[med-svn] [sra-sdk] branch master updated (9df1a87 -> 089dbf0)
Andreas Tille
tille at debian.org
Wed Dec 30 07:52:52 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository sra-sdk.
from 9df1a87 Help configure finding Debian packaged libraries
adds 05ef62f Imported Upstream version 2.4.2-1
new 82d7c33 Imported Upstream version 2.5.7
new e272747 Merge tag 'upstream/2.5.7'
new c9eef4a New upstream version
new 089dbf0 Adapt patches to new version
The 4 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 | 16 +-
GNU-license.txt | 674 ---
LICENSE | 66 +
Makefile | 13 +-
README | 53 +-
README-WINDOWS.txt | 144 -
README-build | 237 -
README-config.txt | 19 -
README-vdb-config.txt => README-vdb-config | 4 -
README-wget.txt | 35 -
README.md | 8 +-
USAGE | 162 -
build/MSVC/2010/abi-dump.vcxproj | 2 -
...d-filter-redact.vcxproj => align-cache.vcxproj} | 76 +-
build/MSVC/2010/align-info.vcxproj | 2 -
build/MSVC/2010/cache-mgr.vcxproj | 4 +-
...q-dump-ngs.vcxproj => dbgap-mount-demo.vcxproj} | 13 +-
build/MSVC/2010/dll-project.props | 59 -
build/MSVC/2010/exe-project.props | 70 +-
build/MSVC/2010/fastq-dump-ngs.vcxproj | 5 +-
build/MSVC/2010/fastq-dump.vcxproj | 2 -
build/MSVC/2010/fastq-loader.vcxproj | 6 +-
.../{kdbmeta.vcxproj => general-loader.vcxproj} | 16 +-
...llumina-diump.vcxproj => illumina-dump.vcxproj} | 0
build/MSVC/2010/kar.vcxproj | 2 -
build/MSVC/2010/kdbmeta.vcxproj | 2 -
build/MSVC/2010/lib-project.props | 68 +-
build/MSVC/2010/md5cp.vcxproj | 4 +-
build/MSVC/2010/prefetch.vcxproj | 5 +-
build/MSVC/2010/qual-recalib-stat.vcxproj | 4 -
build/MSVC/2010/rcexplain.vcxproj | 2 -
build/MSVC/2010/read-filter-redact.vcxproj | 2 -
...astq-dump-ngs.vcxproj => ref-variation.vcxproj} | 84 +-
build/MSVC/2010/sam-dump.vcxproj | 4 +-
build/MSVC/2010/schema-replace.vcxproj | 2 -
build/MSVC/2010/sff-dump.vcxproj | 2 -
build/MSVC/2010/sra-kar.vcxproj | 2 -
build/MSVC/2010/sra-pileup.vcxproj | 4 +-
build/MSVC/2010/sra-stat.vcxproj | 4 +-
build/MSVC/2010/sra-tools.sln | 70 +-
build/MSVC/2010/srapath.vcxproj | 2 -
.../{md5cp.vcxproj => test-align-info.vcxproj} | 23 +-
...tq-loader.vcxproj => test-fastq-loader.vcxproj} | 17 +-
...kdbmeta.vcxproj => test-general-loader.vcxproj} | 22 +-
build/MSVC/2010/test-sra-tools.sln | 66 +
build/MSVC/2010/test-sra.vcxproj | 2 -
...ema-replace.vcxproj => test-vcf-loader.vcxproj} | 21 +-
.../{fastq-dump-ngs.vcxproj => var-expand.vcxproj} | 84 +-
build/MSVC/2010/vdb-common.props | 92 +-
build/MSVC/2010/vdb-config.vcxproj | 9 +-
build/MSVC/2010/vdb-copy.vcxproj | 3 -
build/MSVC/2010/vdb-decrypt.vcxproj | 2 -
.../{vdb-validate.vcxproj => vdb-diff.vcxproj} | 9 +-
build/MSVC/2010/vdb-dump.vcxproj | 3 -
build/MSVC/2010/vdb-encrypt.vcxproj | 2 -
build/MSVC/2010/vdb-lock.vcxproj | 2 -
build/MSVC/2010/vdb-passwd.vcxproj | 2 -
build/MSVC/2010/vdb-unlock.vcxproj | 2 -
build/MSVC/2010/vdb-validate.vcxproj | 2 -
...{fastq-loader.vcxproj => wb-test-fastq.vcxproj} | 17 +-
build/Makefile.clang | 16 +-
build/Makefile.env | 29 +-
build/Makefile.gcc | 16 +-
build/Makefile.install | 56 +-
build/Makefile.linux | 3 +
build/Makefile.mac | 3 +
build/ld.linux.dlib.sh | 4 +-
build/ld.linux.exe.sh | 18 +-
build/ld.linux.gcc.sh | 5 +-
build/ld.mac.clang.sh | 7 +-
build/ld.mac.gcc.sh | 7 +-
build/ld.mac.slib.sh | 35 +-
configure | 6 +-
debian/changelog | 4 +-
debian/patches/10_portability.patch | 15 -
debian/patches/find_configure_libs.patch | 37 +-
debian/patches/hardening.patch | 10 +-
konfigure.perl | 1204 -----
os-arch.perl | 35 -
configure => setup/install | 10 +-
setup/install.perl | 1329 ++++++
setup/install.prl | 38 +
setup/konfigure.perl | 1717 +++++++
setup/os-arch.perl | 22 +
os-arch.pm => setup/os-arch.prl | 12 +-
package.pm => setup/package.prl | 48 +-
configure => setup/s/install | 12 +-
setup/s/os.prl | 2 +
test/Makefile | 38 +-
test/{ => align-info}/Makefile | 30 +-
test/fastq-loader/.gitignore | 1 +
test/fastq-loader/Makefile | 207 +
test/fastq-loader/expected/1.1.stdout | 31 +
test/fastq-loader/expected/1.2.stdout | 31 +
test/fastq-loader/expected/1.3.stderr | 4 +
test/fastq-loader/expected/1.3.stdout | 27 +
test/fastq-loader/expected/1.4.stdout | 90 +
test/fastq-loader/expected/10.0.stdout | 31 +
test/fastq-loader/expected/11.0.stdout | 31 +
test/fastq-loader/expected/11.1.stdout | 31 +
test/fastq-loader/expected/12.0.stdout | 60 +
test/fastq-loader/expected/12.1.stdout | 60 +
test/fastq-loader/expected/12.2.stdout | 31 +
test/fastq-loader/expected/2.1.1.stdout | 44 +
test/fastq-loader/expected/2.1.stdout | 60 +
test/fastq-loader/expected/2.5.stdout | 60 +
test/fastq-loader/expected/2.6.stdout | 31 +
test/fastq-loader/expected/2.7.stdout | 31 +
test/fastq-loader/expected/2.8.1.stdout | 60 +
test/fastq-loader/expected/2.8.stdout | 60 +
test/fastq-loader/expected/2.9.1.stderr | 4 +
test/fastq-loader/expected/2.9.stderr | 4 +
test/fastq-loader/expected/3.1.stdout | 120 +
test/fastq-loader/expected/4.2.stdout | 31 +
test/fastq-loader/expected/4.3.1.stderr | 14 +
test/fastq-loader/expected/4.4.stdout | 66 +
test/fastq-loader/expected/4.5.1.stderr | 8 +
test/fastq-loader/expected/4.5.stderr | 9 +
test/fastq-loader/expected/4.6.1.stderr | 3 +
test/fastq-loader/expected/4.6.stdout | 31 +
test/fastq-loader/expected/4.7.stderr | 2 +
test/fastq-loader/expected/5.0.stdout | 31 +
test/fastq-loader/expected/6.0.stdout | 390 ++
test/fastq-loader/expected/7.1.stdout | 60 +
test/fastq-loader/expected/7.2.stdout | 60 +
test/fastq-loader/expected/7.3.stdout | 60 +
test/fastq-loader/expected/8.0.stdout | 31 +
test/fastq-loader/expected/8.1.stderr | 5 +
test/fastq-loader/expected/9.0.stdout | 60 +
test/fastq-loader/input/1.1.fastq | 5 +
test/fastq-loader/input/1.2.fastq | 5 +
test/fastq-loader/input/1.3.fastq | 5 +
test/fastq-loader/input/1.4.fastq | 24 +
test/fastq-loader/input/10.0.fastq | 4 +
test/fastq-loader/input/11.0.1.fasta | 2 +
test/fastq-loader/input/11.0.2.fasta | 2 +
test/fastq-loader/input/11.1.1.fastq | 4 +
test/fastq-loader/input/11.1.2.fastq | 4 +
test/fastq-loader/input/12.0.fastq | 8 +
test/fastq-loader/input/12.1.fastq | 8 +
test/fastq-loader/input/12.2.fastq | 4 +
test/fastq-loader/input/2.1.1.fastq | 5 +
test/fastq-loader/input/2.1.fastq | 4 +
test/fastq-loader/input/2.2.fastq | 4 +
test/fastq-loader/input/2.3.fastq | 8 +
test/fastq-loader/input/2.4.fastq | 8 +
test/fastq-loader/input/2.5.fastq | 9 +
test/fastq-loader/input/2.6.fastq | 9 +
test/fastq-loader/input/2.7.fastq | 8 +
test/fastq-loader/input/2.8.1.fastq | 4 +
test/fastq-loader/input/2.8.fastq | 4 +
test/fastq-loader/input/2.9.1.fastq | 4 +
test/fastq-loader/input/2.9.fastq | 4 +
test/fastq-loader/input/3.1a.fastq | 8 +
test/fastq-loader/input/3.1b.fastq | 9 +
test/fastq-loader/input/3.2a.fastq | 8 +
test/fastq-loader/input/3.2b.fastq | 8 +
test/fastq-loader/input/3.3a.fastq | 8 +
test/fastq-loader/input/3.3b.fastq | 8 +
test/fastq-loader/input/4.4.fastq | 13 +
test/fastq-loader/input/4.5.1.fastq | 10 +
test/fastq-loader/input/4.5.fastq | 10 +
test/fastq-loader/input/4.fastq | 5 +
test/fastq-loader/input/5.0.fastq.gz | Bin 0 -> 139 bytes
test/fastq-loader/input/6.0.fastq | 52 +
test/fastq-loader/input/7.1.fastq | 9 +
test/fastq-loader/input/7.2.fastq | 8 +
test/fastq-loader/input/7.3.fastq | 8 +
test/fastq-loader/input/8.0.fastq | 9 +
test/fastq-loader/input/8.1.fastq | 17 +
test/fastq-loader/input/9.0.fastq | 16 +
test/fastq-loader/runtestcase.sh | 106 +
test/fastq-loader/test-fastq-loader.cpp | 215 +
test/fastq-loader/wb-test-fastq.cpp | 1376 ++++++
test/general-loader/.gitignore | 3 +
test/general-loader/Makefile | 194 +
test/general-loader/column01 | 3 +
test/general-loader/column02 | 3 +
test/general-loader/expected/1.stdout | 75 +
test/general-loader/expected/1override.stdout | 75 +
test/general-loader/expected/1packed.stdout | 75 +
test/general-loader/expected/2.stderr | 2 +
test/general-loader/expected/2packed.stderr | 2 +
test/general-loader/expected/3.stdout | 16 +
test/general-loader/expected/3packed.stdout | 16 +
test/general-loader/expected/4.stdout | 160 +
test/general-loader/expected/4packed.stdout | 160 +
test/general-loader/expected/5packed.stdout | 16 +
test/general-loader/expected/6.stdout | 1 +
test/general-loader/expected/6packed.stdout | 1 +
test/general-loader/makeinputs.cpp | 226 +
test/general-loader/runtestcase.sh | 108 +
test/general-loader/schema/.gitignore | 4 +
test/general-loader/test-general-loader.cpp | 1698 +++++++
test/general-loader/test-general-writer.cpp | 341 ++
.../general-loader/test-gw-dumper.cpp | 85 +-
test/general-loader/testsource.cpp | 758 +++
test/general-loader/testsource.hpp | 177 +
test/kget/.gitignore | 3 +
configure => test/kget/Makefile | 53 +-
{tools/cg-dump => test/network-test}/Makefile | 48 +-
test/network-test/network-test.c | 105 +
.../network-test/network-test.vers | 0
test/network-test/network-testing.c | 436 ++
.../network-test/network-testing.h | 12 +-
test/ngs-pileup/Makefile | 140 +
test/ngs-pileup/runtestcase.sh | 90 +
test/ngs-pileup/test-ngs-pileup.cpp | 177 +
test/ngs-pileup/valgrind.suppress | 6 +
test/only-remote-repository.kfg | 2 +
test/ref-variation/Makefile | 57 +
test/ref-variation/valgrind.suppress | 6 +
{tools/sra-dbcc => test/samline}/Makefile | 34 +-
test/samline/alig-gen.c | 604 +++
test/samline/cigar.c | 446 ++
.../line_token_iter.h => test/samline/cigar.h | 37 +-
test/samline/example.sh | 64 +
test/samline/refbases.c | 145 +
.../vtblcp-priv.h => test/samline/refbases.h | 9 +-
.../dump-idx.vers => test/samline/samline.vers | 0
test/tarballs/build.xml | 27 +
test/tarballs/test-tarballs.bat | 40 +
test/tarballs/test-tarballs.sh | 97 +
configure => test/vcf-loader/Makefile | 70 +-
test/vcf-loader/test-vcf-loader.cpp | 864 ++++
test/{ => vdb-dump}/Makefile | 29 +-
test/vdb-dump/SRR056386 | Bin 0 -> 14505 bytes
test/vdb-dump/expected/1.0.stdout | 1 +
test/vdb-dump/expected/1.1.stdout | 1 +
test/vschema/Makefile | 115 +
.../vschema/bio-end/bio-end-excl.vschema | 31 +-
.../vschema/bio-end/bio-end-incl.vschema | 31 +-
test/vschema/bio-end/expected/excl-1.stdout | 5 +
test/vschema/bio-end/expected/excl-2.stdout | 5 +
test/vschema/bio-end/expected/excl-3.stdout | 5 +
test/vschema/bio-end/expected/excl-4.stdout | 5 +
test/vschema/bio-end/expected/incl-1.stdout | 5 +
test/vschema/bio-end/makeinputs.cpp | 129 +
test/vschema/idx-text/checklookup.cpp | 323 ++
test/vschema/idx-text/expected/ci-1.stdout | 15 +
test/vschema/idx-text/expected/ci-2.stdout | 18 +
test/vschema/idx-text/expected/ci-3.stdout | 12 +
test/vschema/idx-text/expected/ci-4.stdout | 12 +
test/vschema/idx-text/expected/cs-1.stdout | 18 +
test/vschema/idx-text/expected/cs-2.stdout | 18 +
test/vschema/idx-text/idx-text.vschema | 105 +
test/vschema/idx-text/makeinputs.cpp | 148 +
test/vschema/runtestcase.sh | 126 +
tools/.gitignore | 3 +
tools/Makefile | 66 +-
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/{vtblcp => align-cache}/Makefile | 34 +-
tools/align-cache/align-cache.cpp | 557 +++
.../dump-idx.vers => align-cache/align-cache.vers} | 0
tools/align-cache/align-cache.vers.h | 1 +
tools/align-cache/helper.cpp | 923 ++++
tools/align-cache/helper.h | 390 ++
tools/align-info/align-info.c | 20 +-
tools/align-info/align-info.vers | 2 +-
tools/align-info/align-info.vers.h | 2 +-
tools/bam-loader/Globals.h | 1 +
tools/bam-loader/Makefile | 32 +-
tools/bam-loader/bam-load.3.vers | 1 -
tools/bam-loader/bam-load.vers | 2 +-
tools/bam-loader/bam-loader.c | 63 +-
tools/bam-loader/bam-loader3.c | 1028 -----
tools/bam-loader/bam.c | 4085 ++++++++++++++++
tools/bam-loader/bam.h | 632 +++
tools/bam-loader/config-file.cpp | 195 +
.../key_value.h => bam-loader/config-file.hpp} | 73 +-
tools/bam-loader/fasta-file.cpp | 257 ++
.../idx-mapping.h => bam-loader/fasta-file.hpp} | 68 +-
tools/bam-loader/loader-imp.c | 1426 +++---
tools/bam-loader/loader-imp3.c | 369 --
tools/bam-loader/mem-bank.cpp | 477 ++
.../fastq-reader.h => bam-loader/mem-bank.h} | 29 +-
tools/bam-loader/reference-writer.c | 214 +-
tools/bam-loader/reference-writer.h | 12 +-
tools/bam-loader/sequence-writer.c | 24 +-
tools/cache-mgr/cache-mgr.c | 64 +-
tools/cache-mgr/cache-mgr.vers | 2 +-
tools/cache-mgr/cache-mgr.vers.h | 2 +-
tools/ccextract/Makefile | 25 +-
tools/ccextract/ccextract.c | 16 +-
tools/ccextract/ccextract.vers | 2 +-
tools/cg-dump/cg-dump.c | 1563 -------
tools/cg-dump/cg-dump.vers | 1 -
tools/cg-dump/last_rowid.c | 353 --
tools/cg-dump/line_token_iter.c | 148 -
tools/cg-dump/num-gen.c | 848 ----
tools/cg-dump/num-gen.h | 225 -
tools/cg-dump/progressbar.c | 140 -
tools/cg-dump/progressbar.h | 70 -
tools/cg-dump/sg_lookup.c | 277 --
tools/cg-load/Makefile | 5 +-
tools/cg-load/cg-load.c | 281 +-
tools/cg-load/cg-load.vers | 2 +-
tools/cg-load/defs.h | 41 +-
tools/cg-load/f1_3.c | 1 +
tools/cg-load/f1_5.c | 2 +-
tools/cg-load/{f1_5.c => f1_7.c} | 39 +-
tools/cg-load/f2_0.c | 18 +-
tools/cg-load/f2_2.c | 4 +-
tools/cg-load/f2_5.c | 98 +
tools/cg-load/factory-evidence-dnbs.c | 290 +-
tools/cg-load/factory-evidence-dnbs.h | 3 +
tools/cg-load/factory-evidence-intervals.c | 100 +-
tools/cg-load/factory-evidence-intervals.h | 3 +
tools/cg-load/factory-file.h | 4 +
tools/cg-load/factory-mappings.c | 213 +-
tools/cg-load/factory-mappings.h | 3 +
tools/cg-load/factory-reads.c | 246 +-
tools/cg-load/factory-reads.h | 3 +
tools/cg-load/factory-tag-lfr.c | 183 +-
tools/cg-load/factory-tag-lfr.h | 6 +-
tools/cg-load/file-version-factory.c | 7 +-
tools/cg-load/file.c | 149 +-
tools/cg-load/file.h | 1 +
tools/{vdb-dump/vdb_info.h => cg-load/formats.c} | 37 +-
tools/{vtblcp/vtblcp-priv.h => cg-load/formats.h} | 19 +-
tools/cg-load/writer-algn.c | 128 +-
tools/cg-load/writer-algn.h | 3 +-
tools/cg-load/writer-evidence-dnbs.c | 56 +-
tools/cg-load/writer-evidence-dnbs.h | 19 +-
tools/cg-load/writer-evidence-intervals.c | 25 +-
tools/cg-load/writer-seq.c | 36 +-
tools/cg-load/writer-seq.h | 12 +-
tools/check-blob-size/check-blob-size.c | 332 --
tools/check-blob-size/check-blob-size.vers | 1 -
tools/copycat/Makefile | 28 +-
tools/copycat/cccat.c | 12 +-
tools/copycat/ccsra.c | 2 +-
tools/copycat/cctree.c | 6 +-
tools/copycat/copycat.c | 14 +-
tools/copycat/copycat.vers | 2 +-
tools/{workspace => dbgap-mount}/Makefile | 82 +-
tools/dbgap-mount/demo.c | 360 ++
tools/dbgap-mount/demo.mkfg | 47 +
.../sra-gui/sra-gui.vers => dbgap-mount/demo.vers} | 0
tools/dbgap-mount/demo.vers.h | 1 +
tools/deseq/csra-trim.vers | 1 -
tools/deseq/deseq.c | 521 ---
tools/fastq-dump/Makefile | 18 +-
tools/fastq-dump/args.cpp | 12 +-
tools/fastq-dump/args.hpp | 2 +-
tools/fastq-dump/fastq-dump.cpp | 146 +-
tools/fastq-dump/fastq-dump.vers | 2 +-
tools/fastq-dump/koutstream | 73 +-
tools/fastq-loader/Makefile | 13 +-
tools/fastq-loader/fastq-grammar.c | 714 +--
tools/fastq-loader/fastq-grammar.y | 224 +-
tools/fastq-loader/fastq-lex.c | 749 ++-
tools/fastq-loader/fastq-lex.l | 20 +-
tools/fastq-loader/fastq-loader.c | 80 +-
tools/fastq-loader/fastq-parse.h | 50 +-
tools/fastq-loader/fastq-reader.c | 45 +-
tools/fastq-loader/fastq-reader.h | 9 +-
tools/fastq-loader/latf-load.vers | 2 +-
tools/fastq-loader/latf-load.vers.h | 2 +-
tools/fastq-loader/loader-imp.c | 19 +-
tools/fastq-loader/parsing_rules.txt | 93 +
tools/fix-run-stat/fix-run-stat.c | 355 --
tools/fix-run-stat/fix-run-stat.vers | 1 -
tools/fuse/Makefile | 37 +
tools/fuse/directory.c | 8 +-
tools/fuse/remote-cache.c | 12 +-
tools/fuse/remote-directory.c | 4 +-
tools/fuse/remote-fuser.vers | 2 +-
tools/fuse/sra-fuser-test.vers | 2 +-
tools/fuse/sra-fuser-test.vers.h | 2 +-
tools/fuse/sra-fuser.vers | 2 +-
tools/fuse/sra-list.c | 6 +-
tools/fuse/sra-makeidx.c | 6 +-
tools/fuse/sra-makeidx.vers | 2 +-
tools/fuse/tar-list.c | 4 +-
tools/fuse/unix/sra-fuser-sys.c | 37 +-
tools/{meta-sync => general-loader}/Makefile | 100 +-
tools/general-loader/database-loader.cpp | 895 ++++
tools/general-loader/general-loader.cpp | 223 +
tools/general-loader/general-loader.hpp | 243 +
tools/general-loader/general-loader.vers | 1 +
tools/general-loader/general-loader.vers.h | 1 +
tools/general-loader/general-writer.cpp | 1172 +++++
tools/general-loader/general-writer.h | 1081 +++++
tools/general-loader/general-writer.hpp | 210 +
tools/general-loader/gw-dumper.cpp | 1785 +++++++
tools/general-loader/libgeneral-writer.vers | 1 +
tools/general-loader/main.cpp | 246 +
tools/general-loader/protocol-parser.cpp | 1048 +++++
tools/general-loader/utf8-like-int-codec.c | 687 +++
.../utf8-like-int-codec.h} | 63 +-
tools/kar/kar.c | 21 +-
tools/kar/kar.vers | 2 +-
tools/kar/kar.vers.h | 2 +-
tools/kar/sra-kar.c | 10 +-
tools/kar/sra-kar.vers | 2 +-
tools/kar/sra-kar.vers.h | 2 +-
tools/keyring-srv/keyring-data.c | 8 +-
tools/keyring-srv/keyring-srv.vers | 2 +-
tools/{sra-dbcc => kget}/Makefile | 31 +-
tools/kget/kget.c | 688 +++
tools/{fuse/dump-idx.vers => kget/kget.vers} | 0
tools/kqsh/kqsh.c | 2 +-
tools/kqsh/kqsh.vers | 2 +-
tools/meta-sync/meta-sync.c | 1517 ------
tools/meta-sync/meta-sync.pl | 41 -
tools/meta-sync/meta-sync.vers | 1 -
tools/nenctool/nenctest.c | 10 +-
tools/nenctool/nenctest.vers | 2 +-
tools/nenctool/nenctool.c | 12 +-
tools/nenctool/nenctool.vers | 2 +-
tools/nencvalid/nencvalid.c | 9 +-
tools/nencvalid/nencvalid.vers | 2 +-
tools/{fix-run-stat => ngs-pileup}/Makefile | 46 +-
tools/ngs-pileup/main.cpp | 164 +
tools/ngs-pileup/ngs-pileup.cpp | 206 +
tools/ngs-pileup/ngs-pileup.hpp | 97 +
.../sra-gui.vers => ngs-pileup/ngs-pileup.vers} | 0
tools/ngs-pileup/ngs-pileup.vers.h | 1 +
tools/pacbio-load/Makefile | 8 +-
tools/pacbio-load/pacbio-load.vers | 2 +-
tools/pacbio-load/pl-consensus.c | 227 +-
tools/pacbio-load/pl-context.c | 4 +-
tools/pacbio-load/pl-regions.c | 4 +-
tools/pacbio-load/pl-tools.c | 22 +-
tools/{deseq => pileup-stats}/Makefile | 47 +-
tools/pileup-stats/pileup-stats.cpp | 719 +++
tools/pileup-stats/pileup-stats.vers | 1 +
tools/pore-load/GeneralWriter.py | 312 ++
tools/pore-load/README.md | 10 +
tools/pore-load/pore-load.py | 406 ++
tools/prefetch/Makefile | 3 +-
tools/prefetch/kfile-no-q.c | 215 +
.../loader-imp3.h => prefetch/kfile-no-q.h} | 26 +-
tools/prefetch/prefetch.c | 1020 +++-
tools/prefetch/prefetch.vers | 2 +-
tools/prefetch/prefetch.vers.h | 2 +-
tools/qual-recal/Makefile | 101 -
tools/qual-recal/make_histo_data.sh | 12 -
tools/qual-recal/qual-recal.c | 654 ---
tools/qual-recalib-stat/Makefile | 2 -
tools/qual-recalib-stat/context.c | 6 +-
tools/qual-recalib-stat/context.h | 4 +-
tools/qual-recalib-stat/num-gen.c | 848 ----
tools/qual-recalib-stat/num-gen.h | 225 -
tools/qual-recalib-stat/progressbar.c | 182 -
tools/qual-recalib-stat/progressbar.h | 75 -
tools/qual-recalib-stat/qual-recalib-stat.c | 39 +-
tools/qual-recalib-stat/qual-recalib-stat.vers | 2 +-
tools/qual-recalib-stat/qual-recalib-stat.vers.h | 2 +-
tools/qual-recalib-stat/ref_exclude.c | 8 +-
tools/qual-recalib-stat/stat_mod.c | 4 +-
tools/qual-recalib-stat/stat_mod_1.c | 4 +-
tools/qual-recalib-stat/stat_mod_2.c | 4 +-
tools/qual-recalib-stat/writer.c | 58 +-
tools/qual-recalib-stat/writer.h | 1 -
tools/rd-filter-redact/rd-filter-redact.c | 6 +-
tools/rd-filter-redact/rd-filter-redact.vers | 2 +-
tools/rd-filter-redact/read-filter-redact.c | 6 +-
tools/rd-filter-redact/read-filter-redact.vers | 2 +-
tools/rd-filter-redact/read-filter-redact.vers.h | 2 +-
tools/rd-filter-redact/test-read-write-cursor.vers | 2 +-
tools/{check-blob-size => ref-variation}/Makefile | 73 +-
tools/ref-variation/common.cpp | 70 +
.../vdb_info.h => ref-variation/common.h} | 31 +-
tools/ref-variation/helper.cpp | 1404 ++++++
tools/ref-variation/helper.h | 605 +++
tools/ref-variation/ref-variation.cpp | 2102 +++++++++
.../ref-variation.vers} | 0
tools/ref-variation/ref-variation.vers.h | 1 +
tools/ref-variation/var-expand.cpp | 448 ++
.../sra-gui.vers => ref-variation/var-expand.vers} | 0
tools/ref-variation/var-expand.vers.h | 1 +
tools/refseq-load/refseq-load.vers | 1 +
tools/run-stat/.gitignore | 6 -
tools/run-stat/Makefile | 120 -
tools/run-stat/chart.c | 465 --
tools/run-stat/chart.h | 109 -
tools/run-stat/context.c | 439 --
tools/run-stat/context.h | 98 -
tools/run-stat/helper.c | 715 ---
tools/run-stat/helper.h | 126 -
tools/run-stat/key_value.c | 549 ---
tools/run-stat/mod_cmn.c | 329 --
tools/run-stat/mod_cmn.h | 149 -
tools/run-stat/mod_reads.c | 747 ---
tools/run-stat/mod_reads_defs.h | 128 -
tools/run-stat/mod_reads_helper.c | 575 ---
tools/run-stat/mod_reads_helper.h | 61 -
tools/run-stat/num-gen.c | 497 --
tools/run-stat/progressbar.c | 191 -
tools/run-stat/progressbar.h | 76 -
tools/run-stat/rd_filter.c | 243 -
tools/run-stat/rd_filter.h | 98 -
tools/run-stat/run-stat.c | 703 ---
tools/run-stat/run-stat.vers | 1 -
tools/run-stat/svg.c | 753 ---
tools/run-stat/svg.h | 117 -
tools/sam-dump/debug.h | 34 -
tools/sam-dump/sam-dump.c | 4870 --------------------
tools/sam-dump/sam-dump.vers | 1 -
tools/sra-dbcc/sra-dbcc.c | 1577 -------
tools/sra-dbcc/sra-dbcc.vers | 1 -
tools/sra-dump/abi-dump.vers | 2 +-
tools/sra-dump/abi-dump.vers.h | 2 +-
tools/sra-dump/abi.c | 4 +-
tools/sra-dump/core.c | 9 +-
tools/sra-dump/factory.c | 4 +-
tools/sra-dump/fasta_dump.c | 6 +-
tools/sra-dump/fastq-dump.vers | 2 +-
tools/sra-dump/fastq-dump.vers.h | 2 +-
tools/sra-dump/fastq.c | 4 +-
tools/sra-dump/illumina-dump.vers | 2 +-
tools/sra-dump/illumina-dump.vers.h | 2 +-
tools/sra-dump/sff-dump.vers | 2 +-
tools/sra-dump/sff-dump.vers.h | 2 +-
tools/sra-dump/sra-dump.c | 20 +-
tools/sra-dump/sra-dump.vers | 2 +-
tools/sra-load/Makefile | 19 +-
tools/sra-load/abi-load.vers | 2 +-
tools/sra-load/common-xml.c | 11 +-
tools/sra-load/experiment-xml.c | 6 +-
tools/sra-load/fastq-load.vers | 2 +-
tools/sra-load/helicos-load.vers | 2 +-
tools/sra-load/illumina-load.vers | 2 +-
tools/sra-load/loader.c | 28 +-
tools/sra-load/pacbio-loadxml.vers | 2 +-
tools/sra-load/sff-load.vers | 2 +-
tools/sra-load/srf-absolid.c | 15 +-
tools/sra-load/srf-load.vers | 2 +-
tools/sra-load/writer-illumina.c | 2 +-
tools/sra-load/ztr-huffman.c | 15 +-
tools/sra-pileup/Makefile | 27 +-
tools/sra-pileup/cg_tools.c | 2 +-
tools/sra-pileup/cmdline_cmn.c | 6 +-
tools/sra-pileup/dyn_string.c | 20 +
tools/sra-pileup/dyn_string.h | 1 +
tools/sra-pileup/inputfiles.c | 1 +
tools/sra-pileup/md_flag.c | 268 ++
.../{cg-dump/last_rowid.h => sra-pileup/md_flag.h} | 14 +-
tools/sra-pileup/pileup_counters.c | 4 +-
.../{pileup_varcount.c => pileup_indels.c} | 71 +-
.../vtblcp-priv.h => sra-pileup/pileup_indels.h} | 8 +-
tools/sra-pileup/pileup_options.h | 1 +
tools/sra-pileup/pileup_v2.c | 8 +-
tools/sra-pileup/pileup_varcount.c | 10 +-
tools/sra-pileup/ref_regions.c | 74 +-
tools/sra-pileup/ref_walker_0.c | 20 +-
tools/sra-pileup/report_deletes.c | 2 +-
tools/sra-pileup/reref.c | 208 +-
tools/sra-pileup/sam-aligned.c | 44 +-
tools/sra-pileup/sam-dump-opts.c | 171 +-
tools/sra-pileup/sam-dump-opts.h | 3 +
tools/sra-pileup/sam-dump.c | 14 +-
tools/sra-pileup/sam-dump.vers | 2 +-
tools/sra-pileup/sam-dump.vers.h | 2 +-
tools/sra-pileup/sam-dump2.vers | 2 +-
tools/sra-pileup/sam-dump3.c | 12 +-
tools/sra-pileup/sam-hdr.c | 4 +-
tools/sra-pileup/sam-hdr1.c | 853 ++++
.../last_rowid.h => sra-pileup/sam-hdr1.h} | 18 +-
tools/sra-pileup/sra-pileup.c | 214 +-
tools/sra-pileup/sra-pileup.vers | 2 +-
tools/sra-pileup/sra-pileup.vers.h | 2 +-
tools/sra-pileup/walk_debug.c | 75 +-
tools/{sam-dump => sra-seq-count}/Makefile | 53 +-
tools/sra-seq-count/main_fkt.c | 211 +
.../last_rowid.h => sra-seq-count/options.h} | 24 +-
tools/sra-seq-count/range.hpp | 307 ++
tools/sra-seq-count/sra-seq-count.cpp | 688 +++
.../sra-seq-count.vers} | 0
tools/sra-sort/col-pair.c | 2 +-
tools/sra-sort/idx-mapping.c | 12 +-
tools/sra-sort/idx-mapping.h | 4 +-
tools/sra-sort/meta-pair.c | 12 +-
tools/sra-sort/poslen-col-pair.c | 2 +-
tools/sra-sort/ref-alignid-col.c | 13 +-
tools/sra-sort/sra-sort.c | 10 +-
tools/sra-sort/sra-sort.vers | 2 +-
tools/sra-stat/Makefile | 8 +-
tools/sra-stat/sra-stat.c | 1301 ++++--
.../{run-stat/mod_reads.h => sra-stat/sra-stat.h} | 26 +-
tools/sra-stat/sra-stat.vers | 2 +-
tools/sra-stat/sra-stat.vers.h | 2 +-
tools/sra-stat/sra.c | 446 ++
tools/sra/.cvsignore | 1 +
tools/sra/Makefile | 9 +-
tools/sra/table-vers.c | 4 +-
tools/sra/table-vers.vers | 2 +-
tools/srapath/srapath.c | 51 +-
tools/srapath/srapath.vers | 2 +-
tools/srapath/srapath.vers.h | 2 +-
tools/update-schema/.cvsignore | 1 +
tools/update-schema/Makefile | 4 +-
tools/update-schema/update-schema.c | 14 +-
tools/update-schema/vdb-update-schema.vers | 2 +-
tools/util/Makefile | 39 +-
tools/util/crc32sum.c | 2 +-
tools/util/kdb-index.c | 264 ++
tools/util/kdb-index.vers | 1 +
tools/util/kdbmeta.c | 10 +-
tools/util/kdbmeta.vers | 2 +-
tools/util/kdbmeta.vers.h | 2 +-
tools/util/md5cp.c | 8 +-
tools/util/md5cp.vers | 2 +-
tools/util/md5cp.vers.h | 2 +-
tools/util/pacbio-correct.c | 2 +-
tools/util/pacbio-correct.vers | 2 +-
tools/util/rcexplain.c | 2 +-
tools/util/rcexplain.vers | 2 +-
tools/util/rcexplain.vers.h | 2 +-
tools/util/rowwritetest.c | 4 +-
tools/util/rowwritetest.vers | 2 +-
tools/{sra-sort/idx-mapping.h => util/samview.c} | 74 +-
tools/util/schema-replace.c | 4 +-
tools/util/schema-replace.vers | 2 +-
tools/util/schema-replace.vers.h | 2 +-
tools/util/sortreadtest.c | 6 +-
tools/util/test-sra.c | 1129 ++++-
tools/util/test-sra.vers | 2 +-
tools/util/test-sra.vers.h | 2 +-
tools/util/testld.c | 4 +-
tools/util/testld.vers | 2 +-
tools/util/txt2kdb.c | 8 +-
tools/util/txt2kdb.vers | 2 +-
tools/util/vdb-lock.c | 2 +-
tools/util/vdb-lock.vers | 2 +-
tools/util/vdb-lock.vers.h | 2 +-
tools/util/vdb-passwd.c | 46 +-
tools/util/vdb-passwd.vers | 2 +-
tools/util/vdb-passwd.vers.h | 2 +-
tools/util/vdb-unlock.c | 2 +-
tools/util/vdb-unlock.vers | 2 +-
tools/util/vdb-unlock.vers.h | 2 +-
tools/vcf-loader/.gitignore | 1 +
tools/vcf-loader/Makefile | 9 +-
tools/vcf-loader/vcf-database.c | 5 +-
tools/vcf-loader/vcf-grammar.c | 2 +-
tools/vcf-loader/vcf-grammar.y | 2 +-
tools/vcf-loader/vcf-lex.c | 50 +-
tools/vcf-loader/vcf-lex.l | 12 +-
tools/vcf-loader/vcf-load.vers | 2 +-
tools/vcf-loader/vcf-parse.h | 5 +-
tools/vdb-config/configure.cpp | 56 +-
tools/vdb-config/interactive.cpp | 64 +-
tools/vdb-config/util.cpp | 93 +-
tools/vdb-config/util.hpp | 7 +-
tools/vdb-config/vdb-config-model.cpp | 16 +-
tools/vdb-config/vdb-config-model.hpp | 75 +-
tools/vdb-config/vdb-config.c | 921 ++--
tools/vdb-config/vdb-config.vers | 2 +-
tools/vdb-config/vdb-config.vers.h | 2 +-
tools/vdb-copy/Makefile | 2 -
tools/vdb-copy/context.c | 17 +-
tools/vdb-copy/context.h | 5 +-
tools/vdb-copy/definitions.h | 4 +
tools/vdb-copy/num-gen.c | 4 +-
tools/vdb-copy/progressbar.c | 137 -
tools/vdb-copy/progressbar.h | 70 -
tools/vdb-copy/type_matcher.c | 12 +-
tools/vdb-copy/vdb-copy.c | 50 +-
tools/vdb-copy/vdb-copy.vers | 2 +-
tools/vdb-copy/vdb-copy.vers.h | 2 +-
tools/vdb-decrypt/shared.c | 17 +-
tools/vdb-decrypt/vdb-decrypt.vers | 2 +-
tools/vdb-decrypt/vdb-decrypt.vers.h | 2 +-
tools/vdb-decrypt/vdb-encrypt.vers | 2 +-
tools/vdb-decrypt/vdb-encrypt.vers.h | 2 +-
tools/{sra-dbcc => vdb-diff}/Makefile | 33 +-
tools/vdb-diff/coldefs.c | 211 +
.../vdb-dump-num-gen.h => vdb-diff/coldefs.h} | 87 +-
tools/vdb-diff/namelist_tools.c | 299 ++
.../sg_lookup.h => vdb-diff/namelist_tools.h} | 40 +-
tools/vdb-diff/vdb-diff.c | 1017 ++++
.../{fuse/dump-idx.vers => vdb-diff/vdb-diff.vers} | 0
tools/vdb-diff/vdb-diff.vers.h | 1 +
tools/vdb-dump/Makefile | 1 -
tools/vdb-dump/help.txt | 194 +-
tools/vdb-dump/vdb-boot.vers | 2 +-
tools/vdb-dump/vdb-dump-bin.c | 397 +-
tools/vdb-dump/vdb-dump-bin.h | 2 +
tools/vdb-dump/vdb-dump-coldefs.c | 180 +-
tools/vdb-dump/vdb-dump-coldefs.h | 5 +
tools/vdb-dump/vdb-dump-context.c | 60 +-
tools/vdb-dump/vdb-dump-context.h | 26 +-
tools/vdb-dump/vdb-dump-fastq.c | 958 ++--
tools/vdb-dump/vdb-dump-formats.c | 58 +-
tools/vdb-dump/vdb-dump-helper.c | 118 +-
tools/vdb-dump/vdb-dump-helper.h | 5 +-
tools/vdb-dump/vdb-dump-num-gen.c | 477 --
tools/vdb-dump/vdb-dump-row-context.h | 2 +-
tools/vdb-dump/vdb-dump-str.c | 160 +
tools/vdb-dump/vdb-dump-str.h | 5 +
tools/vdb-dump/vdb-dump-tools.c | 7 +-
tools/vdb-dump/vdb-dump-tools.h | 2 +-
tools/vdb-dump/vdb-dump.c | 778 +++-
tools/vdb-dump/vdb-dump.vers | 2 +-
tools/vdb-dump/vdb-dump.vers.h | 2 +-
tools/vdb-dump/vdb_info.c | 462 +-
tools/vdb-dump/vdb_info.h | 2 +-
tools/vdb-validate/vdb-validate.c | 92 +-
tools/vdb-validate/vdb-validate.vers | 2 +-
tools/vdb-validate/vdb-validate.vers.h | 2 +-
tools/vdbview/b_first.png | Bin 528 -> 0 bytes
tools/vdbview/b_goto.png | Bin 475 -> 0 bytes
tools/vdbview/b_last.png | Bin 519 -> 0 bytes
tools/vdbview/b_next.png | Bin 428 -> 0 bytes
tools/vdbview/b_nextpage.png | Bin 639 -> 0 bytes
tools/vdbview/b_prev.png | Bin 426 -> 0 bytes
tools/vdbview/b_prevpage.png | Bin 636 -> 0 bytes
tools/vdbview/b_search.png | Bin 614 -> 0 bytes
tools/vdbview/background.pas | 277 --
tools/vdbview/buttons.svg | 268 --
tools/vdbview/columnsel.lfm | 90 -
tools/vdbview/columnsel.pas | 115 -
tools/vdbview/dataproxy.pas | 602 ---
tools/vdbview/gotoform.lfm | 56 -
tools/vdbview/gotoform.pas | 47 -
tools/vdbview/jobdef.pas | 27 -
tools/vdbview/linkedlist.pas | 186 -
tools/vdbview/logo_128.png | Bin 1752 -> 0 bytes
tools/vdbview/logo_16.png | Bin 368 -> 0 bytes
tools/vdbview/logo_256.png | Bin 3524 -> 0 bytes
tools/vdbview/logo_32.png | Bin 541 -> 0 bytes
tools/vdbview/logo_64.png | Bin 910 -> 0 bytes
tools/vdbview/mainwindow.lfm | 973 ----
tools/vdbview/mainwindow.pas | 793 ----
tools/vdbview/searchform.lfm | 69 -
tools/vdbview/searchform.pas | 79 -
tools/vdbview/selector_types.pas | 20 -
tools/vdbview/support_unit.pas | 217 -
tools/vdbview/svdb.pas | 676 ---
tools/vdbview/svdb_obj.pas | 339 --
tools/vdbview/vdbview.ico | Bin 25890 -> 0 bytes
tools/vdbview/vdbview.lpi | 343 --
tools/vdbview/vdbview.lpr | 24 -
tools/vdbview/vdbview.res | Bin 27156 -> 0 bytes
tools/vdbview/vdbview1.ico | Bin 25890 -> 0 bytes
tools/vdbview/version.lfm | 40 -
tools/vdbview/version.pas | 33 -
tools/vtblcp/vtblcp.c | 979 ----
tools/vtblcp/vtblcp.vers | 1 -
tools/workspace/.gitignore | 3 -
tools/workspace/path-to-kar-file.cpp | 117 -
tools/workspace/prefs-lex.l | 181 -
tools/workspace/prefs-yacc.y | 189 -
tools/workspace/sra.cpp | 1514 ------
tools/workspace/sra.vers | 1 -
tools/workspace/sratoolkit-exception.cpp | 126 -
tools/workspace/sratoolkit-exception.hpp | 111 -
tools/workspace/token.c | 228 -
tools/workspace/token.h | 99 -
tools/workspace/workspace.cpp | 1116 -----
win-configure.bat | 1 -
757 files changed, 58096 insertions(+), 42785 deletions(-)
delete mode 100644 GNU-license.txt
create mode 100644 LICENSE
delete mode 100644 README-WINDOWS.txt
delete mode 100644 README-build
delete mode 100644 README-config.txt
rename README-vdb-config.txt => README-vdb-config (97%)
delete mode 100644 README-wget.txt
delete mode 100644 USAGE
copy build/MSVC/2010/{read-filter-redact.vcxproj => align-cache.vcxproj} (74%)
mode change 100644 => 100755
copy build/MSVC/2010/{fastq-dump-ngs.vcxproj => dbgap-mount-demo.vcxproj} (71%)
copy build/MSVC/2010/{kdbmeta.vcxproj => general-loader.vcxproj} (68%)
rename build/MSVC/2010/{illumina-diump.vcxproj => illumina-dump.vcxproj} (100%)
copy build/MSVC/2010/{fastq-dump-ngs.vcxproj => ref-variation.vcxproj} (59%)
mode change 100644 => 100755
copy build/MSVC/2010/{md5cp.vcxproj => test-align-info.vcxproj} (55%)
copy build/MSVC/2010/{fastq-loader.vcxproj => test-fastq-loader.vcxproj} (73%)
copy build/MSVC/2010/{kdbmeta.vcxproj => test-general-loader.vcxproj} (60%)
create mode 100644 build/MSVC/2010/test-sra-tools.sln
copy build/MSVC/2010/{schema-replace.vcxproj => test-vcf-loader.vcxproj} (64%)
copy build/MSVC/2010/{fastq-dump-ngs.vcxproj => var-expand.vcxproj} (59%)
mode change 100644 => 100755
copy build/MSVC/2010/{vdb-validate.vcxproj => vdb-diff.vcxproj} (80%)
copy build/MSVC/2010/{fastq-loader.vcxproj => wb-test-fastq.vcxproj} (73%)
delete mode 100644 konfigure.perl
delete mode 100644 os-arch.perl
copy configure => setup/install (83%)
create mode 100644 setup/install.perl
create mode 100644 setup/install.prl
create mode 100644 setup/konfigure.perl
create mode 100644 setup/os-arch.perl
rename os-arch.pm => setup/os-arch.prl (89%)
rename package.pm => setup/package.prl (53%)
copy configure => setup/s/install (82%)
create mode 100644 setup/s/os.prl
copy test/{ => align-info}/Makefile (75%)
create mode 100644 test/fastq-loader/.gitignore
create mode 100644 test/fastq-loader/Makefile
create mode 100644 test/fastq-loader/expected/1.1.stdout
create mode 100644 test/fastq-loader/expected/1.2.stdout
create mode 100644 test/fastq-loader/expected/1.3.stderr
create mode 100644 test/fastq-loader/expected/1.3.stdout
create mode 100755 test/fastq-loader/expected/1.4.stdout
create mode 100644 test/fastq-loader/expected/10.0.stdout
create mode 100644 test/fastq-loader/expected/11.0.stdout
create mode 100644 test/fastq-loader/expected/11.1.stdout
create mode 100644 test/fastq-loader/expected/12.0.stdout
create mode 100644 test/fastq-loader/expected/12.1.stdout
create mode 100644 test/fastq-loader/expected/12.2.stdout
create mode 100644 test/fastq-loader/expected/2.1.1.stdout
create mode 100644 test/fastq-loader/expected/2.1.stdout
create mode 100644 test/fastq-loader/expected/2.5.stdout
create mode 100644 test/fastq-loader/expected/2.6.stdout
create mode 100644 test/fastq-loader/expected/2.7.stdout
create mode 100644 test/fastq-loader/expected/2.8.1.stdout
create mode 100644 test/fastq-loader/expected/2.8.stdout
create mode 100644 test/fastq-loader/expected/2.9.1.stderr
create mode 100644 test/fastq-loader/expected/2.9.stderr
create mode 100644 test/fastq-loader/expected/3.1.stdout
create mode 100644 test/fastq-loader/expected/4.2.stdout
create mode 100644 test/fastq-loader/expected/4.3.1.stderr
create mode 100644 test/fastq-loader/expected/4.4.stdout
create mode 100644 test/fastq-loader/expected/4.5.1.stderr
create mode 100644 test/fastq-loader/expected/4.5.stderr
create mode 100644 test/fastq-loader/expected/4.6.1.stderr
create mode 100644 test/fastq-loader/expected/4.6.stdout
create mode 100644 test/fastq-loader/expected/4.7.stderr
create mode 100644 test/fastq-loader/expected/5.0.stdout
create mode 100644 test/fastq-loader/expected/6.0.stdout
create mode 100644 test/fastq-loader/expected/7.1.stdout
create mode 100644 test/fastq-loader/expected/7.2.stdout
create mode 100644 test/fastq-loader/expected/7.3.stdout
create mode 100644 test/fastq-loader/expected/8.0.stdout
create mode 100644 test/fastq-loader/expected/8.1.stderr
create mode 100644 test/fastq-loader/expected/9.0.stdout
create mode 100644 test/fastq-loader/input/1.1.fastq
create mode 100644 test/fastq-loader/input/1.2.fastq
create mode 100644 test/fastq-loader/input/1.3.fastq
create mode 100644 test/fastq-loader/input/1.4.fastq
create mode 100644 test/fastq-loader/input/10.0.fastq
create mode 100644 test/fastq-loader/input/11.0.1.fasta
create mode 100644 test/fastq-loader/input/11.0.2.fasta
create mode 100644 test/fastq-loader/input/11.1.1.fastq
create mode 100644 test/fastq-loader/input/11.1.2.fastq
create mode 100644 test/fastq-loader/input/12.0.fastq
create mode 100644 test/fastq-loader/input/12.1.fastq
create mode 100644 test/fastq-loader/input/12.2.fastq
create mode 100644 test/fastq-loader/input/2.1.1.fastq
create mode 100644 test/fastq-loader/input/2.1.fastq
create mode 100644 test/fastq-loader/input/2.2.fastq
create mode 100644 test/fastq-loader/input/2.3.fastq
create mode 100644 test/fastq-loader/input/2.4.fastq
create mode 100644 test/fastq-loader/input/2.5.fastq
create mode 100644 test/fastq-loader/input/2.6.fastq
create mode 100644 test/fastq-loader/input/2.7.fastq
create mode 100644 test/fastq-loader/input/2.8.1.fastq
create mode 100644 test/fastq-loader/input/2.8.fastq
create mode 100644 test/fastq-loader/input/2.9.1.fastq
create mode 100644 test/fastq-loader/input/2.9.fastq
create mode 100644 test/fastq-loader/input/3.1a.fastq
create mode 100644 test/fastq-loader/input/3.1b.fastq
create mode 100644 test/fastq-loader/input/3.2a.fastq
create mode 100644 test/fastq-loader/input/3.2b.fastq
create mode 100644 test/fastq-loader/input/3.3a.fastq
create mode 100644 test/fastq-loader/input/3.3b.fastq
create mode 100644 test/fastq-loader/input/4.4.fastq
create mode 100644 test/fastq-loader/input/4.5.1.fastq
create mode 100644 test/fastq-loader/input/4.5.fastq
create mode 100644 test/fastq-loader/input/4.fastq
create mode 100644 test/fastq-loader/input/5.0.fastq.gz
create mode 100644 test/fastq-loader/input/6.0.fastq
create mode 100644 test/fastq-loader/input/7.1.fastq
create mode 100644 test/fastq-loader/input/7.2.fastq
create mode 100644 test/fastq-loader/input/7.3.fastq
create mode 100644 test/fastq-loader/input/8.0.fastq
create mode 100644 test/fastq-loader/input/8.1.fastq
create mode 100644 test/fastq-loader/input/9.0.fastq
create mode 100755 test/fastq-loader/runtestcase.sh
create mode 100644 test/fastq-loader/test-fastq-loader.cpp
create mode 100644 test/fastq-loader/wb-test-fastq.cpp
create mode 100644 test/general-loader/.gitignore
create mode 100644 test/general-loader/Makefile
create mode 100644 test/general-loader/column01
create mode 100644 test/general-loader/column02
create mode 100644 test/general-loader/expected/1.stdout
create mode 100644 test/general-loader/expected/1override.stdout
create mode 100644 test/general-loader/expected/1packed.stdout
create mode 100644 test/general-loader/expected/2.stderr
create mode 100644 test/general-loader/expected/2packed.stderr
create mode 100644 test/general-loader/expected/3.stdout
create mode 100644 test/general-loader/expected/3packed.stdout
create mode 100644 test/general-loader/expected/4.stdout
create mode 100644 test/general-loader/expected/4packed.stdout
create mode 100644 test/general-loader/expected/5packed.stdout
create mode 100644 test/general-loader/expected/6.stdout
create mode 100644 test/general-loader/expected/6packed.stdout
create mode 100644 test/general-loader/makeinputs.cpp
create mode 100755 test/general-loader/runtestcase.sh
create mode 100644 test/general-loader/schema/.gitignore
create mode 100644 test/general-loader/test-general-loader.cpp
create mode 100644 test/general-loader/test-general-writer.cpp
rename tools/run-stat/num-gen.h => test/general-loader/test-gw-dumper.cpp (50%)
create mode 100644 test/general-loader/testsource.cpp
create mode 100644 test/general-loader/testsource.hpp
create mode 100644 test/kget/.gitignore
copy configure => test/kget/Makefile (64%)
mode change 100755 => 100644
rename {tools/cg-dump => test/network-test}/Makefile (83%)
create mode 100644 test/network-test/network-test.c
copy tools/fuse/dump-idx.vers => test/network-test/network-test.vers (100%)
create mode 100644 test/network-test/network-testing.c
copy tools/run-stat/mod_reads.h => test/network-test/network-testing.h (91%)
create mode 100644 test/ngs-pileup/Makefile
create mode 100755 test/ngs-pileup/runtestcase.sh
create mode 100644 test/ngs-pileup/test-ngs-pileup.cpp
create mode 100644 test/ngs-pileup/valgrind.suppress
create mode 100644 test/only-remote-repository.kfg
create mode 100644 test/ref-variation/Makefile
create mode 100644 test/ref-variation/valgrind.suppress
copy {tools/sra-dbcc => test/samline}/Makefile (86%)
create mode 100644 test/samline/alig-gen.c
create mode 100644 test/samline/cigar.c
rename tools/cg-dump/line_token_iter.h => test/samline/cigar.h (63%)
create mode 100755 test/samline/example.sh
create mode 100644 test/samline/refbases.c
copy tools/vtblcp/vtblcp-priv.h => test/samline/refbases.h (88%)
copy tools/fuse/dump-idx.vers => test/samline/samline.vers (100%)
create mode 100644 test/tarballs/build.xml
create mode 100644 test/tarballs/test-tarballs.bat
create mode 100755 test/tarballs/test-tarballs.sh
copy configure => test/vcf-loader/Makefile (58%)
mode change 100755 => 100644
create mode 100644 test/vcf-loader/test-vcf-loader.cpp
copy test/{ => vdb-dump}/Makefile (72%)
create mode 100644 test/vdb-dump/SRR056386
create mode 100644 test/vdb-dump/expected/1.0.stdout
create mode 100644 test/vdb-dump/expected/1.1.stdout
create mode 100644 test/vschema/Makefile
copy tools/vdb-dump/vdb_info.h => test/vschema/bio-end/bio-end-excl.vschema (71%)
copy tools/vdb-dump/vdb_info.h => test/vschema/bio-end/bio-end-incl.vschema (71%)
create mode 100644 test/vschema/bio-end/expected/excl-1.stdout
create mode 100644 test/vschema/bio-end/expected/excl-2.stdout
create mode 100644 test/vschema/bio-end/expected/excl-3.stdout
create mode 100644 test/vschema/bio-end/expected/excl-4.stdout
create mode 100644 test/vschema/bio-end/expected/incl-1.stdout
create mode 100644 test/vschema/bio-end/makeinputs.cpp
create mode 100644 test/vschema/idx-text/checklookup.cpp
create mode 100644 test/vschema/idx-text/expected/ci-1.stdout
create mode 100644 test/vschema/idx-text/expected/ci-2.stdout
create mode 100644 test/vschema/idx-text/expected/ci-3.stdout
create mode 100644 test/vschema/idx-text/expected/ci-4.stdout
create mode 100644 test/vschema/idx-text/expected/cs-1.stdout
create mode 100644 test/vschema/idx-text/expected/cs-2.stdout
create mode 100644 test/vschema/idx-text/idx-text.vschema
create mode 100644 test/vschema/idx-text/makeinputs.cpp
create mode 100755 test/vschema/runtestcase.sh
create mode 100644 tools/agp-load/AGP.py
create mode 100644 tools/agp-load/agp-load.py
create mode 100644 tools/agp-load/agp.vschema
create mode 100644 tools/agp-load/eutils.py
rename tools/{vtblcp => align-cache}/Makefile (86%)
create mode 100644 tools/align-cache/align-cache.cpp
copy tools/{fuse/dump-idx.vers => align-cache/align-cache.vers} (100%)
create mode 100644 tools/align-cache/align-cache.vers.h
create mode 100644 tools/align-cache/helper.cpp
create mode 100644 tools/align-cache/helper.h
delete mode 100644 tools/bam-loader/bam-load.3.vers
delete mode 100644 tools/bam-loader/bam-loader3.c
create mode 100644 tools/bam-loader/bam.c
create mode 100644 tools/bam-loader/bam.h
create mode 100644 tools/bam-loader/config-file.cpp
rename tools/{run-stat/key_value.h => bam-loader/config-file.hpp} (58%)
create mode 100644 tools/bam-loader/fasta-file.cpp
copy tools/{sra-sort/idx-mapping.h => bam-loader/fasta-file.hpp} (57%)
delete mode 100644 tools/bam-loader/loader-imp3.c
create mode 100644 tools/bam-loader/mem-bank.cpp
copy tools/{fastq-loader/fastq-reader.h => bam-loader/mem-bank.h} (64%)
delete mode 100644 tools/cg-dump/cg-dump.c
delete mode 100644 tools/cg-dump/cg-dump.vers
delete mode 100644 tools/cg-dump/last_rowid.c
delete mode 100644 tools/cg-dump/line_token_iter.c
delete mode 100644 tools/cg-dump/num-gen.c
delete mode 100644 tools/cg-dump/num-gen.h
delete mode 100644 tools/cg-dump/progressbar.c
delete mode 100644 tools/cg-dump/progressbar.h
delete mode 100644 tools/cg-dump/sg_lookup.c
copy tools/cg-load/{f1_5.c => f1_7.c} (77%)
create mode 100644 tools/cg-load/f2_5.c
copy tools/{vdb-dump/vdb_info.h => cg-load/formats.c} (67%)
copy tools/{vtblcp/vtblcp-priv.h => cg-load/formats.h} (79%)
delete mode 100644 tools/check-blob-size/check-blob-size.c
delete mode 100644 tools/check-blob-size/check-blob-size.vers
rename tools/{workspace => dbgap-mount}/Makefile (78%)
create mode 100644 tools/dbgap-mount/demo.c
create mode 100755 tools/dbgap-mount/demo.mkfg
copy tools/{sra-shell/sra-gui/sra-gui.vers => dbgap-mount/demo.vers} (100%)
create mode 100644 tools/dbgap-mount/demo.vers.h
delete mode 100644 tools/deseq/csra-trim.vers
delete mode 100644 tools/deseq/deseq.c
create mode 100755 tools/fastq-loader/parsing_rules.txt
delete mode 100644 tools/fix-run-stat/fix-run-stat.c
delete mode 100644 tools/fix-run-stat/fix-run-stat.vers
rename tools/{meta-sync => general-loader}/Makefile (66%)
create mode 100644 tools/general-loader/database-loader.cpp
create mode 100644 tools/general-loader/general-loader.cpp
create mode 100644 tools/general-loader/general-loader.hpp
create mode 100644 tools/general-loader/general-loader.vers
create mode 100644 tools/general-loader/general-loader.vers.h
create mode 100644 tools/general-loader/general-writer.cpp
create mode 100644 tools/general-loader/general-writer.h
create mode 100644 tools/general-loader/general-writer.hpp
create mode 100644 tools/general-loader/gw-dumper.cpp
create mode 100644 tools/general-loader/libgeneral-writer.vers
create mode 100644 tools/general-loader/main.cpp
create mode 100644 tools/general-loader/protocol-parser.cpp
create mode 100644 tools/general-loader/utf8-like-int-codec.c
rename tools/{run-stat/definitions.h => general-loader/utf8-like-int-codec.h} (54%)
copy tools/{sra-dbcc => kget}/Makefile (86%)
create mode 100644 tools/kget/kget.c
copy tools/{fuse/dump-idx.vers => kget/kget.vers} (100%)
delete mode 100644 tools/meta-sync/meta-sync.c
delete mode 100755 tools/meta-sync/meta-sync.pl
delete mode 100644 tools/meta-sync/meta-sync.vers
rename tools/{fix-run-stat => ngs-pileup}/Makefile (83%)
create mode 100644 tools/ngs-pileup/main.cpp
create mode 100644 tools/ngs-pileup/ngs-pileup.cpp
create mode 100644 tools/ngs-pileup/ngs-pileup.hpp
copy tools/{sra-shell/sra-gui/sra-gui.vers => ngs-pileup/ngs-pileup.vers} (100%)
create mode 100644 tools/ngs-pileup/ngs-pileup.vers.h
rename tools/{deseq => pileup-stats}/Makefile (83%)
create mode 100644 tools/pileup-stats/pileup-stats.cpp
create mode 100644 tools/pileup-stats/pileup-stats.vers
create mode 100644 tools/pore-load/GeneralWriter.py
create mode 100644 tools/pore-load/README.md
create mode 100644 tools/pore-load/pore-load.py
create mode 100644 tools/prefetch/kfile-no-q.c
rename tools/{bam-loader/loader-imp3.h => prefetch/kfile-no-q.h} (76%)
delete mode 100644 tools/qual-recal/Makefile
delete mode 100644 tools/qual-recal/make_histo_data.sh
delete mode 100644 tools/qual-recal/qual-recal.c
delete mode 100644 tools/qual-recalib-stat/num-gen.c
delete mode 100644 tools/qual-recalib-stat/num-gen.h
delete mode 100644 tools/qual-recalib-stat/progressbar.c
delete mode 100644 tools/qual-recalib-stat/progressbar.h
rename tools/{check-blob-size => ref-variation}/Makefile (70%)
create mode 100644 tools/ref-variation/common.cpp
copy tools/{vdb-dump/vdb_info.h => ref-variation/common.h} (73%)
create mode 100644 tools/ref-variation/helper.cpp
create mode 100644 tools/ref-variation/helper.h
create mode 100644 tools/ref-variation/ref-variation.cpp
copy tools/{sra-shell/sra-gui/sra-gui.vers => ref-variation/ref-variation.vers} (100%)
create mode 100644 tools/ref-variation/ref-variation.vers.h
create mode 100644 tools/ref-variation/var-expand.cpp
copy tools/{sra-shell/sra-gui/sra-gui.vers => ref-variation/var-expand.vers} (100%)
create mode 100644 tools/ref-variation/var-expand.vers.h
create mode 100644 tools/refseq-load/refseq-load.vers
delete mode 100644 tools/run-stat/.gitignore
delete mode 100644 tools/run-stat/Makefile
delete mode 100644 tools/run-stat/chart.c
delete mode 100644 tools/run-stat/chart.h
delete mode 100644 tools/run-stat/context.c
delete mode 100644 tools/run-stat/context.h
delete mode 100644 tools/run-stat/helper.c
delete mode 100644 tools/run-stat/helper.h
delete mode 100644 tools/run-stat/key_value.c
delete mode 100644 tools/run-stat/mod_cmn.c
delete mode 100644 tools/run-stat/mod_cmn.h
delete mode 100644 tools/run-stat/mod_reads.c
delete mode 100644 tools/run-stat/mod_reads_defs.h
delete mode 100644 tools/run-stat/mod_reads_helper.c
delete mode 100644 tools/run-stat/mod_reads_helper.h
delete mode 100644 tools/run-stat/num-gen.c
delete mode 100644 tools/run-stat/progressbar.c
delete mode 100644 tools/run-stat/progressbar.h
delete mode 100644 tools/run-stat/rd_filter.c
delete mode 100644 tools/run-stat/rd_filter.h
delete mode 100644 tools/run-stat/run-stat.c
delete mode 100644 tools/run-stat/run-stat.vers
delete mode 100644 tools/run-stat/svg.c
delete mode 100644 tools/run-stat/svg.h
delete mode 100644 tools/sam-dump/debug.h
delete mode 100644 tools/sam-dump/sam-dump.c
delete mode 100644 tools/sam-dump/sam-dump.vers
delete mode 100644 tools/sra-dbcc/sra-dbcc.c
delete mode 100644 tools/sra-dbcc/sra-dbcc.vers
create mode 100644 tools/sra-pileup/md_flag.c
copy tools/{cg-dump/last_rowid.h => sra-pileup/md_flag.h} (82%)
copy tools/sra-pileup/{pileup_varcount.c => pileup_indels.c} (55%)
rename tools/{vtblcp/vtblcp-priv.h => sra-pileup/pileup_indels.h} (89%)
create mode 100644 tools/sra-pileup/sam-hdr1.c
copy tools/{cg-dump/last_rowid.h => sra-pileup/sam-hdr1.h} (87%)
rename tools/{sam-dump => sra-seq-count}/Makefile (82%)
create mode 100644 tools/sra-seq-count/main_fkt.c
rename tools/{cg-dump/last_rowid.h => sra-seq-count/options.h} (77%)
create mode 100644 tools/sra-seq-count/range.hpp
create mode 100644 tools/sra-seq-count/sra-seq-count.cpp
copy tools/{fuse/dump-idx.vers => sra-seq-count/sra-seq-count.vers} (100%)
rename tools/{run-stat/mod_reads.h => sra-stat/sra-stat.h} (74%)
create mode 100644 tools/sra-stat/sra.c
create mode 100644 tools/sra/.cvsignore
create mode 100644 tools/update-schema/.cvsignore
create mode 100644 tools/util/kdb-index.c
create mode 100644 tools/util/kdb-index.vers
copy tools/{sra-sort/idx-mapping.h => util/samview.c} (50%)
create mode 100644 tools/vcf-loader/.gitignore
delete mode 100644 tools/vdb-copy/progressbar.c
delete mode 100644 tools/vdb-copy/progressbar.h
rename tools/{sra-dbcc => vdb-diff}/Makefile (87%)
create mode 100644 tools/vdb-diff/coldefs.c
rename tools/{vdb-dump/vdb-dump-num-gen.h => vdb-diff/coldefs.h} (50%)
create mode 100644 tools/vdb-diff/namelist_tools.c
rename tools/{cg-dump/sg_lookup.h => vdb-diff/namelist_tools.h} (57%)
create mode 100644 tools/vdb-diff/vdb-diff.c
copy tools/{fuse/dump-idx.vers => vdb-diff/vdb-diff.vers} (100%)
create mode 100644 tools/vdb-diff/vdb-diff.vers.h
delete mode 100644 tools/vdb-dump/vdb-dump-num-gen.c
delete mode 100644 tools/vdbview/b_first.png
delete mode 100644 tools/vdbview/b_goto.png
delete mode 100644 tools/vdbview/b_last.png
delete mode 100644 tools/vdbview/b_next.png
delete mode 100644 tools/vdbview/b_nextpage.png
delete mode 100644 tools/vdbview/b_prev.png
delete mode 100644 tools/vdbview/b_prevpage.png
delete mode 100644 tools/vdbview/b_search.png
delete mode 100644 tools/vdbview/background.pas
delete mode 100644 tools/vdbview/buttons.svg
delete mode 100644 tools/vdbview/columnsel.lfm
delete mode 100644 tools/vdbview/columnsel.pas
delete mode 100644 tools/vdbview/dataproxy.pas
delete mode 100644 tools/vdbview/gotoform.lfm
delete mode 100644 tools/vdbview/gotoform.pas
delete mode 100644 tools/vdbview/jobdef.pas
delete mode 100644 tools/vdbview/linkedlist.pas
delete mode 100644 tools/vdbview/logo_128.png
delete mode 100644 tools/vdbview/logo_16.png
delete mode 100644 tools/vdbview/logo_256.png
delete mode 100644 tools/vdbview/logo_32.png
delete mode 100644 tools/vdbview/logo_64.png
delete mode 100644 tools/vdbview/mainwindow.lfm
delete mode 100644 tools/vdbview/mainwindow.pas
delete mode 100644 tools/vdbview/searchform.lfm
delete mode 100644 tools/vdbview/searchform.pas
delete mode 100644 tools/vdbview/selector_types.pas
delete mode 100644 tools/vdbview/support_unit.pas
delete mode 100644 tools/vdbview/svdb.pas
delete mode 100644 tools/vdbview/svdb_obj.pas
delete mode 100644 tools/vdbview/vdbview.ico
delete mode 100644 tools/vdbview/vdbview.lpi
delete mode 100644 tools/vdbview/vdbview.lpr
delete mode 100644 tools/vdbview/vdbview.res
delete mode 100644 tools/vdbview/vdbview1.ico
delete mode 100644 tools/vdbview/version.lfm
delete mode 100644 tools/vdbview/version.pas
delete mode 100644 tools/vtblcp/vtblcp.c
delete mode 100644 tools/vtblcp/vtblcp.vers
delete mode 100644 tools/workspace/.gitignore
delete mode 100644 tools/workspace/path-to-kar-file.cpp
delete mode 100644 tools/workspace/prefs-lex.l
delete mode 100644 tools/workspace/prefs-yacc.y
delete mode 100644 tools/workspace/sra.cpp
delete mode 100644 tools/workspace/sra.vers
delete mode 100644 tools/workspace/sratoolkit-exception.cpp
delete mode 100644 tools/workspace/sratoolkit-exception.hpp
delete mode 100644 tools/workspace/token.c
delete mode 100644 tools/workspace/token.h
delete mode 100644 tools/workspace/workspace.cpp
delete mode 100644 win-configure.bat
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sra-sdk.git
More information about the debian-med-commit
mailing list