[med-svn] [sra-sdk] 03/06: Merge tag 'upstream/2.3.5-2+dfsg'
Andreas Tille
tille at debian.org
Wed Jul 30 12:22:35 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository sra-sdk.
commit d8167d7aa66855636bca3e4f319832f85f373cf2
Merge: e03f2ef 888f953
Author: Andreas Tille <tille at debian.org>
Date: Wed Jul 30 13:56:19 2014 +0200
Merge tag 'upstream/2.3.5-2+dfsg'
Upstream version 2.3.5-2+dfsg
README | 3 -
README-build.txt | 20 -
build/Makefile.env | 39 +-
build/Makefile.gcc | 11 +-
build/Makefile.rules | 31 +-
build/Makefile.vc++ | 2 +-
build/ld.win.cmn.sh | 8 +
configuration-assistant.perl | 2 +-
interfaces/align/align-access.h | 22 +-
interfaces/align/bam.h | 26 +-
interfaces/align/reader-refseq.h | 7 +-
interfaces/align/writer-reference.h | 13 +-
interfaces/cc/gcc/i386/arch-impl.h | 16 +
interfaces/cc/gcc/x86_64/arch-impl.h | 31 +
interfaces/cc/vc++/stdint.h | 73 +-
interfaces/insdc/insdc.vschema | 8 +
interfaces/{klib => kfc}/callconv.h | 6 +-
interfaces/kfc/ctx.h | 214 +
interfaces/{klib => kfc}/defs.h | 122 +-
interfaces/kfc/except.h | 149 +
interfaces/{klib => kfc}/extern.h | 20 +-
interfaces/{klib => kfc}/rc.h | 147 +-
libs/vfs/keyring-priv.h => interfaces/kfc/rsrc.h | 60 +-
interfaces/kfc/xc.h | 94 +
interfaces/{kns/manager-ext.h => kfc/xcdefs.h} | 48 +-
.../bsd/syslock-priv.h => interfaces/kfc/xcext.h | 44 +-
interfaces/{kns/url-fetcher.h => kfc/xcgen.h} | 50 +-
interfaces/kfs/file.h | 107 +
interfaces/kfs/impl.h | 7 +
interfaces/kfs/kfs-priv.h | 19 +-
interfaces/klib/callconv.h | 23 +-
interfaces/klib/debug.h | 14 +-
interfaces/klib/defs.h | 69 +-
interfaces/klib/extern.h | 29 +-
libs/kns/stream-priv.h => interfaces/klib/misc.h | 24 +-
interfaces/klib/namelist.h | 16 +
interfaces/klib/rc.h | 314 +-
interfaces/klib/time.h | 8 +-
interfaces/kns/KCurlRequest.h | 69 -
interfaces/kns/ascp.h | 43 +-
interfaces/kns/endpoint.h | 12 +-
interfaces/kns/entrez-fetcher.h | 88 -
interfaces/kns/http.h | 33 +-
interfaces/kns/impl.h | 7 +
interfaces/kns/manager-ext.h | 2 +-
interfaces/kns/manager.h | 26 +-
interfaces/kns/socket.h | 43 +-
interfaces/kns/stream.h | 84 +
interfaces/kproc/cond.h | 3 +-
interfaces/kproc/lock.h | 22 +-
interfaces/krypto/encfile-priv.h | 8 +-
interfaces/krypto/extern.h | 7 +-
interfaces/ktst/test_tools.hpp | 2 +-
interfaces/ktst/unit_test.hpp | 30 +-
interfaces/ktst/unit_test_suite.hpp | 5 +-
.../{kns/curl-file.h => ncbi/vdb-blast-priv.h} | 24 +-
interfaces/ncbi/vdb-blast.h | 489 ++
interfaces/sra/fastq.h | 2 +-
interfaces/vdb/manager.h | 12 +
interfaces/vfs/manager.h | 3 +
interfaces/vfs/resolver.h | 6 +-
libs/Makefile | 1 +
libs/align/align-access.c | 28 +-
libs/align/bam.c | 1114 ++-
libs/align/refseq-mgr.c | 4 +
libs/align/writer-alignment.c | 2 +-
libs/align/writer-reference.c | 48 +-
libs/ascp/linux/ascp-path.c | 28 +
libs/ascp/mac/ascp-path.c | 2 +-
libs/ascp/win/connect.c | 71 +-
libs/{vfs => blast}/Makefile | 63 +-
libs/blast/blast.c | 5243 ++++++++++++++
libs/kapp/args_debug.h | 2 +-
libs/kdb/dbmgr-cmn.c | 112 +-
libs/kdb/dbmgr-priv.h | 2 +
libs/kdb/wmeta.c | 6 +-
libs/kfg/config-lex.c | 330 +-
libs/kfg/config.c | 45 +
libs/kfg/default.kfg | 19 +-
libs/kfs/Makefile | 27 +-
libs/kfs/file.c | 435 +-
libs/kfs/from_to_namelist.c | 307 +
libs/kfs/gzip.c | 65 +-
libs/kfs/win/sysdir-priv.h | 7 +
libs/kfs/win/sysdir.c | 3 +
libs/klib/Makefile | 1 +
libs/klib/printf.c | 2 +-
libs/klib/release-vers.h | 2 +-
libs/klib/report.c | 17 +-
libs/{kns/unix/sysmgr.c => klib/unix/misc.c} | 12 +-
libs/klib/unix/systime.c | 31 +
libs/klib/vector_namelist.c | 36 +-
libs/{kns/unix/sysmgr.c => klib/win/misc.c} | 12 +-
libs/kns/KCurlFile.c | 716 --
libs/kns/KCurlRequest.c | 438 --
libs/kns/Makefile | 56 +-
libs/kns/curlhdr/curl.h | 1600 -----
libs/kns/curlhdr/curlver.h | 56 -
libs/kns/curlhdr/easy.h | 81 -
libs/kns/curlhdr/multi.h | 344 -
libs/kns/curlhdr/types.h | 1 -
libs/kns/entrez-fetcher.c | 221 -
libs/kns/http-priv.h | 25 +-
libs/kns/http-test.c | 4 +-
libs/kns/http.c | 393 +-
libs/kns/kns_manager-ext.c | 21 +-
libs/kns/kns_manager.c | 7 +
libs/kns/kns_mgr_priv.h | 71 -
libs/kns/{unix => linux}/sysendpoint.c | 24 +-
libs/kns/linux/syspoll.c | 107 +
libs/kns/{unix => mac}/sysendpoint.c | 0
libs/kns/mac/syspoll.c | 96 +
libs/kns/manager.c | 307 +
libs/{kproc/win/syslock-priv.h => kns/mgr-priv.h} | 23 +-
interfaces/kns/curl-file.h => libs/kns/poll-priv.h | 20 +-
libs/kns/stream-priv.h | 4 +
libs/kns/stream.c | 474 +-
libs/kns/{unix/sysmgr.c => sysmgr.h} | 20 +-
libs/kns/undyinghttp.c | 362 +
libs/kns/unix/sysmgr.c | 8 +-
libs/kns/unix/syssock.c | 817 ++-
libs/kns/win/sysmgr.c | 44 +-
libs/kns/win/syssock.c | 1388 ++--
libs/kproc/bsd/syslock-priv.h | 12 +-
libs/kproc/bsd/syslock.c | 507 +-
libs/kproc/linux/syslock-priv.h | 6 +
libs/kproc/linux/syslock.c | 123 +-
libs/kproc/win/syslock-priv.h | 11 +
libs/kproc/win/syslock.c | 122 +-
libs/krypto/Makefile | 2 +-
libs/ktst/testenv.cpp | 11 +-
libs/ktst/unix/runprocesstestcase.cpp | 16 +-
libs/ktst/win/runprocesstestcase.cpp | 41 +-
libs/loader/common-writer.c | 25 +-
libs/ncbi-vdb/Makefile | 2 +-
libs/ncbi-vdb/libncbi-vdb.vers | 2 +-
libs/ncbi-vdb/libncbi-wvdb.vers | 2 +-
libs/search/agrep-dp.c | 18 +-
libs/search/agrep-myers.c | 150 +-
libs/search/fgrep-aho.c | 2 +-
libs/search/fgrep-boyermoore.c | 4 +-
libs/search/fgrep-dumb.c | 2 +-
libs/search/search-priv.h | 4 +-
libs/sra/Makefile | 2 +-
libs/sra/reader-abi.c | 14 +-
libs/sra/reader-fastq.c | 20 +-
libs/sra/sra-schema.c | 7238 ++++++++++----------
libs/vdb/blob.c | 14 +-
libs/vdb/cursor-cmn.c | 35 +-
libs/vdb/database-depend.c | 11 +-
libs/vdb/dbmgr-cmn.c | 78 +
libs/vdb/prod-priv.h | 3 +
libs/vdb/report-vdb.c | 2 +-
libs/vdb/table-cmn.c | 2 +-
libs/vdb/wcursor.c | 2 -
libs/vfs/Makefile | 29 +-
libs/vfs/keyring.h | 9 +-
libs/vfs/manager.c | 218 +-
libs/vfs/path.c | 31 +-
libs/vfs/resolver.c | 216 +-
libs/vfs/unix/syskeyring.c | 149 +-
libs/vfs/win/syskeyring.c | 8 +-
tools/align-info/align-info.c | 37 +-
tools/align-info/align-info.vers | 2 +-
tools/bam-loader/bam-load.vers | 2 +-
tools/bam-loader/loader-imp.c | 91 +-
tools/cache-mgr/cache-mgr.vers | 2 +-
tools/cg-load/cg-load.vers | 2 +-
tools/fastq-loader/fastq-grammar.c | 679 +-
tools/fastq-loader/fastq-lex.c | 403 +-
tools/fastq-loader/fastq-loader.c | 6 +-
tools/fastq-loader/fastq-parse.h | 54 +-
tools/fastq-loader/fastq-reader.c | 80 +-
tools/fastq-loader/fastq-tokens.h | 3 +-
tools/fastq-loader/latf-load.vers | 2 +-
tools/kar/kar.vers | 2 +-
tools/kar/sra-kar.vers | 2 +-
tools/nenctool/Makefile | 4 +-
tools/nenctool/nenctest.vers | 2 +-
tools/nenctool/nenctool.vers | 2 +-
tools/nencvalid/Makefile | 2 +-
tools/nencvalid/nencvalid.vers | 2 +-
tools/prefetch/prefetch.c | 55 +-
tools/prefetch/prefetch.vers | 2 +-
tools/sra-dbcc/sra-dbcc.vers | 2 +-
tools/sra-dump/abi-dump.vers | 2 +-
tools/sra-dump/abi.c | 2 +
tools/sra-dump/core.c | 16 +-
tools/sra-dump/core.h | 1 +
tools/sra-dump/factory.c | 4 +
tools/sra-dump/fastq-dump.vers | 2 +-
tools/sra-dump/fastq.c | 29 +-
tools/sra-dump/illumina-dump.vers | 2 +-
tools/sra-dump/sff-dump.vers | 2 +-
tools/sra-dump/sra-dump.vers | 2 +-
tools/sra-load/abi-load.vers | 2 +-
tools/sra-load/fastq-load.vers | 2 +-
tools/sra-load/helicos-load.vers | 2 +-
tools/sra-load/illumina-load.vers | 2 +-
tools/sra-load/pacbio-loadxml.vers | 2 +-
tools/sra-load/sff-load.vers | 2 +-
tools/sra-load/srf-load.vers | 2 +-
tools/sra-load/writer-absolid.c | 6 +-
tools/sra-load/writer-absolid.h | 3 +-
tools/sra-pileup/cg_tools.c | 8 +-
tools/sra-pileup/cg_tools.h | 4 +-
tools/sra-pileup/read_fkt.h | 164 +-
tools/sra-pileup/sam-aligned.c | 6 +-
tools/sra-pileup/sam-aligned.h | 90 +-
tools/sra-pileup/sam-dump-opts.c | 16 +
tools/sra-pileup/sam-dump-opts.h | 7 +-
tools/sra-pileup/sam-dump.vers | 2 +-
tools/sra-pileup/sam-dump3.c | 7 +-
tools/sra-pileup/sam-hdr.c | 416 +-
tools/sra-pileup/sam-unaligned.h | 2 +-
tools/sra-pileup/sra-pileup.vers | 2 +-
tools/sra-sort/sort-defs.h | 15 +
tools/sra-sort/sra-sort.vers | 2 +-
tools/sra-stat/sra-stat.vers | 2 +-
tools/srapath/srapath.vers | 2 +-
tools/util/kdbmeta.c | 74 +-
tools/util/kdbmeta.vers | 2 +-
tools/util/mac/syspass.c | 2 +-
tools/util/md5cp.vers | 2 +-
tools/util/rcexplain.vers | 2 +-
tools/util/rowwritetest.vers | 2 +-
tools/util/schema-replace.vers | 2 +-
tools/util/test-sra.c | 163 +-
tools/util/test-sra.vers | 2 +-
tools/util/testld.vers | 2 +-
tools/util/txt2kdb.vers | 2 +-
tools/util/vdb-lock.vers | 2 +-
tools/util/vdb-passwd.vers | 2 +-
tools/util/vdb-unlock.vers | 2 +-
tools/vdb-config/vdb-config.c | 56 +-
tools/vdb-config/vdb-config.vers | 2 +-
tools/vdb-copy/vdb-copy.vers | 2 +-
tools/vdb-decrypt/vdb-decrypt.vers | 2 +-
tools/vdb-decrypt/vdb-encrypt.vers | 2 +-
tools/vdb-dump/vdb-dump-coldefs.c | 27 +-
tools/vdb-dump/vdb-dump-coldefs.h | 6 +-
tools/vdb-dump/vdb-dump-context.c | 4 +-
tools/vdb-dump/vdb-dump-context.h | 4 +-
tools/vdb-dump/vdb-dump-fastq.c | 3 +
tools/vdb-dump/vdb-dump.c | 86 +-
tools/vdb-dump/vdb-dump.vers | 2 +-
tools/vdb-validate/vdb-validate.c | 569 +-
tools/vdb-validate/vdb-validate.vers | 2 +-
248 files changed, 19551 insertions(+), 11609 deletions(-)
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