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commit 2f5856f36119ac7141f4d68d20f956ee0b745c8e Merge: be7b56c f14de0e Author: Andreas Tille <[email protected]> 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(-) -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/sra-sdk.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
