[med-svn] [ncbi-vdb] 01/07: Updated version 2.8.2-2+dfsg from 'upstream/2.8.2-2+dfsg'
Andreas Tille
tille at debian.org
Thu Oct 19 21:46:52 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to tag debian/2.8.2-2+dfsg-1
in repository ncbi-vdb.
commit 4a6d68def908804fb291fa38712f364ca91df282
Merge: b36a1ec a68f5ec
Author: Andreas Tille <tille at debian.org>
Date: Thu Oct 19 22:48:27 2017 +0200
Updated version 2.8.2-2+dfsg from 'upstream/2.8.2-2+dfsg'
with Debian dir 71f0b74c11896d25b6eb13fe9703468fd074cfee
.gitignore | 1 +
CHANGES.md | 23 +
build/Makefile.env | 12 +-
build/Makefile.install | 91 +-
build/Makefile.vers | 2 +-
interfaces/align/bam.h | 33 +-
interfaces/insdc/sra.vschema | 4 +-
.../libkdb.vers.h => interfaces/kfg/kart-priv.h | 24 +-
interfaces/kfg/kart.h | 40 +-
interfaces/kfs/directory.h | 7 +
interfaces/kfs/filetools.h | 12 +-
libs/ngs/VByteBlob.h => interfaces/kfs/limitfile.h | 34 +-
interfaces/klib/debug.h | 3 +-
interfaces/klib/namelist.h | 7 +
interfaces/klib/time.h | 16 +
interfaces/kns/endpoint.h | 6 +
interfaces/kns/kns-mgr-priv.h | 1 -
interfaces/kns/stream.h | 7 +
interfaces/ktst/unit_test_suite.hpp | 28 +-
interfaces/sra/generic-fastq.vschema | 9 +
interfaces/tui/tui.hpp | 1 +
interfaces/vfs/path.h | 11 +-
interfaces/vfs/resolver.h | 14 +-
.../VByteBlob.h => interfaces/vfs/services-priv.h | 40 +-
interfaces/vfs/services.h | 138 +
libs/align/align-access.c | 55 +-
libs/align/bam.c | 610 +--
libs/ascp/ascp.c | 2 +-
libs/blast/blast-mgr.c | 2 +-
libs/blast/reference.c | 5 +-
libs/kdb/libkdb.vers.h | 2 +-
libs/kfg/config.c | 87 +-
libs/kfg/kart.c | 331 +-
libs/kfg/keystore.c | 6 +
libs/kfs/Makefile | 3 +-
libs/kfs/cacheteefile.c | 129 +-
libs/kfs/from_to_namelist.c | 55 +-
libs/kfs/gzip.c | 110 +-
libs/kfs/limitfile.c | 206 ++
libs/kfs/unix/sysdir.c | 24 +
libs/klib/log.c | 28 +-
libs/klib/release-vers.h | 2 +-
libs/klib/time.c | 28 +
libs/klib/unix/systime.c | 66 +-
libs/klib/vector_namelist.c | 59 +
libs/kns/Makefile | 1 +
libs/kns/http-client.c | 113 +-
libs/kns/http-file.c | 54 +-
libs/kns/http-priv.h | 16 +-
libs/kns/http.c | 1 -
libs/kns/linux/sysendpoint.c | 10 +
libs/kns/manager.c | 110 +-
libs/kns/mgr-priv.h | 7 +
libs/kns/stream-from-buffer.c | 192 +
libs/kns/tls.c | 158 +-
libs/kns/unix/syssock.c | 11 +
libs/ktst/testcase.cpp | 2 +-
libs/ktst/testenv.cpp | 15 +
libs/ncbi-vdb/libncbi-vdb.vers | 2 +-
libs/ngs/BAM_ReadCollection.c | 191 +-
libs/ngs/CSRA1_Alignment.c | 2 +-
libs/ngs/CSRA1_Read.c | 101 +-
libs/ngs/CSRA1_ReadCollection.c | 4 +-
libs/ngs/CSRA1_Reference.c | 33 +-
libs/ngs/CSRA1_Reference.h | 7 +-
libs/ngs/CSRA1_ReferenceWindow.c | 185 +-
libs/ngs/Makefile | 6 +-
libs/ngs/NGS_FragmentBlob.c | 26 +-
libs/ngs/NGS_FragmentBlob.h | 6 +
libs/ngs/NGS_FragmentBlobIterator.c | 6 +
libs/ngs/NGS_ReadCollection.c | 8 +-
libs/ngs/NGS_Reference.c | 127 +-
libs/ngs/NGS_Reference.h | 31 +-
libs/ngs/NGS_ReferenceBlob.c | 296 ++
libs/ngs/NGS_ReferenceBlob.h | 100 +
...tBlobIterator.c => NGS_ReferenceBlobIterator.c} | 76 +-
libs/ngs/NGS_ReferenceBlobIterator.h | 82 +
libs/ngs/SRA_DB_ReadCollection.c | 10 +-
libs/ngs/SRA_Read.c | 1 +
libs/ngs/SRA_Read.h | 5 +-
libs/ngs/SRA_ReadCollection.c | 10 +-
libs/ngs/VByteBlob.c | 31 +-
libs/ngs/VByteBlob.h | 4 +-
libs/tui/tui_dlg_helper.c | 128 +-
libs/vdb/cursor-cmn.c | 2 +-
libs/vdb/libvdb.vers.h | 2 +-
libs/vfs/Makefile | 5 +-
libs/vfs/manager.c | 38 +-
libs/vfs/path-priv.h | 79 +
libs/vfs/path.c | 290 +-
libs/vfs/remote-services.c | 3905 ++++++++++++++++++++
libs/vfs/resolver-priv.h | 7 +-
libs/vfs/resolver.c | 315 +-
libs/vfs/services-priv.h | 126 +
libs/vfs/services.c | 280 ++
libs/vfs/srv-response.c | 580 +++
py_vdb/L1-manager.py | 57 +
py_vdb/L10-fastq.py | 81 +
py_vdb/L2-table_read.py | 80 +
py_vdb/L3-table_write.py | 94 +
py_vdb/L4-database_read.py | 58 +
py_vdb/L5-database_write.py | 111 +
py_vdb/L6-meta_read.py | 47 +
py_vdb/L7-table-rnd-write.py | 49 +
py_vdb/L8-import-csv.py | 44 +
py_vdb/L9-index_usage.py | 57 +
py_vdb/custom_fastq.py | 27 +
py_vdb/ref_var.py | 375 ++
py_vdb/tst_config.py | 48 +
py_vdb/vdb.py | 2229 +++++++++++
setup/konfigure.perl | 99 +-
setup/package.prl | 12 +-
test/Makefile | 1 +
build/Makefile.vers => test/align-access/Makefile | 35 +-
test/align-access/align-access.hpp | 182 +
.../release-vers.h => test/align-access/main.c | 37 +-
test/align-access/test.cpp | 192 +
test/align-access/test.pl | 132 +
test/install/.gitignore | 2 +
test/install/Makefile | 139 +
test/kdb/kdbtest.cpp | 31 +-
test/kfg/flat-sra-kfg.cpp | 4 +-
test/kfg/keystoretest.cpp | 48 +-
test/kfg/kfgtest.cpp | 3 +-
test/kfs/Makefile | 70 +-
test/kfs/cachetee-out-of-space.cpp | 187 +
test/kfs/cacheteetest.cpp | 4 +-
test/kfs/fuse_proxy.c | 668 ++++
test/kfs/kdf.cpp | 303 ++
test/kfs/run-cachetee-out-of-space-test.sh | 87 +
test/klib/Makefile | 13 +
test/klib/test-log.cpp | 36 +
test/klib/test-time.cpp | 87 +
test/kns/Makefile | 98 +-
test/kns/test-proxy-with-scheme.cpp | 162 +
test/kns/test-proxy.cpp | 16 +
.../env-with-schema-and-port/environment | 1 +
.../test-proxy/env-with-schema-and-port/expected | 1 +
test/kns/test-proxy/env-with-schema/environment | 1 +
test/kns/test-proxy/env-with-schema/expected | 1 +
.../kns/test-proxy/kfg-with-schema-and-port/config | 1 +
.../test-proxy/kfg-with-schema-and-port/expected | 1 +
test/kns/test-proxy/kfg-with-schema/config | 1 +
test/kns/test-proxy/kfg-with-schema/expected | 1 +
test/krypto/Makefile | 10 +-
test/ktst/ktsttest.cpp | 52 +
test/ngs-java/ngs_test_CSRA1.java | 292 +-
test/ngs/Makefile | 43 +-
test/ngs/ngs_c_fixture.hpp | 2 +-
test/ngs/ngstest_byteblob.cpp | 314 ++
test/ngs/ngstest_csra1.cpp | 502 ---
test/ngs/ngstest_fragmentblob.cpp | 29 +-
test/ngs/ngstest_reference.cpp | 582 ++-
test/ngs/ngstest_referenceblob.cpp | 773 ++++
test/vdb/Makefile | 22 +-
test/vdb/test-VDB-3060.cpp | 2 +-
test/vdb/test-VDB-3061.cpp | 40 +-
test/vdb/test-VDB-3305.cpp | 161 +
test/vdb/test-vdb.cpp | 90 +-
test/vfs/Makefile | 26 +-
.../redirect-rejected-names-cgi-http-to-https.cpp | 10 +-
test/vfs/resolvertest.cpp | 12 +-
test/vfs/test-caching.cpp | 4 +-
test/vfs/test-names-30.cpp | 503 +++
vdb3/itf/kfc/except.hpp | 36 +-
vdb3/itf/kfc/memmgr.hpp | 9 +-
vdb3/itf/kfc/ptr.hpp | 20 +-
vdb3/itf/kfc/rsrc.hpp | 15 +-
vdb3/itf/kfc/string.hpp | 9 +-
vdb3/src/kfc/Makefile | 16 +-
vdb3/src/kfc/rsrc.cpp | 1 +
vdb3/src/kfc/string.cpp | 80 +-
172 files changed, 17841 insertions(+), 1998 deletions(-)
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