[med-svn] [sra-sdk] 01/03: Merge branch 'master' into debian/jessie-backports
Andreas Tille
tille at debian.org
Wed Jun 7 19:30:59 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch debian/jessie-backports
in repository sra-sdk.
commit 36543b558618cf19adc496e6dd236397a4453008
Merge: 6aee0f3 eb51dd1
Author: Andreas Tille <tille at debian.org>
Date: Wed Jun 7 14:21:04 2017 +0200
Merge branch 'master' into debian/jessie-backports
.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 -
build/MSVC/2010/schema-replace.vcxproj | 36 -
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 --
build/MSVC/2013/vdb-config.vcxproj | 20 -
build/MSVC/2013/vdb-copy.vcxproj | 17 -
build/MSVC/2013/vdb-decrypt.vcxproj | 17 -
build/MSVC/2013/vdb-diff.vcxproj | 15 -
build/MSVC/2013/vdb-dump.vcxproj | 17 -
build/MSVC/2013/vdb-encrypt.vcxproj | 17 -
build/MSVC/2013/vdb-lock.vcxproj | 17 -
build/MSVC/2013/vdb-passwd.vcxproj | 17 -
build/MSVC/2013/vdb-unlock.vcxproj | 17 -
build/MSVC/2013/vdb-validate.vcxproj | 17 -
build/MSVC/2013/wb-test-fastq.vcxproj | 18 -
build/MSVC/abi-dump.files | 9 -
build/MSVC/align-cache.files | 8 -
build/MSVC/align-info.files | 6 -
build/MSVC/build.xml | 69 -
build/MSVC/cache-mgr.files | 6 -
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 | 45 +
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/link_debian_packaged_libmbed.patch | 16 +
debian/patches/seek_dynamic_libs.patch | 22 +
debian/patches/series | 4 +-
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 +-
tools/{ref-variation/common.h => cg-load/f2_4.c} | 20 +-
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/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 +-
387 files changed, 4170 insertions(+), 17325 deletions(-)
diff --cc debian/changelog
index 2df91d4,0d36f5a..f3f6144
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,10 -1,48 +1,55 @@@
+ sra-sdk (2.8.1-2+dfsg-2) unstable; urgency=medium
+
+ * Fix install dir by using DEB_HOST_MULTIARCH instead of DEB_BUILD_GNU_TYPE
+ (thanks for the patch to Graham Inggs <ginggs at debian.org>)
+ Closes: #859261
+
+ -- Andreas Tille <tille at debian.org> Sat, 01 Apr 2017 23:06:00 +0200
+
+ sra-sdk (2.8.1-2+dfsg-1) unstable; urgency=medium
+
+ * New upstream bugfix release
+
+ -- Andreas Tille <tille at debian.org> Tue, 24 Jan 2017 09:05:43 +0100
+
+ sra-sdk (2.8.1+dfsg-3) unstable; urgency=medium
+
+ * Upstream suggested a different name to resolve #851219: vdb-get
+
+ -- Andreas Tille <tille at debian.org> Sat, 14 Jan 2017 14:41:57 +0100
+
+ sra-sdk (2.8.1+dfsg-2) unstable; urgency=medium
+
+ * Deal with name space conflict with kget
+ Closes: #851219
+
+ -- Andreas Tille <tille at debian.org> Fri, 13 Jan 2017 09:23:03 +0100
+
+ sra-sdk (2.8.1+dfsg-1) unstable; urgency=medium
+
+ * New upstream version
+ Closes: #846461
+ * For whatever reason configure is checking for libfuse-dev so add it to
+ Build-Depends
+ * Build-Depends: libhdf5-dev, libmagic-dev, libxml2-dev
+
+ -- Andreas Tille <tille at debian.org> Wed, 11 Jan 2017 23:06:42 +0100
+
+ sra-sdk (2.7.0-2) unstable; urgency=medium
+
+ * d/rules: Remove -pie to adapt to latest changes in dpkg
+ * link against Debian packaged libmbedtls-dev
+ * Enable build using ncbi-vdb version 2.8.0
+
+ -- Andreas Tille <tille at debian.org> Fri, 25 Nov 2016 19:08:25 +0100
+
+sra-sdk (2.7.0-1~bpo8+1) jessie-backports; urgency=medium
+
+ * Rebuild for jessie-backports.
+ * Adjust versioned Build-Depends: libncbi-vdb-dev
+
+ -- Andreas Tille <tille at debian.org> Fri, 14 Oct 2016 20:38:02 +0200
+
sra-sdk (2.7.0-1) unstable; urgency=medium
[ Andreas Tille ]
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