[med-svn] [sra-sdk] branch master updated (41b9a17 -> 7e2f365)
Andreas Tille
tille at debian.org
Thu Oct 19 22:15:20 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository sra-sdk.
from 41b9a17 Added references to registries.
new 03cd16f New upstream version 2.8.2-3+dfsg
new 82aa437 Updated version 2.8.2-3+dfsg from 'upstream/2.8.2-3+dfsg'
new e3ee2ae New upstream version
new 087262b cme fix dpkg-control, Standards-Version: 4.1.1
new 61d3527 debhelper 10
new 27b7b08 Refresh patches
new 7e2f365 Avoid issues occuring when parallel build is forced by debhelper 10
The 7 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 +-
debian/changelog | 11 +-
debian/compat | 2 +-
debian/control | 9 +-
debian/patches/find_configure_libs.patch | 2 +-
debian/patches/find_hdf5_serial.patch | 2 +-
debian/patches/find_ncbi-vdb.patch | 4 +-
debian/patches/find_ngs-sdk.patch | 4 +-
.../ignore_failing_tests_for_the_moment.patch | 4 +-
debian/rules | 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 ++--
78 files changed, 6328 insertions(+), 348 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
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