[med-svn] [sra-sdk] 02/03: Merge tag 'upstream/2.3.3-4_dfsg'
Charles Plessy
plessy at alioth.debian.org
Mon Oct 21 09:16:55 UTC 2013
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch master
in repository sra-sdk.
commit 3228669bad660f0edb55c6450caf31795c85446c
Merge: 8ee4a69 a84ff91
Author: Charles Plessy <plessy at debian.org>
Date: Mon Oct 21 18:10:49 2013 +0900
Merge tag 'upstream/2.3.3-4_dfsg'
Upstream version 2.3.3-4~dfsg
# gpg: Signature made Mon 21 Oct 2013 18:10:44 JST using RSA key ID B3443334
# gpg: Good signature from "Charles Plessy <plessy at riken.jp>"
Makefile | 39 +-
build/BUILD.linux | 2 +-
build/COMP.mac | 2 +-
build/LNKG.linux | 2 +-
build/Makefile.env | 30 +-
build/Makefile.shell | 22 +-
libs/Makefile => build/Makefile.targets | 99 +-
build/ld.linux.cmn.sh | 5 +-
build/ld.linux.dlib.sh | 14 +-
build/ld.linux.exe.sh | 12 +
build/ld.linux.slib.sh | 6 +-
build/ld.mac.cmn.sh | 5 +-
build/ld.mac.dlib.sh | 73 +-
build/ld.mac.exe.sh | 12 +
build/ld.mac.slib.sh | 6 +-
build/ld.sh | 122 +-
build/ld.unix.slib.sh | 6 +-
build/ld.win.cmn.sh | 62 +-
build/ld.win.dlib.sh | 2 +-
build/ld.win.exe.sh | 2 +-
build/sra-dflt-schema.sh | 41 +-
build/win-cc.sh | 35 +-
configuration-assistant.perl | 2 +-
interfaces/align/bam.h | 14 +-
interfaces/align/iterator.h | 8 +-
interfaces/align/reference.h | 2 +-
interfaces/align/refseq-mgr.h | 2 +-
interfaces/align/writer-alignment.h | 36 +-
interfaces/align/writer-reference.h | 14 +-
interfaces/align/writer-refseq.h | 7 +-
interfaces/align/writer-sequence.h | 3 +-
interfaces/cc/vc++/compiler.h | 2 +-
interfaces/kdb/kdb-priv.h | 13 +-
interfaces/kfg/config.h | 11 +-
interfaces/kfg/kart.h | 87 +
interfaces/{kfs/kfs-priv.h => kfg/keystore-priv.h} | 79 +-
interfaces/kfg/keystore.h | 155 +
interfaces/kfg/repository.h | 31 +-
interfaces/kfs/arrayfile.h | 18 +
interfaces/kfs/directory.h | 16 +-
interfaces/kfs/impl.h | 5 +
interfaces/kfs/kfs-priv.h | 15 +-
interfaces/kfs/sra.h | 1 +
interfaces/klib/data-buffer.h | 20 +
interfaces/klib/defs.h | 29 +
interfaces/klib/log.h | 24 +-
interfaces/klib/namelist.h | 12 +-
interfaces/klib/printf.h | 19 +-
interfaces/klib/ptrie.h | 2 +-
interfaces/klib/text.h | 2 +-
interfaces/klib/writer.h | 4 +-
interfaces/kns/KCurlRequest.h | 2 +-
interfaces/{kfs/kfs-priv.h => kns/adapt.h} | 60 +-
.../kns/ascp.h | 102 +-
interfaces/kns/endpoint.h | 117 +
interfaces/kns/http.h | 278 +
interfaces/kns/socket.h | 98 +
interfaces/ktst/unit_test_suite.hpp | 8 +-
interfaces/loader/alignment-writer.h | 18 +-
interfaces/loader/common-writer.h | 16 +-
interfaces/loader/reference-writer.h | 2 +-
interfaces/ncbi/wgs-contig.vschema | 2 +-
interfaces/sra/sradb-priv.h | 88 +-
interfaces/vdb/dependencies.h | 22 +-
interfaces/vdb/vdb-priv.h | 15 +
interfaces/vdb/vdb.vschema | 4 +-
interfaces/vdb/xform.h | 4 +-
interfaces/vfs/extern.h | 5 +
interfaces/vfs/manager-priv.h | 22 +-
interfaces/vfs/manager.h | 60 +-
interfaces/vfs/path-priv.h | 211 +-
interfaces/vfs/path.h | 337 +-
interfaces/vfs/resolver.h | 75 +-
libs/Makefile | 71 +-
libs/align/Makefile | 58 +-
libs/align/bam.c | 332 +-
libs/align/pl_iterator.c | 15 +
libs/align/ref_iterator.c | 8 +-
libs/align/reference.c | 40 +-
libs/align/writer-alignment.c | 105 +-
libs/align/writer-cmn.c | 21 +-
libs/align/writer-priv.h | 7 +-
libs/align/writer-reference.c | 42 +-
libs/align/writer-refseq.c | 11 +-
libs/align/writer-sequence.c | 27 +-
libs/{ktst => ascp}/Makefile | 38 +-
.../definitions.h => libs/ascp/ascp-priv.h | 45 +-
libs/ascp/ascp.c | 692 +
libs/ascp/linux/ascp-path.c | 61 +
libs/ascp/mac/ascp-path.c | 65 +
libs/ascp/unix/connect.c | 555 +
libs/ascp/win/ascp-path.c | 26 +
libs/ascp/win/connect.c | 520 +
libs/axf/Makefile | 27 +-
libs/axf/align-ref-pos.c | 4 +-
libs/axf/cigar.c | 4 +-
libs/axf/ref-tbl-sub-select.c | 309 +-
libs/{ktst => ext}/Makefile | 67 +-
libs/{kapp => ext/bzip2}/Makefile | 134 +-
libs/{ktst => ext/curl}/Makefile | 69 +-
libs/{kapp => ext/zlib}/Makefile | 139 +-
libs/kapp/Makefile | 34 +-
libs/kapp/tokenizer.c | 2 +-
libs/kdb/Makefile | 54 +-
libs/kdb/btree.c | 2 +-
libs/kdb/column.c | 11 +-
libs/kdb/database-cmn.c | 7 +-
libs/kdb/database.c | 4 +-
libs/kdb/dbmgr-cmn.c | 41 +-
libs/kdb/dbmgr-priv.h | 3 +-
libs/kdb/dbmgr.c | 29 +-
libs/kdb/index.c | 2 +-
libs/kdb/kdb.c | 6 +-
libs/{kns/stream-priv.h => kdb/libkdb.vers.h} | 7 +-
libs/{kns/stream-priv.h => kdb/libwkdb.vers.h} | 7 +-
libs/kdb/meta.c | 17 +-
libs/kdb/table.c | 8 +-
libs/kdb/wcolumn.c | 11 +-
libs/kdb/wdatabase.c | 4 +-
libs/kdb/wdbmgr.c | 2 +-
libs/kdb/wkdb.c | 6 +-
libs/kdb/wmeta.c | 15 +-
libs/kdb/wtable.c | 5 +-
libs/kfg/Makefile | 63 +-
libs/kfg/config-lex.c | 4 +-
libs/kfg/config.c | 131 +-
libs/kfg/kart.c | 608 +
libs/kfg/keystore.c | 836 +
libs/kfg/report.c | 433 -
libs/kfg/repository.c | 109 +-
libs/kfs/Makefile | 46 +-
libs/kfs/arrayfile.c | 41 +
libs/kfs/directory.c | 2 +-
libs/kfs/file.c | 2 +-
libs/kfs/lockfile.c | 2 +-
libs/kfs/mmap.c | 2 +-
libs/kfs/pmem.c | 5 +
libs/kfs/ramfile.c | 17 +-
libs/kfs/sra.c | 3 +-
libs/kfs/toc.c | 14 +-
libs/kfs/tocdir.c | 18 +-
libs/kfs/unix/sysdll.c | 12 +-
libs/kfs/win/sysdir.c | 178 +-
libs/kfs/win/sysdll.c | 25 +-
libs/klib/Makefile | 24 +-
libs/klib/data-buffer.c | 23 +-
libs/klib/judy/Makefile | 19 +-
libs/klib/printf.c | 98 +-
libs/klib/status-rc.c | 4 +-
libs/klib/status.c | 2 +-
libs/klib/text.c | 8 +-
libs/klib/unix/syswriter.c | 1 +
libs/klib/vector_namelist.c | 34 +-
libs/klib/writer.c | 2 +-
libs/kns/KCurlRequest.c | 2 +-
libs/kns/Makefile | 46 +-
libs/kns/endpoint.c | 109 +
libs/kns/entrez-fetcher.c | 2 +-
interfaces/kfs/kfs-priv.h => libs/kns/http-priv.h | 86 +-
libs/kns/http-test.c | 368 +
libs/kns/http.c | 3002 +
libs/kns/kns_manager.c | 64 +-
libs/kns/kns_mgr_priv.h | 8 +
libs/kns/stream-priv.h | 4 +
libs/kns/stream.c | 2 +-
libs/kns/unix/sysendpoint.c | 169 +
.../definitions.h => libs/kns/unix/sysmgr.c | 34 +-
libs/kns/unix/syssock.c | 552 +
libs/kns/unix/sysstream.c | 251 +
libs/kns/win/sysendpoint.c | 185 +
.../sra-pileup/cg_tools.h => libs/kns/win/sysmgr.c | 59 +-
libs/kns/win/syssock.c | 663 +
libs/kns/win/sysstream.c | 232 +
libs/kproc/Makefile | 61 +-
libs/kproc/procmgr.c | 2 +-
libs/kproc/task.c | 2 +-
libs/krypto/Makefile | 45 +-
libs/krypto/aes-ncbi.aes-ni.pic.o.list |38295 ----------
libs/krypto/aes-ncbi.vec.pic.o.list |74023 -------------------
libs/krypto/aes-ncbi.vecreg.pic.o.list |75192 --------------------
libs/krypto/aes_core.c | 2 +-
libs/krypto/cipher-vec.aes-ni.pic.o.list |10909 ---
libs/krypto/cipher-vec.vec.pic.o.list |10959 ---
libs/krypto/cipher-vec.vecreg.pic.o.list |10919 ---
libs/krypto/cipher.c | 12 +-
libs/krypto/compile-test.aes-ni.pic.o.list | 592 -
libs/krypto/compile-test.vec.pic.o.list | 590 -
libs/krypto/compile-test.vecreg.pic.o.list | 592 -
libs/krypto/encfilev2.c | 2 +-
libs/krypto/no-null-ncbi.aes-ni.pic.o.list | 2539 -
libs/krypto/no-null-ncbi.vec.pic.o.list | 2540 -
libs/krypto/no-null-ncbi.vecreg.pic.o.list | 2540 -
libs/krypto/null-ncbi.vec.pic.o.list | 4406 --
libs/krypto/null-ncbi.vecreg.pic.o.list | 4406 --
libs/krypto/wgaencrypt.c | 2 +-
libs/ktst/Makefile | 13 +-
libs/ktst/testenv.cpp | 2 +
libs/ktst/unix/runprocesstestcase.cpp | 27 +-
libs/ktst/win/runprocesstestcase.cpp | 11 +
libs/kxml/Makefile | 57 +-
libs/loader/Makefile | 16 +-
libs/loader/alignment-writer.c | 56 +-
libs/loader/common-reader.c | 2 +-
libs/loader/common-writer.c | 236 +-
libs/loader/reference-writer.c | 11 +-
libs/{search => ncbi-vdb}/Makefile | 130 +-
libs/ncbi-vdb/libncbi-vdb.vers | 1 +
libs/ncbi-vdb/libncbi-wvdb.vers | 1 +
libs/search/Makefile | 31 +-
libs/search/agrep-myersunltd.c | 6 +-
libs/search/fgrep-dumb.c | 2 +-
libs/sra/Makefile | 102 +-
libs/{kns/stream-priv.h => sra/libsradb.vers.h} | 7 +-
libs/sra/reader-cmn.c | 24 +-
libs/sra/reader-fastq.c | 2 +-
libs/sra/sra-schema.c | 4083 ++
libs/sra/sracache.c | 175 +-
libs/sra/sramgr-cmn.c | 249 +-
libs/sra/sraschema.c | 1 -
libs/sra/sratbl-cmn.c | 114 +-
libs/sraxf/Makefile | 27 +-
libs/sraxf/v0-decompress-local.h | 2 +-
libs/vdb/Makefile | 54 +-
libs/vdb/blob.c | 71 +-
libs/vdb/column-cmn.c | 14 +
libs/vdb/column-priv.h | 2 +
libs/vdb/cursor-cmn.c | 35 +-
libs/vdb/database-cmn.c | 4 +-
libs/vdb/database-depend.c | 159 +-
libs/vdb/dbmgr-cmn.c | 4 +-
libs/vdb/dbmgr.c | 10 +-
libs/vdb/delta_average.c | 4 +-
libs/{kns/stream-priv.h => vdb/libvdb.vers.h} | 7 +-
libs/{kns/stream-priv.h => vdb/libwvdb.vers.h} | 7 +-
libs/vdb/linker-cmn.c | 11 +-
libs/vdb/linker-int.c | 392 +-
libs/vdb/linker-priv.h | 3 +
libs/vdb/phys-cmn.c | 35 +-
libs/vdb/phys-priv.h | 5 +
libs/vdb/prod-cmn.c | 62 +-
libs/vdb/prod-priv.h | 5 +
libs/vdb/schema.c | 4 +-
libs/vdb/table-cmn.c | 4 +-
libs/vdb/wcolumn.c | 2 +-
libs/vdb/wlinker.c | 41 +-
libs/vdb/xform-priv.h | 43 +-
libs/vfs/Makefile | 72 +-
.../fastq-reader.h => libs/vfs/keyring-priv.h | 14 +-
libs/vfs/keyring.c | 133 +
libs/vfs/keyring.h | 110 +
libs/vfs/manager.c | 1723 +-
libs/vfs/path-priv.h | 146 +-
libs/vfs/path.c | 4664 +-
libs/vfs/resolver.c | 1974 +-
libs/vfs/unix/syskeyring.c | 174 +
libs/vfs/unix/syspath.c | 168 +-
.../fastq-reader.h => libs/vfs/win/syskeyring.c | 48 +-
libs/vfs/win/syspath.c | 474 +-
libs/vxf/Makefile | 67 +-
libs/vxf/integral.c | 6 +-
libs/vxf/{integral.c => integral_0.c} | 16 +-
libs/vxf/rand_4na_2na.c | 3 +-
libs/vxf/unzip.c | 10 +-
libs/wgsxf/Makefile | 34 +-
libs/wgsxf/build_scaffold.c | 101 +-
tools/Makefile | 59 +-
tools/align-info/Makefile | 15 +-
tools/align-info/align-info.c | 1 -
tools/align-info/align-info.vers | 2 +-
tools/bam-loader/Makefile | 43 +-
tools/bam-loader/bam-load.vers | 2 +-
tools/bam-loader/loader-imp.c | 9 +-
tools/bam-loader/reference-writer.c | 6 +-
tools/{refseq-load => cache-mgr}/Makefile | 47 +-
tools/cache-mgr/cache-mgr.c | 1332 +
tools/cache-mgr/cache-mgr.vers | 1 +
tools/cg-load/Makefile | 19 +-
tools/cg-load/cg-load.c | 2 +-
tools/cg-load/cg-load.vers | 2 +-
tools/fastq-loader/Makefile | 90 +-
tools/fastq-loader/fastq-grammar.c | 299 +-
tools/fastq-loader/fastq-lex.c | 1 +
tools/fastq-loader/fastq-loader.c | 6 +-
tools/fastq-loader/fastq-parse.h | 9 +-
tools/fastq-loader/fastq-reader.c | 9 +-
tools/fastq-loader/fastq-reader.h | 2 +-
tools/fastq-loader/latf-load.vers | 2 +-
tools/fastq-loader/loader-imp.c | 14 +-
tools/kar/Makefile | 12 +-
tools/kar/kar.c | 16 +-
tools/kar/kar.vers | 2 +-
tools/kar/sra-kar.vers | 2 +-
tools/nenctool/nenctest.c | 4 +-
tools/nenctool/nenctest.vers | 2 +-
tools/nenctool/nenctool.c | 4 +-
tools/nenctool/nenctool.vers | 2 +-
tools/nencvalid/nencvalid.c | 88 +-
tools/nencvalid/nencvalid.vers | 2 +-
tools/prefetch/Makefile | 15 +-
tools/prefetch/prefetch.c | 1274 +-
tools/prefetch/prefetch.vers | 2 +-
tools/refseq-load/context.c | 339 -
tools/refseq-load/context.h | 99 -
tools/refseq-load/refseq-load.c | 819 -
tools/refseq-load/refseq-load.vers | 1 -
tools/sra-dump/Makefile | 52 +-
tools/sra-dump/abi-dump.vers | 2 +-
tools/sra-dump/core.c | 262 +-
tools/sra-dump/factory.c | 131 +-
tools/sra-dump/factory.h | 6 +
tools/sra-dump/fastq-dump.vers | 2 +-
tools/sra-dump/fastq.c | 453 +-
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 | 21 +-
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/sff-load.vers | 2 +-
tools/sra-load/srf-load.vers | 2 +-
tools/sra-pileup/Makefile | 30 +-
tools/sra-pileup/cg_tools.c | 486 +-
tools/sra-pileup/cg_tools.h | 68 +-
tools/sra-pileup/cmdline_cmn.c | 30 +-
tools/sra-pileup/cmdline_cmn.h | 3 +-
tools/sra-pileup/matecache.c | 2 +-
tools/sra-pileup/read_fkt.c | 816 +-
tools/sra-pileup/read_fkt.h | 49 +-
tools/sra-pileup/reref.c | 33 +-
tools/sra-pileup/sam-aligned.c | 1204 +-
tools/sra-pileup/sam-dump-opts.c | 25 +-
tools/sra-pileup/sam-dump-opts.h | 5 +
tools/sra-pileup/sam-dump.c | 131 +-
tools/sra-pileup/sam-dump.vers | 2 +-
tools/sra-pileup/sam-dump3.c | 32 +-
tools/sra-pileup/sam-unaligned.c | 289 +-
tools/sra-pileup/sra-pileup.c | 1639 +-
tools/sra-pileup/sra-pileup.vers | 2 +-
tools/sra-sort/Makefile | 15 +-
tools/sra-sort/ctx.h | 4 +
tools/sra-sort/sra-sort.vers | 2 +-
tools/sra-stat/Makefile | 15 +-
tools/sra-stat/sra-stat.vers | 2 +-
tools/srapath/srapath.c | 42 +-
tools/srapath/srapath.vers | 2 +-
tools/util/Makefile | 57 +-
tools/util/kdbmeta.c | 5 +-
tools/util/kdbmeta.vers | 2 +-
tools/util/rcexplain.vers | 2 +-
tools/util/test-sra.c | 838 +-
tools/util/test-sra.vers | 2 +-
tools/util/vdb-lock.vers | 2 +-
tools/util/vdb-passwd.c | 2 +-
tools/util/vdb-passwd.vers | 2 +-
tools/util/vdb-unlock.vers | 2 +-
tools/vdb-config/Makefile | 14 +-
tools/vdb-config/vdb-config.c | 138 +-
tools/vdb-config/vdb-config.vers | 2 +-
tools/vdb-copy/Makefile | 16 +-
tools/vdb-copy/vdb-copy.vers | 2 +-
tools/vdb-decrypt/vdb-decrypt.c | 5 +-
tools/vdb-decrypt/vdb-decrypt.vers | 2 +-
tools/vdb-decrypt/vdb-encrypt.c | 6 +-
tools/vdb-decrypt/vdb-encrypt.vers | 2 +-
tools/vdb-dump/Makefile | 15 +-
tools/vdb-dump/vdb-dump-coldefs.h | 4 +
tools/vdb-dump/vdb-dump-context.c | 2 +
tools/vdb-dump/vdb-dump-context.h | 6 +
tools/vdb-dump/vdb-dump-filter.h | 4 +
tools/vdb-dump/vdb-dump-formats.h | 4 +
tools/vdb-dump/vdb-dump-helper.h | 4 +
tools/vdb-dump/vdb-dump-num-gen.h | 4 +
tools/vdb-dump/vdb-dump-row-context.h | 5 +
tools/vdb-dump/vdb-dump-str.h | 4 +
tools/vdb-dump/vdb-dump-tools.c | 1 +
tools/vdb-dump/vdb-dump-tools.h | 4 +
tools/vdb-dump/vdb-dump.c | 36 +
tools/vdb-dump/vdb-dump.vers | 2 +-
tools/vdb-validate/Makefile | 15 +-
tools/vdb-validate/vdb-validate.c | 473 +-
tools/vdb-validate/vdb-validate.vers | 2 +-
383 files changed, 32219 insertions(+), 250081 deletions(-)
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