[med-svn] [sra-sdk] branch upstream updated (ae3e130 -> d4dc8c4)
Andreas Tille
tille at debian.org
Fri Jul 22 13:24:07 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository sra-sdk.
from ae3e130 Imported Upstream version 2.7.0+dfsg
new d4dc8c4 Imported Upstream version 2.7.0
The 1 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 | 27 +-
CHANGES | 83 +-
CHANGES.md | 80 +-
LICENSE | 13 +-
Makefile | 44 +-
README | 18 +-
README-blastn | 133 +
README-vdb-config | 115 +
README.md | 16 +-
build/.gitignore | 8 +-
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 +
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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 +
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build/MSVC/2013/vdb-unlock.vcxproj | 17 +
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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.clang | 17 +-
build/Makefile.deb | 108 +
build/Makefile.env | 73 +-
build/Makefile.gcc | 18 +-
build/Makefile.install | 111 +-
build/Makefile.linux | 5 +-
build/Makefile.mac | 84 +
build/Makefile.rpm | 164 +
build/Makefile.rules | 5 +-
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.../asm-trace/asm-trace.xcodeproj/project.pbxproj | 4444 ++++
build/Xcode/old-toolkit/.gitignore | 1 +
.../old-toolkit.xcodeproj/project.pbxproj | 2153 ++
build/check-exit-code.py | 131 +
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interfaces/align/align.h | 70 -
interfaces/align/align.vschema | 1610 --
interfaces/align/alignsrc.h | 71 -
interfaces/align/bam.h | 836 -
interfaces/align/dna-reverse-cmpl.h | 43 -
interfaces/align/extern.h | 41 -
interfaces/align/iterator.h | 610 -
interfaces/align/iterator_examples.txt | 148 -
interfaces/align/manager.h | 69 -
interfaces/align/mate-cache.vschema | 99 -
interfaces/align/pileup-stats.vschema | 120 -
interfaces/align/qstat.vschema | 87 -
interfaces/align/quality-quantizer.h | 49 -
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interfaces/align/reference.h | 150 -
interfaces/align/refseq-mgr.h | 88 -
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tools/fuse/tar-list.c | 598 +
tools/fuse/tar-list.h | 49 +
tools/fuse/tar-node.c | 320 +
tools/fuse/tar-node.h | 35 +
tools/fuse/text-file.c | 134 +
tools/fuse/text-file.h | 36 +
tools/fuse/unix/remote-fuser-sys.c | 696 +
tools/fuse/unix/sra-fuser-sys.c | 637 +
tools/fuse/xml.c | 516 +
tools/fuse/xml.h | 60 +
tools/fuse/zlib-simple.c | 65 +
tools/fuse/zlib-simple.h | 33 +
tools/general-loader/Makefile | 131 +
tools/general-loader/database-loader.cpp | 894 +
tools/general-loader/general-loader.cpp | 223 +
tools/general-loader/general-loader.hpp | 243 +
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/main.cpp | 239 +
tools/general-loader/protocol-parser.cpp | 1048 +
tools/general-loader/utf8-like-int-codec.c | 687 +
tools/general-loader/utf8-like-int-codec.h | 69 +
tools/kar/Makefile | 99 +
tools/kar/kar-args.c | 428 +
tools/kar/kar-args.h | 98 +
tools/kar/kar.c | 2063 ++
tools/kar/sra-kar.c | 431 +
tools/keyring-srv/Makefile | 110 +
tools/keyring-srv/keyring-data.c | 346 +
tools/keyring-srv/keyring-data.h | 130 +
tools/keyring-srv/keyring-database.c | 441 +
tools/keyring-srv/keyring-database.h | 45 +
tools/keyring-srv/keyring-srv-main.c | 333 +
tools/keyring-srv/keyring-srv.c | 522 +
tools/keyring-srv/keyring-srv.h | 101 +
tools/kget/Makefile | 77 +
tools/kget/examples.sh | 62 +
tools/kget/kget.c | 968 +
tools/kqsh/.gitignore | 7 +
tools/kqsh/Makefile | 207 +
tools/kqsh/kqsh-alter.c | 347 +
tools/kqsh/kqsh-close.c | 186 +
tools/kqsh/kqsh-create.c | 680 +
tools/kqsh/kqsh-help.c | 1292 ++
tools/kqsh/kqsh-load.c | 410 +
tools/kqsh/kqsh-open.c | 199 +
tools/kqsh/kqsh-parse.c | 198 +
tools/kqsh/kqsh-print.c | 170 +
tools/kqsh/kqsh-priv.h | 151 +
tools/kqsh/kqsh-show.c | 290 +
tools/kqsh/kqsh-thunk.pl | 662 +
tools/kqsh/kqsh-tok.c | 99 +
tools/kqsh/kqsh-tok.h | 155 +
tools/kqsh/kqsh-write.c | 321 +
tools/kqsh/kqsh.c | 516 +
tools/nenctool/Makefile | 119 +
tools/nenctool/nenctest.c | 489 +
tools/nenctool/nenctool.c | 435 +
tools/nencvalid/Makefile | 88 +
tools/nencvalid/nencvalid.c | 593 +
tools/ngs-pileup/Makefile | 82 +
tools/ngs-pileup/main.cpp | 152 +
tools/ngs-pileup/ngs-pileup.cpp | 206 +
tools/ngs-pileup/ngs-pileup.hpp | 97 +
tools/pacbio-load/.gitignore | 7 +
tools/pacbio-load/Makefile | 117 +
tools/pacbio-load/pacbio-load.c | 650 +
tools/pacbio-load/pl-basecalls_cmn.c | 97 +
tools/pacbio-load/pl-basecalls_cmn.h | 60 +
tools/pacbio-load/pl-consensus.c | 472 +
tools/pacbio-load/pl-consensus.h | 83 +
tools/pacbio-load/pl-context.c | 211 +
tools/pacbio-load/pl-context.h | 87 +
tools/pacbio-load/pl-metrics.c | 779 +
tools/pacbio-load/pl-metrics.h | 83 +
tools/pacbio-load/pl-passes.c | 437 +
tools/pacbio-load/pl-passes.h | 70 +
tools/pacbio-load/pl-progress.c | 195 +
tools/pacbio-load/pl-progress.h | 70 +
tools/pacbio-load/pl-regions.c | 1048 +
tools/pacbio-load/pl-regions.h | 140 +
tools/pacbio-load/pl-sequence.c | 928 +
tools/pacbio-load/pl-sequence.h | 110 +
tools/pacbio-load/pl-tools.c | 624 +
tools/pacbio-load/pl-tools.h | 291 +
tools/pacbio-load/pl-zmw.c | 221 +
tools/pacbio-load/pl-zmw.h | 105 +
tools/pacbio-load/verify/ins_nl.pl | 15 +
tools/pacbio-load/verify/ins_nl_1.pl | 30 +
tools/pacbio-load/verify/ins_nl_2.pl | 24 +
tools/pacbio-load/verify/ins_nl_4.pl | 24 +
tools/pacbio-load/verify/ins_nl_f.pl | 27 +
tools/pileup-stats/Makefile | 81 +
tools/pileup-stats/pileup-stats.cpp | 787 +
tools/pore-load/GeneralWriter.py | 312 +
tools/pore-load/README.md | 10 +
tools/pore-load/pore-load.py | 406 +
tools/prefetch/Makefile | 93 +
tools/prefetch/kfile-no-q.c | 215 +
tools/prefetch/kfile-no-q.h | 44 +
tools/prefetch/prefetch.c | 3601 ++++
tools/qual-recalib-stat/.gitignore | 3 +
tools/qual-recalib-stat/Makefile | 84 +
tools/qual-recalib-stat/columns.c | 94 +
tools/qual-recalib-stat/columns.h | 67 +
tools/qual-recalib-stat/context.c | 330 +
tools/qual-recalib-stat/context.h | 120 +
tools/qual-recalib-stat/fasta_dump.pl | 81 +
tools/qual-recalib-stat/namelist_tools.c | 187 +
tools/qual-recalib-stat/namelist_tools.h | 53 +
tools/qual-recalib-stat/qual-recalib-stat.c | 418 +
tools/qual-recalib-stat/reader.c | 241 +
tools/qual-recalib-stat/reader.h | 88 +
tools/qual-recalib-stat/ref_exclude.c | 561 +
tools/qual-recalib-stat/ref_exclude.h | 71 +
tools/qual-recalib-stat/ref_grab.pl | 82 +
tools/qual-recalib-stat/spot_position.c | 121 +
tools/qual-recalib-stat/spot_position.h | 68 +
tools/qual-recalib-stat/stat_mod.c | 883 +
tools/qual-recalib-stat/stat_mod.h | 148 +
tools/qual-recalib-stat/stat_mod_1.c | 962 +
tools/qual-recalib-stat/stat_mod_1.h | 160 +
tools/qual-recalib-stat/stat_mod_2.c | 1041 +
tools/qual-recalib-stat/stat_mod_2.h | 141 +
tools/qual-recalib-stat/writer.c | 480 +
tools/qual-recalib-stat/writer.h | 79 +
tools/rd-filter-redact/Makefile | 95 +
tools/rd-filter-redact/rd-filter-redact.c | 1350 ++
tools/rd-filter-redact/read-filter-redact.c | 861 +
tools/rd-filter-redact/test-read-write-cursor.c | 220 +
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/.gitignore | 1 +
tools/sra-dump/Makefile | 128 +
tools/sra-dump/abi.c | 907 +
tools/sra-dump/core.c | 1717 ++
tools/sra-dump/core.h | 74 +
tools/sra-dump/debug.h | 34 +
tools/sra-dump/factory.c | 1069 +
tools/sra-dump/factory.h | 194 +
tools/sra-dump/fasta_dump.c | 752 +
tools/sra-dump/fasta_dump.h | 36 +
tools/sra-dump/fastq.c | 3800 ++++
tools/sra-dump/illumina.c | 536 +
tools/sra-dump/sff.c | 200 +
tools/sra-dump/sra-dump.c | 1011 +
tools/sra-load/Makefile | 209 +
tools/sra-load/absolid-fmt.c | 573 +
tools/sra-load/common-xml.c | 871 +
tools/sra-load/common-xml.h | 183 +
tools/sra-load/debug.h | 34 +
tools/sra-load/experiment-xml.c | 1255 ++
tools/sra-load/experiment-xml.h | 77 +
tools/sra-load/fastq-fmt.c | 700 +
tools/sra-load/helicos-fmt.c | 273 +
tools/sra-load/illumina-fmt.c | 847 +
tools/sra-load/loader-file.c | 191 +
tools/sra-load/loader-file.h | 113 +
tools/sra-load/loader-fmt.c | 165 +
tools/sra-load/loader-fmt.h | 171 +
tools/sra-load/loader.c | 1135 ++
tools/sra-load/pacbio-fmt.c | 140 +
tools/sra-load/pstring.c | 208 +
tools/sra-load/pstring.h | 58 +
tools/sra-load/run-xml.c | 487 +
tools/sra-load/run-xml.h | 90 +
tools/sra-load/sff-fmt.c | 490 +
tools/sra-load/sra-writer.c | 370 +
tools/sra-load/sra-writer.h | 92 +
tools/sra-load/srf-absolid.c | 497 +
tools/sra-load/srf-fmt.c | 267 +
tools/sra-load/srf-fmt.h | 46 +
tools/sra-load/srf-illumina.c | 452 +
tools/sra-load/srf.c | 229 +
tools/sra-load/srf.h | 146 +
tools/sra-load/writer-454.c | 262 +
tools/sra-load/writer-454.h | 46 +
tools/sra-load/writer-absolid.c | 501 +
tools/sra-load/writer-absolid.h | 94 +
tools/sra-load/writer-helicos.c | 135 +
tools/sra-load/writer-helicos.h | 41 +
tools/sra-load/writer-illumina.c | 720 +
tools/sra-load/writer-illumina.h | 92 +
tools/sra-load/writer-ion-torrent.c | 262 +
tools/sra-load/writer-ion-torrent.h | 46 +
tools/sra-load/ztr-absolid.c | 656 +
tools/sra-load/ztr-absolid.h | 124 +
tools/sra-load/ztr-huffman.c | 664 +
tools/sra-load/ztr-huffman.h | 45 +
tools/sra-load/ztr-illumina.c | 1367 ++
tools/sra-load/ztr-illumina.h | 136 +
tools/sra-load/ztr.h | 182 +
tools/sra-pileup/.gitignore | 2 +
tools/sra-pileup/4na_ascii.c | 95 +
tools/sra-pileup/4na_ascii.h | 44 +
tools/sra-pileup/Makefile | 133 +
tools/sra-pileup/cg_tools.c | 1723 ++
tools/sra-pileup/cg_tools.h | 137 +
tools/sra-pileup/cmdline_cmn.c | 711 +
tools/sra-pileup/cmdline_cmn.h | 150 +
tools/sra-pileup/debug.h | 34 +
tools/sra-pileup/dyn_string.c | 206 +
tools/sra-pileup/dyn_string.h | 55 +
tools/sra-pileup/inputfiles.c | 377 +
tools/sra-pileup/inputfiles.h | 99 +
tools/sra-pileup/make_opt.pl | 13 +
tools/sra-pileup/matecache.c | 439 +
tools/sra-pileup/matecache.h | 119 +
tools/sra-pileup/md_flag.c | 268 +
tools/sra-pileup/md_flag.h | 48 +
tools/sra-pileup/out_redir.c | 120 +
tools/sra-pileup/out_redir.h | 64 +
tools/sra-pileup/perf_log.c | 273 +
tools/sra-pileup/perf_log.h | 52 +
tools/sra-pileup/pileup_counters.c | 447 +
tools/sra-pileup/pileup_counters.h | 41 +
tools/sra-pileup/pileup_indels.c | 120 +
tools/sra-pileup/pileup_indels.h | 40 +
tools/sra-pileup/pileup_index.c | 122 +
tools/sra-pileup/pileup_index.h | 40 +
tools/sra-pileup/pileup_options.h | 62 +
tools/sra-pileup/pileup_stat.c | 391 +
tools/sra-pileup/pileup_stat.h | 40 +
tools/sra-pileup/pileup_v2.c | 382 +
tools/sra-pileup/pileup_v2.h | 40 +
tools/sra-pileup/pileup_varcount.c | 139 +
tools/sra-pileup/pileup_varcount.h | 40 +
tools/sra-pileup/read_fkt.c | 718 +
tools/sra-pileup/read_fkt.h | 82 +
tools/sra-pileup/ref_regions.c | 825 +
tools/sra-pileup/ref_regions.h | 71 +
tools/sra-pileup/ref_walker.c | 1028 +
tools/sra-pileup/ref_walker.h | 147 +
tools/sra-pileup/ref_walker_0.c | 231 +
tools/sra-pileup/ref_walker_0.h | 107 +
tools/sra-pileup/report_deletes.c | 259 +
tools/sra-pileup/report_deletes.h | 41 +
tools/sra-pileup/reref.c | 550 +
tools/sra-pileup/reref.h | 43 +
tools/sra-pileup/rna_splice_log.c | 374 +
tools/sra-pileup/rna_splice_log.h | 87 +
tools/sra-pileup/sam-aligned.c | 2367 +++
tools/sra-pileup/sam-aligned.h | 46 +
tools/sra-pileup/sam-dump-opts.c | 1676 ++
tools/sra-pileup/sam-dump-opts.h | 306 +
tools/sra-pileup/sam-dump.c | 4905 +++++
tools/sra-pileup/sam-dump3.c | 563 +
tools/sra-pileup/sam-hdr.c | 728 +
tools/sra-pileup/sam-hdr.h | 41 +
tools/sra-pileup/sam-hdr1.c | 872 +
tools/sra-pileup/sam-hdr1.h | 42 +
tools/sra-pileup/sam-unaligned.c | 1565 ++
tools/sra-pileup/sam-unaligned.h | 44 +
tools/sra-pileup/splitfastq.pl | 46 +
tools/sra-pileup/sra-pileup.c | 1640 ++
tools/sra-pileup/walk_debug.c | 147 +
tools/sra-pileup/walk_debug.h | 42 +
tools/sra-pileup/writer.c | 137 +
tools/sra-pileup/writer.h | 32 +
tools/sra-seq-count/Makefile | 83 +
tools/sra-seq-count/main_fkt.c | 203 +
tools/sra-seq-count/options.h | 56 +
tools/sra-seq-count/range.hpp | 307 +
tools/sra-seq-count/sra-seq-count.cpp | 688 +
tools/sra-shell/Makefile | 58 +
tools/sra-shell/guilib/Makefile | 71 +
tools/sra-shell/job-exec/Makefile | 71 +
tools/sra-shell/parser/Makefile | 71 +
tools/sra-shell/parser/sra-shell-lex.l | 103 +
tools/sra-shell/parser/sra-shell.y | 54 +
tools/sra-shell/sra-gui/Makefile | 80 +
tools/sra-shell/sra-gui/sra-gui.c | 49 +
tools/sra-shell/sra-shell/Makefile | 87 +
tools/sra-shell/sra-shell/sra-shell.c | 49 +
tools/sra-shell/turboVision/Makefile | 71 +
tools/sra-sort/Makefile | 125 +
tools/sra-sort/Makefile.cc | 24 +
tools/sra-sort/Makefile.clang | 27 +
tools/sra-sort/Makefile.gcc | 27 +
tools/sra-sort/Makefile.vc++ | 24 +
tools/sra-sort/buff-writer.c | 789 +
tools/sra-sort/buff-writer.h | 64 +
tools/sra-sort/caps.c | 125 +
tools/sra-sort/caps.h | 70 +
tools/sra-sort/capture-first-half-aligned.c | 192 +
tools/sra-sort/col-pair.c | 818 +
tools/sra-sort/col-pair.h | 323 +
tools/sra-sort/csra-pair.c | 228 +
tools/sra-sort/csra-pair.h | 87 +
tools/sra-sort/csra-tbl.c | 798 +
tools/sra-sort/csra-tbl.h | 83 +
tools/sra-sort/ctx.h | 109 +
tools/sra-sort/db-pair.c | 885 +
tools/sra-sort/db-pair.h | 208 +
tools/sra-sort/dir-pair.c | 504 +
tools/sra-sort/dir-pair.h | 124 +
tools/sra-sort/dump-blob-boundaries.c | 203 +
tools/sra-sort/except.c | 231 +
tools/sra-sort/except.h | 160 +
tools/sra-sort/gcc-ped.sh | 39 +
tools/sra-sort/glob-poslen.c | 349 +
tools/sra-sort/glob-poslen.h | 95 +
tools/sra-sort/id-mapper-col.c | 260 +
tools/sra-sort/id-mapper-col.h | 55 +
tools/sra-sort/idx-mapping.c | 88 +
tools/sra-sort/idx-mapping.h | 59 +
tools/sra-sort/map-file.c | 1192 ++
tools/sra-sort/map-file.h | 172 +
tools/sra-sort/mapping-row-set.c | 496 +
tools/sra-sort/mem.c | 68 +
tools/sra-sort/mem.h | 128 +
tools/sra-sort/membank-priv.h | 44 +
tools/sra-sort/membank.c | 296 +
tools/sra-sort/meta-pair.c | 458 +
tools/sra-sort/meta-pair.h | 109 +
tools/sra-sort/paged-membank.c | 244 +
tools/sra-sort/paged-mmapbank.c | 399 +
tools/sra-sort/poslen-col-pair.c | 559 +
tools/sra-sort/poslen-col-pair.h | 63 +
tools/sra-sort/ref-alignid-col.c | 702 +
tools/sra-sort/ref-alignid-col.h | 53 +
tools/sra-sort/row-set-priv.h | 44 +
tools/sra-sort/row-set.c | 208 +
tools/sra-sort/row-set.h | 215 +
tools/sra-sort/run.c | 388 +
tools/sra-sort/simple-row-set.c | 212 +
tools/sra-sort/sort-defs.h | 109 +
tools/sra-sort/sorting-row-set.c | 405 +
tools/sra-sort/sra-sort.c | 746 +
tools/sra-sort/sra-sort.h | 171 +
tools/sra-sort/status.h | 48 +
tools/sra-sort/tbl-pair.c | 1055 +
tools/sra-sort/tbl-pair.h | 209 +
tools/sra-sort/xcheck-ref-align.c | 411 +
tools/sra-sort/xcheck.h | 49 +
tools/sra-stat/Makefile | 80 +
tools/sra-stat/sra-stat.c | 3634 ++++
tools/sra-stat/sra-stat.h | 42 +
tools/sra-stat/sra.c | 446 +
libs/svdb/.gitignore => tools/sra/.cvsignore | 0
tools/sra/Makefile | 77 +
tools/sra/sra-dbcc.c | 435 +
tools/sra/table-vers.c | 232 +
tools/srapath/Makefile | 79 +
tools/srapath/cgi_request.c | 853 +
tools/srapath/cgi_request.h | 129 +
tools/srapath/helper.c | 464 +
tools/srapath/helper.h | 108 +
tools/srapath/line_iter.c | 241 +
tools/srapath/line_iter.h | 71 +
tools/srapath/srapath.c | 439 +
.../.gitignore => tools/update-schema/.cvsignore | 0
tools/update-schema/Makefile | 77 +
tools/update-schema/update-schema.c | 454 +
tools/util/Makefile | 392 +
tools/util/crc32sum.c | 272 +
tools/util/kdb-index.c | 257 +
tools/util/kdbmeta.c | 1332 ++
tools/util/mac/syspass.c | 48 +
tools/util/md5cp.c | 702 +
tools/util/pacbio-correct.c | 208 +
tools/util/pseudo-aligner.cpp | 515 +
tools/util/rcexplain.c | 127 +
tools/util/rowwritetest.c | 433 +
tools/util/samview.c | 80 +
tools/util/schema-replace.c | 379 +
tools/util/sortreadtest.c | 351 +
tools/util/syspass-priv.h | 44 +
tools/util/test-sra-priv.h | 46 +
tools/util/test-sra.c | 3380 ++++
tools/util/testld.c | 249 +
tools/util/txt2kdb.c | 579 +
tools/util/unix/PrintOS.c | 66 +
tools/util/unix/syspass.c | 62 +
tools/util/vdb-lock.c | 154 +
tools/util/vdb-passwd.c | 307 +
tools/util/vdb-unlock.c | 156 +
tools/util/win/PrintOS.c | 60 +
tools/util/win/syspass.c | 53 +
tools/vcf-loader/.gitignore | 1 +
tools/vcf-loader/Makefile | 128 +
tools/vcf-loader/vcf-database.c | 168 +
tools/vcf-loader/vcf-database.h | 40 +
tools/vcf-loader/vcf-grammar.c | 1686 ++
tools/vcf-loader/vcf-grammar.h | 61 +
tools/vcf-loader/vcf-grammar.y | 123 +
tools/vcf-loader/vcf-lex.c | 2528 +++
tools/vcf-loader/vcf-lex.l | 132 +
tools/vcf-loader/vcf-loader.c | 124 +
tools/vcf-loader/vcf-parse.h | 89 +
tools/vcf-loader/vcf-reader.c | 438 +
tools/vcf-loader/vcf-reader.h | 110 +
tools/vdb-config/Makefile | 82 +
tools/vdb-config/configure.cpp | 815 +
tools/vdb-config/configure.h | 49 +
tools/vdb-config/interactive.cpp | 1084 +
tools/vdb-config/interactive.h | 50 +
tools/vdb-config/util.cpp | 1125 ++
tools/vdb-config/util.hpp | 702 +
tools/vdb-config/vdb-config-model.cpp | 440 +
tools/vdb-config/vdb-config-model.hpp | 482 +
tools/vdb-config/vdb-config.c | 1740 ++
tools/vdb-config/vdb-config2.cpp | 30 +
tools/vdb-config/vdb-config2.h | 29 +
tools/vdb-copy/.gitignore | 17 +
tools/vdb-copy/Makefile | 91 +
tools/vdb-copy/coldefs.c | 775 +
tools/vdb-copy/coldefs.h | 250 +
tools/vdb-copy/column_match.c | 31 +
tools/vdb-copy/column_match.h | 42 +
tools/vdb-copy/config_values.c | 54 +
tools/vdb-copy/config_values.h | 49 +
tools/vdb-copy/context.c | 473 +
tools/vdb-copy/context.h | 183 +
tools/vdb-copy/copy_context.c | 47 +
tools/vdb-copy/copy_context.h | 58 +
tools/vdb-copy/copy_meta.c | 517 +
tools/vdb-copy/copy_meta.h | 46 +
tools/vdb-copy/definitions.h | 112 +
tools/vdb-copy/get_platform.c | 168 +
tools/vdb-copy/get_platform.h | 46 +
tools/vdb-copy/helper.c | 919 +
tools/vdb-copy/helper.h | 225 +
tools/vdb-copy/matcher_input.h | 55 +
tools/vdb-copy/namelist_tools.c | 187 +
tools/vdb-copy/namelist_tools.h | 52 +
tools/vdb-copy/num-gen.c | 848 +
tools/vdb-copy/num-gen.h | 225 +
tools/vdb-copy/redactval.c | 230 +
tools/vdb-copy/redactval.h | 120 +
tools/vdb-copy/type_matcher.c | 850 +
tools/vdb-copy/type_matcher.h | 71 +
tools/vdb-copy/vdb-copy-includes.h | 121 +
tools/vdb-copy/vdb-copy.c | 1456 ++
tools/vdb-copy/vdb-copy.kfg | 94 +
tools/vdb-decrypt/Makefile | 102 +
tools/vdb-decrypt/shared.c | 1271 ++
tools/vdb-decrypt/shared.h | 93 +
tools/vdb-decrypt/vdb-decrypt.c | 269 +
tools/vdb-decrypt/vdb-encrypt.c | 215 +
tools/vdb-diff/Makefile | 79 +
tools/vdb-diff/coldefs.c | 211 +
tools/vdb-diff/coldefs.h | 105 +
tools/vdb-diff/namelist_tools.c | 299 +
tools/vdb-diff/namelist_tools.h | 59 +
tools/vdb-diff/vdb-diff.c | 1002 +
tools/vdb-dump/.gitignore | 2 +
tools/vdb-dump/Makefile | 92 +
tools/vdb-dump/help.txt | 352 +
tools/vdb-dump/vdb-boot.c | 448 +
tools/vdb-dump/vdb-boot.vschema | 52 +
tools/vdb-dump/vdb-dump-bin.c | 1496 ++
tools/vdb-dump/vdb-dump-bin.h | 46 +
tools/vdb-dump/vdb-dump-coldefs.c | 846 +
tools/vdb-dump/vdb-dump-coldefs.h | 110 +
tools/vdb-dump/vdb-dump-context.c | 649 +
tools/vdb-dump/vdb-dump-context.h | 220 +
tools/vdb-dump/vdb-dump-fastq.c | 1132 ++
tools/vdb-dump/vdb-dump-fastq.h | 47 +
tools/vdb-dump/vdb-dump-filter.c | 116 +
tools/vdb-dump/vdb-dump-filter.h | 82 +
tools/vdb-dump/vdb-dump-formats.c | 383 +
tools/vdb-dump/vdb-dump-formats.h | 51 +
tools/vdb-dump/vdb-dump-helper.c | 772 +
tools/vdb-dump/vdb-dump-helper.h | 107 +
tools/vdb-dump/vdb-dump-interact.c | 265 +
tools/vdb-dump/vdb-dump-interact.h | 50 +
tools/vdb-dump/vdb-dump-print.c | 1349 ++
tools/vdb-dump/vdb-dump-print.h | 86 +
tools/vdb-dump/vdb-dump-redir.c | 120 +
tools/vdb-dump/vdb-dump-redir.h | 64 +
tools/vdb-dump/vdb-dump-repo.c | 281 +
tools/vdb-dump/vdb-dump-repo.h | 46 +
tools/vdb-dump/vdb-dump-row-context.h | 71 +
tools/vdb-dump/vdb-dump-str.c | 540 +
tools/vdb-dump/vdb-dump-str.h | 100 +
tools/vdb-dump/vdb-dump-tools.c | 528 +
tools/vdb-dump/vdb-dump-tools.h | 60 +
tools/vdb-dump/vdb-dump.c | 2335 +++
tools/vdb-dump/vdb_info.c | 1528 ++
tools/vdb-dump/vdb_info.h | 47 +
tools/vdb-validate/Makefile | 96 +
tools/vdb-validate/check-corrupt.cpp | 764 +
tools/vdb-validate/vdb-validate.c | 3351 ++++
vdb3/itf/kfc/array.hpp | 127 -
vdb3/itf/kfc/atomic-ia32.hpp | 500 -
vdb3/itf/kfc/atomic-x86_64.hpp | 356 -
vdb3/itf/kfc/atomic.hpp | 133 -
vdb3/itf/kfc/callstk.hpp | 117 -
vdb3/itf/kfc/caps.hpp | 59 -
vdb3/itf/kfc/defs.hpp | 113 -
vdb3/itf/kfc/except.hpp | 174 -
vdb3/itf/kfc/fd.hpp | 102 -
vdb3/itf/kfc/fdmgr.hpp | 95 -
vdb3/itf/kfc/integer.hpp | 191 -
vdb3/itf/kfc/log.hpp | 118 -
vdb3/itf/kfc/memmgr.hpp | 133 -
vdb3/itf/kfc/memory.hpp | 149 -
vdb3/itf/kfc/ptr.hpp | 174 -
vdb3/itf/kfc/ref.hpp | 155 -
vdb3/itf/kfc/refcount.hpp | 94 -
vdb3/itf/kfc/rsrc.hpp | 150 -
vdb3/itf/kfc/stream.hpp | 135 -
vdb3/itf/kfc/string.hpp | 252 -
vdb3/itf/kfc/syserr.hpp | 57 -
vdb3/itf/kfc/task-impl.hpp | 139 -
vdb3/itf/kfc/task.hpp | 124 -
vdb3/itf/kfc/time.hpp | 299 -
vdb3/itf/kfc/timemgr.hpp | 94 -
vdb3/itf/kfc/vers.hpp | 101 -
vdb3/src/kfc/Makefile | 88 -
vdb3/src/kfc/array.cpp | 152 -
vdb3/src/kfc/callstk.cpp | 60 -
vdb3/src/kfc/except.cpp | 222 -
vdb3/src/kfc/fd.cpp | 204 -
vdb3/src/kfc/fdmgr.cpp | 101 -
vdb3/src/kfc/integer.cpp | 137 -
vdb3/src/kfc/log.cpp | 142 -
vdb3/src/kfc/memmgr.cpp | 162 -
vdb3/src/kfc/memory.cpp | 392 -
vdb3/src/kfc/pfdmgr.cpp | 64 -
vdb3/src/kfc/pfdmgr.hpp | 68 -
vdb3/src/kfc/plogger.cpp | 148 -
vdb3/src/kfc/plogger.hpp | 72 -
vdb3/src/kfc/pmemmgr.cpp | 315 -
vdb3/src/kfc/pmemmgr.hpp | 75 -
vdb3/src/kfc/ptimemgr.cpp | 81 -
vdb3/src/kfc/ptimemgr.hpp | 64 -
vdb3/src/kfc/ptr.cpp | 206 -
vdb3/src/kfc/ref.cpp | 140 -
vdb3/src/kfc/refcount.cpp | 113 -
vdb3/src/kfc/rsrc.cpp | 141 -
vdb3/src/kfc/stream.cpp | 395 -
vdb3/src/kfc/string.cpp | 1324 --
vdb3/src/kfc/syserr.cpp | 97 -
vdb3/src/kfc/task-impl.cpp | 352 -
vdb3/src/kfc/task.cpp | 109 -
vdb3/src/kfc/time.cpp | 290 -
vdb3/src/kfc/timemgr.cpp | 105 -
vdb3/src/kfc/vers.cpp | 85 -
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