[med-svn] [sra-sdk] 02/07: Merge tag 'upstream/2.3.4-2+dfsg'
Andreas Tille
tille at debian.org
Tue Dec 24 07:59:16 UTC 2013
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository sra-sdk.
commit 2f5856f36119ac7141f4d68d20f956ee0b745c8e
Merge: be7b56c f14de0e
Author: Andreas Tille <tille at debian.org>
Date: Mon Dec 23 22:36:54 2013 +0100
Merge tag 'upstream/2.3.4-2+dfsg'
Upstream version 2.3.4-2+dfsg
build/Makefile.env | 10 +-
build/Makefile.mac | 4 +
build/ld.linux.exe.sh | 7 +-
build/ld.mac.exe.sh | 7 +-
build/win-cc.sh | 33 +-
configuration-assistant.perl | 19 +-
interfaces/kfg/kart.h | 3 +
interfaces/kfg/keystore.h | 2 -
interfaces/kfg/kfg-priv.h | 35 +-
interfaces/kfs/kfs-priv.h | 8 +
interfaces/klib/refcount.h | 9 +-
interfaces/klib/report.h | 5 +
.../klib/{report.h => sra-release-version.h} | 93 +-
interfaces/kns/KCurlRequest.h | 4 +
interfaces/kns/ascp.h | 9 +-
.../reref.h => interfaces/kns/manager-ext.h | 37 +-
interfaces/kns/manager.h | 13 +
interfaces/kns/socket.h | 67 +-
interfaces/krypto/extern.h | 33 +-
interfaces/ktst/unit_test_suite.hpp | 11 +-
interfaces/ncbi/wgs-contig.h | 25 +-
interfaces/ncbi/wgs-contig.vschema | 71 +-
interfaces/os/mac/os-native.h | 2 +-
interfaces/vdb/vdb-priv.h | 5 +
interfaces/vfs/manager-priv.h | 5 -
interfaces/vfs/path.h | 11 +
libs/align/Makefile | 30 +-
libs/align/bam.c | 21 +-
libs/align/libalign-access.vers | 1 -
libs/align/libalign-reader.vers | 1 -
libs/align/libncbi-bam.vers | 1 -
libs/align/reference.c | 26 +-
libs/align/writer-reference.c | 14 +-
libs/align/writer-refseq.c | 5 +-
libs/ascp/ascp.c | 71 +-
libs/ascp/win/ascp-path.c | 4 +-
libs/ascp/win/connect.c | 23 +-
libs/axf/libaxf.vers | 1 -
libs/axf/libwaxf.vers | 1 -
libs/ext/Makefile | 55 -
libs/ext/bzip2/Makefile | 143 --
libs/ext/curl/Makefile | 103 -
libs/ext/zlib/Makefile | 150 --
libs/kapp/args.c | 2 +-
libs/kapp/libkapp.vers | 1 -
libs/kapp/libload.vers | 1 -
libs/kapp/loader-file.c | 10 +-
libs/kapp/progressbar.c | 2 +-
libs/kapp/tokenizer.c | 4 +-
libs/kapp/unix/sysmain.c | 6 +
libs/kapp/win/sysmain.c | 1 +
libs/kdb/btree.c | 42 +-
libs/kdb/column-cc.c | 2 +-
libs/kdb/database.c | 4 +-
libs/kdb/libkdb.vers | 1 -
libs/kdb/libwkdb.vers | 1 -
libs/kdb/trieidx-v2.c | 70 +-
libs/kfg/Makefile | 10 +-
libs/kfg/config-grammar.c | 109 +-
libs/kfg/config-lex.c | 128 +-
libs/kfg/config-tokens.h | 4 +-
libs/kfg/config.c | 416 ++--
libs/kfg/kart.c | 131 +-
libs/kfg/keystore.c | 14 +-
libs/kfg/libkfg.vers | 1 -
libs/kfg/report-kfg.c | 9 +-
libs/kfg/repository.c | 10 +-
libs/kfs/bzip.c | 6 +-
libs/kfs/cacheteefile.c | 2 +-
libs/kfs/gzip.c | 6 +-
libs/kfs/libkdl.vers | 1 -
libs/kfs/libkff.vers | 1 -
libs/kfs/libkfs.vers | 1 -
libs/kfs/quickmount.c | 6 +-
libs/kfs/tocentry.c | 2 +-
libs/kfs/win/lnk_tools.c | 4 +-
libs/kfs/win/sysdir-priv.h | 7 -
libs/kfs/win/sysdir.c | 6 +-
libs/kfs/win/sysdll.c | 2 +-
libs/kfs/win/sysfile.c | 15 +-
libs/klib/Makefile | 3 +-
libs/klib/libkascii.vers | 1 -
libs/klib/libklib.vers | 1 -
libs/klib/libktlog.vers | 1 -
libs/klib/libkutf8.vers | 1 -
libs/klib/log.c | 4 +-
libs/klib/maybeswap.h | 34 +-
libs/klib/pbstree-impl.c | 198 +-
libs/klib/printf.c | 27 +-
libs/klib/refcount.c | 29 +-
.../sra-pileup/reref.h => libs/klib/release-vers.h | 31 +-
libs/klib/report.c | 45 +-
libs/klib/sra-release-version.c | 328 +++
libs/klib/win/syserrcode.c | 2 +-
libs/klib/win/systime.c | 1 -
libs/klib/win/syswriter.c | 6 +-
libs/kns/KCurlFile.c | 4 +-
libs/kns/Makefile | 1 +
libs/kns/http-priv.h | 2 +-
libs/kns/http-test.c | 8 +-
libs/kns/http.c | 131 +-
libs/kns/kns_manager-ext.c | 140 ++
libs/kns/kns_manager.c | 29 +-
libs/kns/kns_mgr_priv.h | 10 +-
libs/kns/libkns.vers | 1 -
libs/kns/libkurl.vers | 1 -
libs/kns/unix/sysendpoint.c | 87 +-
libs/kns/unix/syssock.c | 160 +-
libs/kns/win/sysendpoint.c | 101 +-
libs/kns/win/syssock.c | 105 +-
libs/kproc/libkproc.vers | 1 -
libs/kproc/libkq.vers | 1 -
libs/kproc/libksproc.vers | 1 -
libs/kproc/unix/systimeout.c | 4 +-
libs/kproc/win/syscond.c | 4 +-
libs/krypto/Makefile | 29 +-
libs/krypto/cipher-byte.c | 2 +-
libs/krypto/cipher.c | 4 +-
libs/krypto/encfile-priv.h | 2 +-
libs/krypto/encfile.c | 4 +-
libs/krypto/encfilev2.c | 2 +-
libs/krypto/libkrypto.vers | 1 -
libs/krypto/libkryptotest.vers | 1 -
libs/krypto/reencfile.c | 2 +-
libs/krypto/wgaencrypt.c | 10 +-
libs/kxml/libkxfs.vers | 1 -
libs/kxml/libkxml.vers | 1 -
libs/kxml/xtoc.c | 4 +-
libs/loader/common-writer.c | 8 +-
libs/ncbi-vdb/Makefile | 4 +-
libs/ncbi-vdb/libncbi-vdb.vers | 2 +-
libs/ncbi-vdb/libncbi-wvdb.vers | 2 +-
libs/search/libksrch.vers | 1 -
libs/search/libnucstrstr.vers | 1 -
libs/search/search.c | 18 +-
libs/sra/libsra-schema.vers | 1 -
libs/sra/libsradb.vers | 1 -
libs/sra/libsrareader.vers | 1 -
libs/sra/libsraschema.vers | 1 -
libs/sra/libwsra-schema.vers | 1 -
libs/sra/libwsradb.vers | 1 -
libs/sra/libwsraschema.vers | 1 -
libs/sra/sracache.c | 2 +-
libs/sraxf/libsraxf.vers | 1 -
libs/sraxf/libwsraxf.vers | 1 -
libs/vdb/column-priv.h | 3 +-
libs/vdb/cursor-cmn.c | 63 +-
libs/vdb/cursor-priv.h | 9 +-
libs/vdb/cursor.c | 2 +-
libs/vdb/database-cmn.c | 12 +
libs/vdb/libvdb.vers | 1 -
libs/vdb/libwvdb.vers | 1 -
libs/vdb/page-map.h | 4 +-
libs/vdb/prod-cmn.c | 32 +-
libs/vdb/prod-expr.c | 6 +-
libs/vdb/prod-expr.h | 3 +
libs/vdb/prod-func.c | 235 +-
libs/vdb/prod.c | 2 +-
libs/vdb/schema-eval.c | 80 +-
libs/vdb/schema-expr.c | 14 +-
libs/vdb/schema-expr.h | 6 +-
libs/vdb/schema-func.c | 437 ++--
libs/vdb/schema-parse.h | 8 +-
libs/vdb/schema-priv.h | 42 +-
libs/vdb/schema-prod.c | 16 +-
libs/vdb/schema-type.c | 21 +-
libs/vdb/schema.c | 1 +
libs/vdb/wcolumn.c | 6 +-
libs/vdb/wcursor.c | 23 +-
libs/vdb/wprod.c | 8 +-
libs/vfs/Makefile | 3 +-
libs/vfs/keyring.c | 189 +-
libs/vfs/libsrapath.vers | 1 -
libs/vfs/libvfs.vers | 1 -
libs/vfs/manager.c | 91 +-
libs/vfs/path-priv.h | 4 +-
libs/vfs/path.c | 6 +-
libs/vfs/resolver.c | 512 +++-
libs/vfs/unix/syspath.c | 2 +-
libs/vfs/win/syspath.c | 5 +-
libs/vxf/libvxf.vers | 1 -
libs/vxf/libwvxf.vers | 1 -
libs/vxf/simple-sub-select.c | 170 +-
libs/wgsxf/libwgsxf.vers | 1 -
libs/wgsxf/libwwgsxf.vers | 1 -
tools/Makefile | 12 -
tools/align-info/align-info.vers | 2 +-
tools/bam-loader/bam-load.3.vers | 1 +
tools/bam-loader/bam-load.vers | 2 +-
tools/bam-loader/loader-imp.c | 27 +-
tools/cache-mgr/Makefile | 23 +-
tools/cache-mgr/cache-mgr.c | 8 +-
tools/cache-mgr/cache-mgr.vers | 2 +-
tools/cg-load/Makefile | 19 +-
tools/cg-load/cg-load.c | 132 +-
tools/cg-load/cg-load.vers | 2 +-
tools/cg-load/defs.h | 4 +
tools/cg-load/f1_5.c | 10 +-
tools/cg-load/f2_0.c | 9 +-
tools/cg-load/f2_2.c | 9 +-
tools/cg-load/factory-cmn.h | 2 +-
tools/cg-load/factory-evidence-dnbs.c | 2 +
tools/cg-load/factory-evidence-intervals.c | 2 +
tools/cg-load/factory-mappings.c | 2 +
tools/cg-load/factory-reads.c | 1 +
tools/cg-load/file-version-factory.c | 1 +
tools/cg-load/file.c | 16 +
tools/cg-load/file.h | 3 +
tools/fastq-loader/Makefile | 8 -
tools/fastq-loader/fastq-lex.c | 56 +-
tools/fastq-loader/latf-load.vers | 2 +-
tools/kar/Makefile | 28 +-
tools/kar/kar.c | 60 +-
tools/kar/kar.vers | 2 +-
tools/kar/sra-kar.vers | 2 +-
tools/nenctool/nenctest.vers | 2 +-
tools/nenctool/nenctool.vers | 2 +-
tools/nencvalid/Makefile | 10 -
tools/nencvalid/nencvalid.vers | 2 +-
tools/prefetch/prefetch.c | 2634 +++++++++++++-------
tools/prefetch/prefetch.vers | 2 +-
tools/sam-dump/sam-dump.c | 2 +-
tools/sra-dbcc/Makefile | 15 +-
tools/sra-dbcc/sra-dbcc.vers | 2 +-
tools/sra-dump/Makefile | 19 -
tools/sra-dump/abi-dump.vers | 2 +-
tools/sra-dump/core.c | 83 +-
tools/sra-dump/fastq-dump.vers | 2 +-
tools/sra-dump/illumina-dump.vers | 2 +-
tools/sra-dump/sff-dump.vers | 2 +-
tools/sra-dump/sra-dump.vers | 2 +-
tools/sra-load/Makefile | 8 -
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 | 1 +
tools/sra-load/sff-load.vers | 2 +-
tools/sra-load/srf-load.vers | 2 +-
tools/sra-pileup/Makefile | 2 +
tools/sra-pileup/cmdline_cmn.c | 382 +--
tools/sra-pileup/cmdline_cmn.h | 27 +-
tools/sra-pileup/ref_regions.c | 491 ++++
.../manager.h => tools/sra-pileup/ref_regions.h | 65 +-
tools/sra-pileup/ref_walker.c | 997 ++++++++
tools/sra-pileup/ref_walker.h | 128 +
tools/sra-pileup/reref.c | 22 +-
tools/sra-pileup/reref.h | 5 -
tools/sra-pileup/sam-aligned.c | 244 +-
tools/sra-pileup/sam-dump-opts.c | 10 +-
tools/sra-pileup/sam-dump-opts.h | 6 +-
tools/sra-pileup/sam-dump.c | 2 +-
tools/sra-pileup/sam-dump.vers | 2 +-
tools/sra-pileup/sam-dump3.c | 99 +-
tools/sra-pileup/sam-hdr.c | 8 +-
tools/sra-pileup/sam-unaligned.c | 4 +-
tools/sra-pileup/sra-pileup.c | 315 ++-
tools/sra-pileup/sra-pileup.vers | 2 +-
tools/sra-sort/sra-sort.vers | 2 +-
tools/sra-stat/sra-stat.vers | 2 +-
tools/srapath/Makefile | 8 +-
tools/srapath/srapath.vers | 2 +-
tools/util/Makefile | 20 +-
tools/util/kdbmeta.c | 47 +-
tools/util/kdbmeta.vers | 2 +-
tools/util/md5cp.vers | 1 +
tools/util/rcexplain.vers | 2 +-
tools/util/rowwritetest.vers | 2 +-
tools/util/schema-replace.vers | 1 +
tools/{sra-pileup/reref.h => util/test-sra-priv.h} | 26 +-
tools/util/test-sra.c | 977 ++++++--
tools/util/test-sra.vers | 2 +-
tools/util/testld.vers | 2 +-
tools/util/txt2kdb.vers | 2 +-
.../krypto/extern.h => tools/util/unix/PrintOS.c | 64 +-
tools/util/vdb-lock.vers | 2 +-
tools/util/vdb-passwd.vers | 2 +-
tools/util/vdb-unlock.vers | 2 +-
tools/{sra-pileup/reref.h => util/win/PrintOS.c} | 46 +-
tools/vdb-config/Makefile | 10 -
tools/vdb-config/vdb-config.c | 27 +-
tools/vdb-config/vdb-config.vers | 2 +-
tools/vdb-copy/vdb-copy.vers | 2 +-
tools/vdb-decrypt/Makefile | 16 +-
tools/vdb-decrypt/vdb-decrypt.c | 2 +-
tools/vdb-decrypt/vdb-decrypt.vers | 2 +-
tools/vdb-decrypt/vdb-encrypt.vers | 2 +-
tools/vdb-dump/Makefile | 2 +
tools/vdb-dump/vdb-dump-context.c | 89 +-
tools/vdb-dump/vdb-dump-context.h | 25 +-
tools/vdb-dump/vdb-dump-fastq.c | 498 ++++
.../reref.h => vdb-dump/vdb-dump-fastq.h} | 21 +-
tools/vdb-dump/vdb-dump-redir.c | 120 +
.../reref.h => vdb-dump/vdb-dump-redir.h} | 32 +-
tools/vdb-dump/vdb-dump.c | 274 +-
tools/vdb-dump/vdb-dump.vers | 2 +-
tools/vdb-validate/vdb-validate.vers | 2 +-
297 files changed, 9988 insertions(+), 4270 deletions(-)
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