[med-svn] [ncbi-vdb] 04/10: Merge tag 'upstream/2.7.0+dfsg'
Andreas Tille
tille at debian.org
Wed Jul 20 15:30:40 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository ncbi-vdb.
commit 91db2e1fbee5840c9ab1baf89155dcaa7412e7b9
Merge: e868533 cd33d97
Author: Andreas Tille <tille at debian.org>
Date: Wed Jul 20 16:39:23 2016 +0200
Merge tag 'upstream/2.7.0+dfsg'
Upstream version 2.7.0+dfsg
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libs/ext/bzip2/decompress.c | 646 -
libs/ext/bzip2/dlltest.c | 175 -
libs/ext/bzip2/huffman.c | 205 -
libs/ext/bzip2/mk251.c | 31 -
libs/ext/bzip2/randtable.c | 84 -
libs/ext/bzip2/spewG.c | 54 -
libs/ext/bzip2/unzcrash.c | 141 -
libs/ext/magic/.gitignore | 1 -
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libs/ext/magic/apprentice.c | 2381 ---
libs/ext/magic/apptype.c | 168 -
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libs/ext/magic/cdf_time.c | 192 -
libs/ext/magic/compress.c | 496 -
libs/ext/magic/config.h | 269 -
libs/ext/magic/elfclass.h | 69 -
libs/ext/magic/encoding.c | 500 -
libs/ext/magic/file.c | 482 -
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libs/ext/magic/fsmagic.c | 363 -
libs/ext/magic/funcs.c | 426 -
libs/ext/magic/getopt_long.c | 498 -
libs/ext/magic/is_tar.c | 157 -
libs/ext/magic/libmagic.vers | 1 -
libs/ext/magic/magic.c | 412 -
libs/ext/magic/mygetopt.h | 68 -
libs/ext/magic/names.h | 173 -
libs/ext/magic/patchlevel.h | 355 -
libs/ext/magic/print.c | 240 -
libs/ext/magic/readcdf.c | 284 -
libs/ext/magic/readelf.c | 1192 --
libs/ext/magic/readelf.h | 312 -
libs/ext/magic/softmagic.c | 2012 ---
libs/ext/magic/strlcat.c | 58 -
libs/ext/magic/strlcpy.c | 54 -
libs/ext/magic/tar.h | 73 -
libs/ext/magic/vasprintf.c | 642 -
libs/ext/regex/Makefile | 114 -
libs/ext/regex/libregex.def | 18 -
libs/ext/regex/regcomp.c | 3796 ----
libs/ext/regex/regex.c | 74 -
libs/ext/regex/regex_internal.c | 1717 --
libs/ext/regex/regex_internal.h | 782 -
libs/ext/regex/regexec.c | 4330 -----
libs/ext/szip/.gitignore | 4 -
libs/ext/szip/Makefile | 117 -
libs/ext/zlib/.gitignore | 4 -
libs/ext/zlib/Makefile | 162 -
libs/ext/zlib/adler32.c | 179 -
libs/ext/zlib/compress.c | 80 -
libs/ext/zlib/crc32.c | 425 -
libs/ext/zlib/crc32.h | 441 -
libs/ext/zlib/deflate.c | 1967 ---
libs/ext/zlib/deflate.h | 346 -
libs/ext/zlib/gzclose.c | 25 -
libs/ext/zlib/gzguts.h | 213 -
libs/ext/zlib/gzlib.c | 634 -
libs/ext/zlib/gzread.c | 594 -
libs/ext/zlib/gzwrite.c | 577 -
libs/ext/zlib/infback.c | 640 -
libs/ext/zlib/inffast.c | 340 -
libs/ext/zlib/inffast.h | 11 -
libs/ext/zlib/inffixed.h | 94 -
libs/ext/zlib/inflate.c | 1512 --
libs/ext/zlib/inflate.h | 122 -
libs/ext/zlib/inftrees.c | 306 -
libs/ext/zlib/inftrees.h | 62 -
libs/ext/zlib/sun/stdlib.h | 7 -
libs/ext/zlib/trees.c | 1226 --
libs/ext/zlib/trees.h | 128 -
libs/ext/zlib/uncompr.c | 59 -
libs/ext/zlib/zconf.h | 511 -
libs/ext/zlib/zlib-1.2.8.diff | 10 -
libs/ext/zlib/zlib.h | 1768 --
libs/ext/zlib/zutil.c | 324 -
libs/ext/zlib/zutil.h | 253 -
libs/hdf5/Makefile | 4 +-
libs/hdf5/libkdf5.vers | 1 -
libs/kapp/main.c | 2 +-
libs/kdb/colidx.c | 14 +-
libs/kdb/column.c | 194 +-
libs/kdb/libkdb.vers.h | 2 +-
libs/kdb/table.c | 12 +
libs/kdb/wcolidx.c | 18 +-
libs/kdb/wcolumn.c | 179 +-
libs/kdb/wdbmgr.c | 2 +-
libs/kdb/wmeta.c | 2 +-
libs/kdb/wtable.c | 9 +
libs/kfc/unix/sysrsrc.c | 4 +-
libs/kfg/config.c | 37 +-
libs/kfg/default.kfg | 4 +-
libs/kfg/repository.c | 170 +
libs/kfs/arc.c | 14 +
libs/kfs/cacheteefile.c | 5 +
libs/kfs/pmem.c | 1247 +-
libs/klib/btree.c | 10 +-
libs/klib/release-vers.h | 2 +-
libs/klib/report-klib.c | 3 +-
libs/klib/vector_namelist.c | 284 +-
libs/kns/Makefile | 17 +-
libs/kns/http-client.c | 70 +-
libs/kns/http-file.c | 5 +
libs/kns/libkns.vers | 1 -
libs/kns/libkns.vers.h | 1 -
libs/kns/manager.c | 4 +-
libs/kproc/unix/syscond.c | 2 +-
libs/loader/Makefile | 1 -
libs/loader/common-writer.c | 91 +-
libs/ncbi-vdb/Makefile | 9 +-
libs/ncbi-vdb/libncbi-vdb.vers | 2 +-
libs/ncbi-vdb/libncbi-wvdb.vers | 1 -
libs/ngs-c++/Makefile | 2 +-
libs/ngs-c++/NCBI-NGS.cpp | 5 +-
libs/ngs-c++/libncbi-ngs-c++.vers | 1 -
libs/ngs-jni/jni_Manager.c | 4 +-
libs/ngs-jni/libncbi-ngs-jni.vers | 1 -
libs/ngs-py/py_Manager.c | 4 +-
libs/ngs/CSRA1_Alignment.c | 352 +-
libs/ngs/CSRA1_ReadCollection.c | 156 +-
libs/ngs/Makefile | 4 +-
libs/ngs/NGS_Cursor.c | 138 +-
libs/ngs/NGS_FragmentBlob.c | 476 +
libs/ngs/NGS_FragmentBlob.h | 125 +
libs/ngs/NGS_FragmentBlobIterator.c | 185 +
.../ngs/NGS_FragmentBlobIterator.h | 51 +-
libs/ngs/NGS_ReadCollection.c | 22 +-
libs/ngs/NGS_ReadCollection.h | 22 +-
libs/ngs/SRA_DB_ReadCollection.c | 67 +-
libs/ngs/SRA_ReadCollection.c | 52 +-
libs/search/sw-search.c | 5 +
libs/sraxf/Makefile | 1 +
libs/sraxf/tokenize-spot_name-generic-fastq.c | 82 +
libs/svdb/Makefile | 4 +-
libs/svdb/libsvdb.vers | 1 -
libs/vdb/dbmgr-cmn.c | 60 +
libs/vdb/libvdb.vers.h | 2 +-
libs/vdb/libwvdb.vers.h | 27 -
libs/vdb/linker-int.c | 2 +
libs/vdb/phys-cmn.c | 64 +-
libs/vdb/prod-cmn.c | 105 +-
libs/vdb/schema-eval.c | 6 +-
libs/vdb/schema-priv.h | 2 +-
libs/vdb/table-cmn.c | 2 +
libs/vdb/table-priv.h | 3 +
libs/vdb/wdbmgr.c | 4 +-
libs/vdb/wtable.c | 2 +
libs/vfs/manager.c | 117 +
libs/vfs/resolver-priv.h | 11 +-
libs/vfs/resolver.c | 165 +-
libs/vxf/deriv.c | 22 +-
libs/vxf/integral.c | 22 +-
libs/vxf/integral_0.c | 22 +-
setup/konfigure.perl | 201 +-
setup/package.prl | 1 -
test/ext/magic/Makefile | 61 -
test/ext/magic/magictest.cpp | 85 -
test/kapp/Makefile | 41 +-
.../libwkdb.vers.h => test/kapp/report-kns-agent.c | 33 +-
test/{ext/Makefile => kapp/run-kns-agent.sh} | 63 +-
test/kfg/Makefile | 15 +-
test/kfg/flat-sra-kfg.cpp | 415 +
test/kfg/flat-sra-kfg/aux_root/empty.kfg | 1 +
test/kfg/flat-sra-kfg/new/sraFlat.kfg | 1 +
test/kfg/flat-sra-kfg/old/fuse1000.kfg | 1 +
test/kfg/ncbi-home-from-env.cpp | 27 +
test/klib/Makefile | 40 +-
test/klib/test-vnamelist.cpp | 364 +
test/kns/httptest.cpp | 65 +-
test/loader/Makefile | 4 +-
test/loader/sequence-writer.c | 366 +
test/ngs-java/Makefile | 14 +-
test/ngs-java/build.xml | 38 +-
test/ngs-java/ngs_test_CSRA1.java | 27 +
test/ngs-java/ngs_test_lib_load.java | 246 +
test/ngs-python/build.xml | 26 +-
test/ngs/Makefile | 61 +-
test/ngs/data/.gitignore | 1 +
test/ngs/ngs_c_fixture.hpp | 23 +-
test/ngs/ngstest.cpp | 280 +-
test/ngs/ngstest_csra1.cpp | 379 +-
test/ngs/ngstest_csra1_refwin.cpp | 10 +-
test/ngs/ngstest_fragmentblob.cpp | 597 +
test/ngs/ngstest_makedb.cpp | 196 +
test/ngs/ngstest_sra.cpp | 436 +-
test/ngs/ngstest_sradb.cpp | 312 +-
test/search/test-agrep.cpp | 8 +-
test/vdb/Makefile | 55 +-
test/vdb/db/blob_val_inv_chsum.sra | Bin 0 -> 196213 bytes
test/vdb/test-VDB-3060.cpp | 380 +
test/vdb/test-blob-val.cpp | 185 +
test/vdb/test-sparse-col.cpp | 0
test/vdb/test-vdb.cpp | 285 +-
test/vdb/test-wvdb.cpp | 169 +-
test/vfs/Makefile | 19 +-
test/vfs/caching-kfg/incomplete.kfg | 4 +
test/vfs/repo/wgs/WGS/YY/ZZ/YYZZ10 | 0
test/vfs/repo/wgs/WGS/YY/ZZ/YYZZ99 | 0
test/vfs/repo/wgs2/WGS/YY/ZZ/YYZZ20 | 0
test/vfs/repo/wgs2/WGS/YY/ZZ/YYZZ99 | 0
test/vfs/resolvertest.cpp | 138 +-
test/vfs/test-caching.cpp | 615 +
612 files changed, 10261 insertions(+), 213868 deletions(-)
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