[med-svn] [sra-sdk] branch upstream updated (5bdf64f -> 03cd16f)
Andreas Tille
tille at debian.org
Thu Oct 19 22:15:23 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository sra-sdk.
from 5bdf64f New upstream version 2.8.1-2+dfsg
new 03cd16f New upstream version 2.8.2-3+dfsg
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:
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 +
.../general-loader/VDB-3250}/Makefile | 73 ++--
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
.../VDB-3250/test_data.vschema} | 39 +-
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 +++++++++++
.../Makefile.gcc => test/vdb-config/Makefile | 10 +-
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, 6305 insertions(+), 331 deletions(-)
create mode 100644 test/dbgap-mount/jaba/App.java
create mode 100644 test/dbgap-mount/jaba/AppTerminator.java
create mode 100644 test/dbgap-mount/jaba/DbGapMountTest.java
create mode 100644 test/dbgap-mount/jaba/DbGapMountTestEnv.java
create mode 100644 test/dbgap-mount/jaba/Utils.java
create mode 100644 test/dbgap-mount/jaba/WrapCmd.java
create mode 100644 test/dbgap-mount/jaba/platform/Platform.java
create mode 100644 test/dbgap-mount/jaba/platform/PlatformLinux.java
create mode 100644 test/dbgap-mount/jaba/platform/PlatformMac.java
create mode 100644 test/dbgap-mount/jaba/platform/PlatformSuper.java
create mode 100644 test/dbgap-mount/jaba/platform/PlatformWin.java
create mode 100644 test/dbgap-mount/jaba/test/Test.java
create mode 100644 test/dbgap-mount/jaba/test/TestBasicBase.java
create mode 100644 test/dbgap-mount/jaba/test/TestFunctionality.java
create mode 100644 test/dbgap-mount/jaba/test/TestRunStopBadConfig.java
create mode 100644 test/dbgap-mount/jaba/test/TestRunStopDaemon.java
create mode 100644 test/dbgap-mount/jaba/test/TestRunStopGoodConfig.java
create mode 100644 test/dbgap-mount/jaba/test/TestRunStopNoConfig.java
create mode 100644 test/dbgap-mount/jaba/test/TestRunStopNoParameters.java
create mode 100644 test/dbgap-mount/jaba/test/TestSuper.java
create mode 100644 test/dbgap-mount/jaba/test/TestWorkspace.java
create mode 100644 test/dbgap-mount/jaba/test/Tests.java
create mode 100644 test/dbgap-mount/py/main.py
create mode 100644 test/dbgap-mount/py/platform/__init__.py
create mode 100644 test/dbgap-mount/py/platform/base.py
create mode 100644 test/dbgap-mount/py/platform/lin.py
create mode 100644 test/dbgap-mount/py/platform/mac.py
create mode 100644 test/dbgap-mount/py/platform/win.py
create mode 100644 test/dbgap-mount/py/test/__init__.py
create mode 100644 test/dbgap-mount/py/test/base.py
create mode 100644 test/dbgap-mount/py/test/test.py
create mode 100644 test/dbgap-mount/py/test/utils.py
copy {tools/pileup-stats => test/general-loader/VDB-3250}/Makefile (65%)
create mode 100644 test/general-loader/VDB-3250/check_test_result.cpp
create mode 100644 test/general-loader/VDB-3250/prepare_test_data.cpp
create mode 100755 test/general-loader/VDB-3250/prepare_test_data.sh
create mode 100644 test/general-loader/VDB-3250/test_data.bin
copy test/{vschema/bio-end/bio-end-excl.vschema => general-loader/VDB-3250/test_data.vschema} (56%)
create mode 100755 test/sra-pileup/test_all_sam_dump_has_spotgroup.py
create mode 100755 test/sra-pileup/test_diff_fastq_dump_vs_sam_dump.py
copy tools/sra-sort/Makefile.gcc => test/vdb-config/Makefile (83%)
create mode 100755 test/vdb-config/test-vdb-config.pl
create mode 100644 tools/bam-loader/sam.l
create mode 100644 tools/bam-loader/sam.y
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sra-sdk.git
More information about the debian-med-commit
mailing list