[med-svn] [sra-sdk] 02/07: Updated version 2.8.2-3+dfsg from 'upstream/2.8.2-3+dfsg'
Andreas Tille
tille at debian.org
Thu Oct 19 22:15:21 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository sra-sdk.
commit 82aa43785de34cc5751d5bc4e96aff2e01e5730d
Merge: 41b9a17 03cd16f
Author: Andreas Tille <tille at debian.org>
Date: Thu Oct 19 23:58:18 2017 +0200
Updated version 2.8.2-3+dfsg from 'upstream/2.8.2-3+dfsg'
with Debian dir 84cddd546b09799cd64f085fe5fc3476566e44a9
CHANGES.md | 30 ++
build/Makefile.vers | 2 +-
setup/konfigure.perl | 96 +++--
shared/toolkit.vers | 2 +-
shared/toolkit.vers.h | 2 +-
test/Makefile | 1 +
test/dbgap-mount/jaba/App.java | 212 ++++++++++
test/dbgap-mount/jaba/AppTerminator.java | 11 +
test/dbgap-mount/jaba/DbGapMountTest.java | 54 +++
test/dbgap-mount/jaba/DbGapMountTestEnv.java | 242 +++++++++++
test/dbgap-mount/jaba/Utils.java | 396 +++++++++++++++++
test/dbgap-mount/jaba/WrapCmd.java | 280 ++++++++++++
test/dbgap-mount/jaba/platform/Platform.java | 85 ++++
test/dbgap-mount/jaba/platform/PlatformLinux.java | 33 ++
test/dbgap-mount/jaba/platform/PlatformMac.java | 40 ++
test/dbgap-mount/jaba/platform/PlatformSuper.java | 166 ++++++++
test/dbgap-mount/jaba/platform/PlatformWin.java | 78 ++++
test/dbgap-mount/jaba/test/Test.java | 30 ++
test/dbgap-mount/jaba/test/TestBasicBase.java | 120 ++++++
test/dbgap-mount/jaba/test/TestFunctionality.java | 97 +++++
.../jaba/test/TestRunStopBadConfig.java | 92 ++++
test/dbgap-mount/jaba/test/TestRunStopDaemon.java | 124 ++++++
.../jaba/test/TestRunStopGoodConfig.java | 106 +++++
.../dbgap-mount/jaba/test/TestRunStopNoConfig.java | 92 ++++
.../jaba/test/TestRunStopNoParameters.java | 87 ++++
test/dbgap-mount/jaba/test/TestSuper.java | 467 +++++++++++++++++++++
test/dbgap-mount/jaba/test/TestWorkspace.java | 179 ++++++++
test/dbgap-mount/jaba/test/Tests.java | 171 ++++++++
test/dbgap-mount/py/main.py | 17 +
test/dbgap-mount/py/platform/__init__.py | 14 +
test/dbgap-mount/py/platform/base.py | 123 ++++++
test/dbgap-mount/py/platform/lin.py | 9 +
test/dbgap-mount/py/platform/mac.py | 12 +
test/dbgap-mount/py/platform/win.py | 33 ++
test/dbgap-mount/py/test/__init__.py | 7 +
test/dbgap-mount/py/test/base.py | 160 +++++++
test/dbgap-mount/py/test/test.py | 125 ++++++
test/dbgap-mount/py/test/utils.py | 79 ++++
test/general-loader/Makefile | 2 +
.../VDB-3250}/Makefile | 57 ++-
test/general-loader/VDB-3250/check_test_result.cpp | 385 +++++++++++++++++
test/general-loader/VDB-3250/prepare_test_data.cpp | 257 ++++++++++++
test/general-loader/VDB-3250/prepare_test_data.sh | 190 +++++++++
test/general-loader/VDB-3250/test_data.bin | Bin 0 -> 122136 bytes
test/general-loader/VDB-3250/test_data.vschema | 65 +++
test/sra-pileup/Makefile | 18 +
test/sra-pileup/test_all_sam_dump_has_spotgroup.py | 92 ++++
.../sra-pileup/test_diff_fastq_dump_vs_sam_dump.py | 245 +++++++++++
build/Makefile.vers => test/vdb-config/Makefile | 13 +-
test/vdb-config/test-vdb-config.pl | 12 +
tools/bam-loader/bam.c | 2 +
tools/bam-loader/loader-imp.c | 10 +
tools/bam-loader/sam.l | 172 ++++++++
tools/bam-loader/sam.y | 396 +++++++++++++++++
tools/bam-loader/samview.c | 1 +
tools/general-loader/general-loader.hpp | 2 +-
tools/general-loader/protocol-parser.cpp | 2 +-
tools/prefetch/prefetch.c | 16 +-
tools/sra-dump/fastq.c | 4 +-
tools/sra-pileup/sam-aligned.c | 2 +-
tools/sra-pileup/sam-unaligned.c | 96 ++++-
tools/sra-stat/sra-stat.c | 69 ++-
tools/util/pseudo-aligner.cpp | 35 +-
tools/util/test-sra.c | 356 +++++++++++-----
tools/vdb-config/configure.cpp | 52 ++-
tools/vdb-config/util.cpp | 108 +++--
tools/vdb-config/util.hpp | 5 +
tools/vdb-config/vdb-config-model.cpp | 25 +-
tools/vdb-config/vdb-config.c | 86 ++--
69 files changed, 6350 insertions(+), 299 deletions(-)
--
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