[med-svn] [sra-sdk] branch debian/jessie-backports updated (6aee0f3 -> 481731e)
Andreas Tille
tille at debian.org
Wed Jun 7 19:30:58 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch debian/jessie-backports
in repository sra-sdk.
from 6aee0f3 Adjust versioned Build-Depends: libncbi-vdb-dev
adds 2efb80c Imported Upstream version 2.8.0+dfsg
adds cdb43d1 Merge tag 'upstream/2.8.0+dfsg'
adds 41bdaca New upstream version
adds 1fd37c4 Bump versioned Build-Depends libncbi-vdb-dev
adds b06c408 Try to adapt patches to version 2.8.0
adds d4b9169 Revert previous commits where attempting to upgrade to next upstream version since we need to fix bugs in old version first
adds 227b159 Imported Upstream version 2.7.0
adds b6dd557 Imported Upstream version 2.7.0
adds cc93870 Merge tag 'upstream/2.7.0'
adds 03e5a49 d/rules: Remove -pie to adapt to latest changes in dpkg
adds 51d668a link against Debian packaged libmbedtls-dev
adds e53d167 Enable build using ncbi-vdb version 2.8.0
adds 5c5aaa0 Upload to unstable
adds 67dbdf6 Try to apply patches for new upstream version (not working yet)
adds 06555f9 New upstream version 2.8.1
adds 075ea1d Merge tag 'upstream/2.8.1'
adds 321e7d9 New upstream version
adds 5eec480 New upstream version 2.8.1+dfsg
adds d52a303 Merge tag 'upstream/2.8.1+dfsg'
adds 9abe735 Adapt patches
adds 60abcfc Refresh versioned depends
adds d282547 Remove cruft
adds 2179a63 Update patches
adds 703ee90 New Build-Depends
adds ab243ea Hack to enable finding includes
adds 2077049 Seek for dynamic lib rather than static one
adds 820ad56 Hack to make sure ncbi-vdb lib will be found
adds 0a20868 Point to correct location of kfg config files in libncbi-vdb2 package
adds e380339 s/hdf5/hdf5_serial/
adds 512cef2 Do not use static lib
adds 3042df0 Properly create /etc/ncbi
adds e507313 Install all existing README* files
adds f054e8c Fix Build-Depends, upload to unstable and close bug
adds e08bfaa Deal with name space conflict of kget
adds 4ab1f9b upload to unstable
adds 192346a Upstream suggested a different name to resolve #851219: vdb-get
adds 6b2bea2 Corrected EDAM annotation file
adds ef5c382 Corrected EDAM annotation file
adds e013b5f Upload to unstable
adds 5bdf64f New upstream version 2.8.1-2+dfsg
adds 0d01a16 Merge tag 'upstream/2.8.1-2+dfsg'
adds 2c0dc32 New upstream bugfix release
adds 3553ace Graham Inggs <ginggs at debian.org>
adds eb51dd1 Upload to unstable
new 36543b5 Merge branch 'master' into debian/jessie-backports
new c0d6d86 Rebuild for jessie-backports
new 481731e Brute-force some object files building with -fPIC
The 3 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:
.gitignore | 1 +
CHANGES | 127 --
CHANGES.md | 69 +
README | 57 -
README.md | 25 +-
build/MSVC/2010/.gitignore | 6 -
build/MSVC/2010/abi-dump.vcxproj | 31 -
build/MSVC/2010/align-cache.vcxproj | 32 -
build/MSVC/2010/align-info.vcxproj | 36 -
build/MSVC/2010/build.xml | 73 -
build/MSVC/2010/cache-mgr.vcxproj | 36 -
build/MSVC/2010/dbgap-mount-demo.vcxproj | 41 -
build/MSVC/2010/dbgap-mount-tool.vcxproj | 42 -
build/MSVC/2010/dll-project.props | 31 -
build/MSVC/2010/exe-project.props | 45 -
build/MSVC/2010/fastq-dump-ngs.vcxproj | 39 -
build/MSVC/2010/fastq-dump.vcxproj | 35 -
build/MSVC/2010/fastq-loader.vcxproj | 42 -
build/MSVC/2010/general-loader.vcxproj | 34 -
build/MSVC/2010/illumina-dump.vcxproj | 38 -
build/MSVC/2010/kar.vcxproj | 36 -
build/MSVC/2010/kdbmeta.vcxproj | 36 -
build/MSVC/2010/lib-project.props | 30 -
build/MSVC/2010/md5cp.vcxproj | 35 -
build/MSVC/2010/prefetch.vcxproj | 37 -
build/MSVC/2010/qual-recalib-stat.vcxproj | 36 -
build/MSVC/2010/rcexplain.vcxproj | 36 -
build/MSVC/2010/read-filter-redact.vcxproj | 36 -
build/MSVC/2010/ref-variation.vcxproj | 35 -
build/MSVC/2010/sam-dump.vcxproj | 36 -
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build/MSVC/2010/sff-dump.vcxproj | 36 -
build/MSVC/2010/sra-kar.vcxproj | 36 -
build/MSVC/2010/sra-pileup.vcxproj | 36 -
build/MSVC/2010/sra-stat.vcxproj | 37 -
build/MSVC/2010/sra-tools.sln | 507 -----
build/MSVC/2010/srapath.vcxproj | 36 -
build/MSVC/2010/test-align-info.log | 18 -
build/MSVC/2010/test-align-info.vcxproj | 28 -
build/MSVC/2010/test-fastq-loader.vcxproj | 39 -
build/MSVC/2010/test-general-loader.vcxproj | 41 -
build/MSVC/2010/test-project.props | 15 -
build/MSVC/2010/test-sra-tools.sln | 66 -
build/MSVC/2010/test-sra.vcxproj | 36 -
build/MSVC/2010/test-vcf-loader.vcxproj | 39 -
build/MSVC/2010/tk-version.vcxproj | 30 -
build/MSVC/2010/var-expand.vcxproj | 35 -
build/MSVC/2010/vcf-loader.vcxproj | 30 -
build/MSVC/2010/vdb-common.props | 94 -
build/MSVC/2010/vdb-config.vcxproj | 39 -
build/MSVC/2010/vdb-copy.vcxproj | 36 -
build/MSVC/2010/vdb-decrypt.vcxproj | 36 -
build/MSVC/2010/vdb-diff.vcxproj | 38 -
build/MSVC/2010/vdb-dump.vcxproj | 36 -
build/MSVC/2010/vdb-encrypt.vcxproj | 36 -
build/MSVC/2010/vdb-lock.vcxproj | 36 -
build/MSVC/2010/vdb-passwd.vcxproj | 36 -
build/MSVC/2010/vdb-unlock.vcxproj | 35 -
build/MSVC/2010/vdb-validate.vcxproj | 36 -
build/MSVC/2010/wb-test-fastq.vcxproj | 38 -
build/MSVC/2013/.gitignore | 7 -
build/MSVC/2013/abi-dump.vcxproj | 13 -
build/MSVC/2013/align-cache.vcxproj | 14 -
build/MSVC/2013/align-info.vcxproj | 17 -
build/MSVC/2013/build.xml | 73 -
build/MSVC/2013/cache-mgr.vcxproj | 17 -
build/MSVC/2013/dbgap-mount-demo.vcxproj | 22 -
build/MSVC/2013/dbgap-mount-tool.vcxproj | 23 -
build/MSVC/2013/dll-project.props | 31 -
build/MSVC/2013/exe-project.props | 45 -
build/MSVC/2013/fastq-dump-ngs.vcxproj | 20 -
build/MSVC/2013/fastq-dump.vcxproj | 16 -
build/MSVC/2013/fastq-loader.vcxproj | 23 -
build/MSVC/2013/general-loader.vcxproj | 16 -
build/MSVC/2013/illumina-dump.vcxproj | 19 -
build/MSVC/2013/kar.vcxproj | 17 -
build/MSVC/2013/kdbmeta.vcxproj | 17 -
build/MSVC/2013/lib-project.props | 30 -
build/MSVC/2013/md5cp.vcxproj | 17 -
build/MSVC/2013/prefetch.vcxproj | 18 -
build/MSVC/2013/qual-recalib-stat.vcxproj | 17 -
build/MSVC/2013/rcexplain.vcxproj | 17 -
build/MSVC/2013/read-filter-redact.vcxproj | 17 -
build/MSVC/2013/ref-variation.vcxproj | 17 -
build/MSVC/2013/sam-dump.vcxproj | 17 -
build/MSVC/2013/schema-replace.vcxproj | 17 -
build/MSVC/2013/sff-dump.vcxproj | 17 -
build/MSVC/2013/sra-kar.vcxproj | 17 -
build/MSVC/2013/sra-pileup.vcxproj | 17 -
build/MSVC/2013/sra-stat.vcxproj | 18 -
build/MSVC/2013/sra-tools.sln | 507 -----
build/MSVC/2013/srapath.vcxproj | 17 -
build/MSVC/2013/test-align-info.vcxproj | 10 -
build/MSVC/2013/test-fastq-loader.vcxproj | 18 -
build/MSVC/2013/test-general-loader.vcxproj | 22 -
build/MSVC/2013/test-project.props | 15 -
build/MSVC/2013/test-sra-tools.sln | 66 -
build/MSVC/2013/test-sra.vcxproj | 16 -
build/MSVC/2013/test-vcf-loader.vcxproj | 19 -
build/MSVC/2013/tk-version.vcxproj | 31 -
build/MSVC/2013/var-expand.vcxproj | 17 -
build/MSVC/2013/vcf-loader.vcxproj | 10 -
build/MSVC/2013/vdb-common.props | 115 --
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build/MSVC/2013/vdb-copy.vcxproj | 17 -
build/MSVC/2013/vdb-decrypt.vcxproj | 17 -
build/MSVC/2013/vdb-diff.vcxproj | 15 -
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build/MSVC/2013/vdb-lock.vcxproj | 17 -
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build/MSVC/align-info.files | 6 -
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build/MSVC/dbgap-mount-demo.files | 6 -
build/MSVC/dbgap-mount-tool.files | 8 -
build/MSVC/fastq-dump-ngs.files | 8 -
build/MSVC/fastq-dump.files | 9 -
build/MSVC/fastq-loader.files | 10 -
build/MSVC/general-loader.files | 10 -
build/MSVC/illumina-dump.files | 9 -
build/MSVC/kar.files | 7 -
build/MSVC/kdbmeta.files | 6 -
build/MSVC/md5cp.files | 6 -
build/MSVC/prefetch.files | 7 -
build/MSVC/qual-recalib-stat.files | 14 -
build/MSVC/rcexplain.files | 6 -
build/MSVC/read-filter-redact.files | 6 -
build/MSVC/ref-variation.files | 11 -
build/MSVC/sam-dump.files | 20 -
build/MSVC/schema-replace.files | 6 -
build/MSVC/sff-dump.files | 9 -
build/MSVC/sra-kar.files | 6 -
build/MSVC/sra-pileup.files | 24 -
build/MSVC/sra-stat.files | 7 -
build/MSVC/srapath.files | 9 -
build/MSVC/test-fastq-loader.files | 9 -
build/MSVC/test-general-loader.files | 7 -
build/MSVC/test-sra.files | 7 -
build/MSVC/test-vcf-loader.files | 6 -
build/MSVC/tk-version.files | 6 -
build/MSVC/var-expand.files | 11 -
build/MSVC/vcf-loader.files | 9 -
build/MSVC/vdb-config.files | 10 -
build/MSVC/vdb-copy.files | 16 -
build/MSVC/vdb-decrypt.files | 7 -
build/MSVC/vdb-diff.files | 8 -
build/MSVC/vdb-dump.files | 20 -
build/MSVC/vdb-encrypt.files | 7 -
build/MSVC/vdb-lock.files | 6 -
build/MSVC/vdb-passwd.files | 7 -
build/MSVC/vdb-unlock.files | 6 -
build/MSVC/vdb-validate.files | 6 -
build/MSVC/wb-test-fastq.files | 9 -
build/Makefile.deb | 14 +-
build/Makefile.env | 14 +-
build/Makefile.install | 33 +-
build/Makefile.mac | 84 -
build/Makefile.rpm | 14 +-
build/Makefile.sun | 96 -
build/Makefile.sun.cc | 155 --
build/Makefile.sun.gcc | 138 --
build/Makefile.tools | 1 +
build/Makefile.vc++ | 81 -
build/Makefile.vers | 2 +-
build/Makefile.win | 79 -
build/ld.mac.clang.sh | 58 -
build/ld.mac.cmn.sh | 159 --
build/ld.mac.dlib.sh | 361 ----
build/ld.mac.exe.sh | 340 ----
build/ld.mac.gcc.sh | 58 -
build/ld.mac.ln.sh | 103 -
build/ld.mac.slib.sh | 101 -
build/ld.win.cmn.sh | 225 ---
build/ld.win.dlib.sh | 327 ---
build/ld.win.exe.sh | 321 ---
build/ld.win.slib.sh | 135 --
build/ld.win.stub.sh | 60 -
build/ld.win.vc++.sh | 65 -
build/sun-c++.sh | 100 -
build/sun-cc.sh | 93 -
build/win-cc.sh | 257 ---
debian/README.Debian | 36 +
debian/changelog | 52 +
debian/control | 7 +-
debian/docs | 2 +-
debian/patches/certs.kfg.patch | 27 +
debian/patches/do_not_link_statically.patch | 11 -
debian/patches/dont_use_static_lib.patch | 51 +-
debian/patches/find_configure_libs.patch | 2 +-
debian/patches/find_hdf5_serial.patch | 33 +-
debian/patches/find_ncbi-vdb.patch | 27 +-
debian/patches/find_ngs-sdk.patch | 6 +-
debian/patches/fix_tests.patch | 21 -
debian/patches/hardening.patch | 2 +-
.../ignore_failing_tests_for_the_moment.patch | 20 +-
debian/patches/jessie_force_fPIC.patch | 73 +
debian/patches/link_debian_packaged_libmbed.patch | 16 +
debian/patches/seek_dynamic_libs.patch | 22 +
debian/patches/series | 5 +-
debian/patches/set_explicit_path_to_schemata.patch | 40 +-
debian/rules | 14 +-
debian/sra-toolkit.links | 1 +
debian/upstream/edam | 17 +-
setup/konfigure.perl | 9 +-
shared/toolkit.vers | 2 +-
shared/toolkit.vers.h | 2 +-
test/Makefile | 9 +-
test/align-cache/Makefile | 4 +-
test/fastq-loader/Makefile | 67 +-
test/fastq-loader/expected/15.0.stderr | 1 +
test/fastq-loader/expected/15.0.stdout | 30 +
test/fastq-loader/expected/2.9.1.stderr | 4 +-
test/fastq-loader/expected/2.9.stderr | 4 +-
test/fastq-loader/input/15.0.fastq | 4 +
test/fastq-loader/test-fastq-loader.cpp | 22 +-
test/fastq-loader/wb-test-fastq.cpp | 4 +-
test/fuse/cfg/standard.cfg | 5 +
test/fuse/kart-util.sh | 166 ++
test/fuse/remote_fuser_clean.sh | 404 ++++
test/fuse/remote_fuser_common.sh | 282 +++
test/fuse/remote_fuser_test.sh | 351 +---
test/general-loader/Makefile | 4 +
test/general-loader/test-general-loader.cpp | 781 ++++----
test/general-loader/testsource.cpp | 2 +-
test/kget/Makefile | 10 +-
test/kget/resolver.kfg | 1 +
test/kget/test_kget.py | 4 +-
test/network-test/analyze_strace_log.py | 128 ++
test/network-test/network-testing.c | 6 +-
test/ref-variation/Makefile | 62 -
test/ref-variation/expected/ref-variation.out | 192 --
test/ref-variation/expected/var-expand.out | 1 -
test/ref-variation/have-access.sh | 25 -
test/ref-variation/ref-variation.in | 4 -
test/ref-variation/ref-variation.sh | 29 -
test/samline/refbases.c | 2 +-
test/tarballs/test-tarballs.bat | 8 +-
test/tarballs/test-tarballs.sh | 4 +-
test/vcf-loader/Makefile | 8 +-
test/{ => vcf-loader}/only-remote-repository.kfg | 0
test/vcf-loader/test-vcf-loader.cpp | 6 +-
test/vdb-dump/Makefile | 36 +-
test/vschema/Makefile | 3 +
test/vschema/runtestcase.sh | 2 +-
tools/Makefile | 3 +-
tools/agp-load/AGP.py | 668 -------
tools/agp-load/agp-load.py | 173 --
tools/agp-load/agp.vschema | 45 -
tools/agp-load/eutils.py | 112 --
tools/bam-loader/KVPFile.c | 2 +-
tools/bam-loader/analysis.c | 2 +-
tools/bam-loader/bam-loader.c | 2 +-
tools/bam-loader/bam-priv.h | 24 +-
tools/bam-loader/bam.c | 130 +-
tools/bam-loader/bam.h | 7 +-
tools/bam-loader/loader-imp.c | 574 +++---
tools/bam-loader/mate-distance-stats.cpp | 23 +
tools/bam-loader/mate-distance-stats.hpp | 20 +
tools/bam-loader/quality-quantizer.cpp | 107 +
tools/bam-loader/quality-quantizer.hpp | 10 +
tools/bam-loader/reference-writer.c | 5 -
tools/bam-loader/reference-writer.h | 2 -
tools/bam-loader/sequence-writer.c | 2 +-
tools/ccextract/ccextract.c | 2 +-
tools/cg-load/Makefile | 1 +
tools/cg-load/cg-load.c | 2 +-
.../{vdb-config/vdb-config2.cpp => cg-load/f2_4.c} | 11 +-
tools/cg-load/factory-cmn.h | 6 +-
tools/cg-load/factory-evidence-dnbs.c | 8 +-
tools/cg-load/factory-file.h | 2 +
tools/cg-load/file-version-factory.c | 2 +
tools/cg-load/file.h | 2 +-
tools/copycat/cccat.c | 4 +-
tools/copycat/cccopy.c | 2 +-
tools/copycat/ccproc.c | 2 +-
tools/copycat/ccprocone.c | 2 +-
tools/copycat/ccsra.c | 6 +-
tools/copycat/ccsubchunk.c | 2 +-
tools/copycat/cctar.c | 2 +-
tools/copycat/cctree-dump.c | 4 +-
tools/copycat/copycat.c | 6 +-
tools/dbgap-mount/Makefile | 26 +-
tools/dbgap-mount/demo.c | 17 +-
tools/fastdump/cmn_iter.h | 1 +
tools/fastdump/fastdump.c | 19 +-
tools/fastq-loader/common-writer.c | 195 +-
tools/fastq-loader/fastq-reader.c | 4 +-
tools/fastq-loader/parsing_rules.txt | 75 +-
tools/fastq-loader/sequence-writer.c | 18 +-
tools/fuse/directory.c | 2 +-
tools/fuse/formats.c | 8 +-
tools/fuse/log.c | 9 +-
tools/fuse/remote-cache.c | 4 +-
tools/fuse/remote-xml.c | 3 +-
tools/fuse/sra-fastq.c | 2 +-
tools/fuse/sra-list.c | 2 +-
tools/fuse/sra-makeidx.c | 6 +-
tools/fuse/sra-sff.c | 2 +-
tools/fuse/tar-list.c | 18 +-
tools/fuse/tar-node.c | 2 +-
tools/fuse/text-file.c | 2 +-
tools/fuse/unix/remote-fuser-sys.c | 8 +-
tools/fuse/unix/sra-fuser-sys.c | 8 +-
tools/fuse/xml.c | 2 +-
tools/general-loader/general-writer.cpp | 2 +-
tools/general-loader/general-writer.h | 10 +-
tools/kar/kar.c | 10 +-
tools/kget/Makefile | 2 +-
tools/kget/kget.c | 33 +-
tools/pacbio-load/pacbio-load.c | 2 +-
tools/pacbio-load/pl-tools.c | 4 +-
tools/pileup-stats/pileup-stats.cpp | 31 +-
tools/pore-load/GeneralWriter.py | 312 ---
tools/pore-load/README.md | 10 -
tools/pore-load/pore-load.py | 406 ----
tools/prefetch/prefetch.c | 145 +-
tools/qual-recalib-stat/ref_exclude.c | 2 +-
tools/ref-variation/Makefile | 113 --
tools/ref-variation/common.cpp | 69 -
tools/ref-variation/common.h | 43 -
tools/ref-variation/helper.cpp | 1458 --------------
tools/ref-variation/helper.h | 603 ------
tools/ref-variation/ref-variation.cpp | 2097 --------------------
tools/ref-variation/var-expand.cpp | 417 ----
tools/sra-dump/abi.c | 2 +-
tools/sra-dump/core.c | 2 +-
tools/sra-dump/factory.h | 2 +-
tools/sra-dump/fastq.c | 4 +-
tools/sra-load/experiment-xml.c | 2 +-
tools/sra-load/fastq-fmt.c | 1 +
tools/sra-load/illumina-fmt.c | 1 +
tools/sra-load/pacbio-fmt.c | 1 +
tools/sra-load/run-xml.c | 6 +-
tools/sra-load/sff-fmt.c | 7 +-
tools/sra-load/srf-fmt.c | 2 +-
tools/sra-load/srf-illumina.c | 1 +
tools/sra-load/writer-absolid.c | 2 +-
tools/sra-load/writer-illumina.c | 6 +-
tools/sra-load/ztr-illumina.c | 14 +-
tools/sra-pileup/cg_tools.c | 4 +-
tools/sra-pileup/ref_walker.c | 2 +-
tools/sra-pileup/reref.c | 4 +-
tools/sra-pileup/rna_splice_log.c | 4 +-
tools/sra-pileup/sam-aligned.c | 45 +-
tools/sra-pileup/sam-dump.c | 34 +-
tools/sra-pileup/sam-hdr1.c | 194 +-
tools/sra-pileup/sra-pileup.c | 2 +-
tools/sra-sort/Makefile.vc++ | 24 -
tools/sra-sort/buff-writer.c | 16 +-
tools/sra-sort/except.c | 3 +-
tools/sra-sort/id-mapper-col.c | 2 +-
tools/sra-sort/map-file.c | 8 +-
tools/sra-sort/poslen-col-pair.c | 4 +-
tools/sra-sort/ref-alignid-col.c | 2 +-
tools/sra-sort/sorting-row-set.c | 2 +-
tools/sra-sort/status.h | 2 +
tools/sra-stat/sra-stat.c | 14 +-
tools/sra/sra-dbcc.c | 4 +-
tools/srapath/cgi_request.c | 4 +-
tools/srapath/srapath.c | 2 +-
tools/util/Makefile | 21 +-
tools/util/kdbmeta.c | 2 +-
tools/util/pseudo-aligner.cpp | 465 +++--
tools/util/schema-replace.c | 4 +-
tools/util/test-sra.c | 592 ++++--
tools/util/vdb-passwd.c | 6 +-
tools/vdb-config/configure.cpp | 7 +-
tools/vdb-config/interactive.cpp | 20 +-
tools/vdb-config/util.cpp | 87 +-
tools/vdb-config/util.hpp | 1 +
tools/vdb-config/vdb-config-model.cpp | 23 +
tools/vdb-config/vdb-config-model.hpp | 33 +-
tools/vdb-config/vdb-config.c | 38 +-
tools/vdb-copy/copy_meta.c | 1 +
tools/vdb-copy/get_platform.c | 6 +-
tools/vdb-copy/helper.c | 2 +-
tools/vdb-copy/num-gen.c | 2 +-
tools/vdb-copy/redactval.c | 4 +-
tools/vdb-decrypt/shared.c | 2 +-
tools/vdb-dump/vdb-dump-helper.c | 8 +-
tools/vdb-dump/vdb-dump.c | 100 +-
tools/vdb-dump/vdb_info.c | 2 +-
tools/vdb-validate/vdb-validate.c | 2 +-
389 files changed, 4253 insertions(+), 17357 deletions(-)
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