[med-svn] [sra-sdk] 02/07: Updated version 2.8.2-3+dfsg from 'upstream/2.8.2-3+dfsg'

[Andreas Tille]

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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