7c544e 13e12c1
Author: Andreas Tille <tille at debian.org>
Date: Tue Jul 12 15:21:28 2016 +0200
Merge tag 'debian/1.2.4-2' into debian/jessie-backports
ngs-sdk Debian release 1.2.4-2
Conflicts:
debian/changelog
.gitignore | 9 +
Makefile => CHANGES | 56 +-
CHANGES.md | 16 +
Makefile | 1 -
configure | 2 +-
debian/changelog | 19 +
debian/control | 4 +-
debian/libngs-java.poms | 29 +
debian/ngs-java.pom | 34 +
debian/ngs-java.pom.asc | 17 +
debian/rules | 17 +-
debian/source/include-binaries | 1 +
debian/sra-tools.gpg | Bin 0 -> 2262 bytes
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 +
.../examples/{RefTest.py => DumpReferenceFASTA.py} | 64 +-
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 +-
139 files changed, 6645 insertions(+), 2497 deletions(-)
diff --cc debian/changelog
index 55f2d08,0f57548..0b61671
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,16 +1,28 @@@
++ngs-sdk (1.2.4-2~bpo8+1) jessie-backports; urgency=medium
++
++ * Rebuild for jessie-backports.
++
++ -- Andreas Tille <tille at debian.org> Tue, 12 Jul 2016 15:21:16 +0200
++
+ ngs-sdk (1.2.4-2) unstable; urgency=medium
+
+ * Add a maven2 pom file for libjava-ngs
+
+ -- Vincent Danjean <vdanjean at debian.org> Wed, 06 Jul 2016 21:57:29 +0200
+
+ ngs-sdk (1.2.4-1) unstable; urgency=medium
+
+ * New upstream version
+ * Add missing header files to devel package
+
+ -- Andreas Tille <tille at debian.org> Mon, 06 Jun 2016 12:54:51 +0200
+
+ngs-sdk (1.2.3-3~bpo8+1) jessie-backports; urgency=medium
+
+ * Rebuild for jessie-backports.
+
+ -- Andreas Tille <tille at debian.org> Wed, 13 Apr 2016 14:32:12 +0200
+
ngs-sdk (1.2.3-3) unstable; urgency=medium
[ Andreas Tille ]
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