[med-svn] [sra-sdk] branch upstream updated (f14de0e -> 888f953)
Andreas Tille
tille at debian.org
Wed Jul 30 12:22:36 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository sra-sdk.
from f14de0e Imported Upstream version 2.3.4-2+dfsg
new 888f953 Imported Upstream version 2.3.5-2+dfsg
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:
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 +-
tools/sra-sort/caps.h => interfaces/kfc/rsrc.h | 46 +-
interfaces/kfc/xc.h | 94 +
libs/kdb/trieidx-priv.h => interfaces/kfc/xcdefs.h | 57 +-
interfaces/{kfs/quickmount.h => kfc/xcext.h} | 41 +-
interfaces/{os/linux/os-native.h => kfc/xcgen.h} | 35 +-
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 +-
.../util/syspass-priv.h => interfaces/klib/misc.h | 12 +-
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/kns/url-fetcher.h | 66 -
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 +-
.../ncbi/vdb-blast-priv.h | 19 +-
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/{ktst => blast}/Makefile | 36 +-
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 +-
.../cc/icc/compiler.h => libs/klib/unix/misc.c | 14 +-
libs/klib/unix/systime.c | 31 +
libs/klib/vector_namelist.c | 36 +-
.../cc/icc/compiler.h => libs/klib/win/misc.c | 14 +-
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 +-
interfaces/cc/gcc/compiler.h => libs/kns/sysmgr.h | 10 +-
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-priv.h | 46 -
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 +-
250 files changed, 19508 insertions(+), 11691 deletions(-)
copy interfaces/{klib => kfc}/callconv.h (95%)
create mode 100644 interfaces/kfc/ctx.h
copy interfaces/{klib => kfc}/defs.h (65%)
create mode 100644 interfaces/kfc/except.h
copy interfaces/{klib => kfc}/extern.h (84%)
copy interfaces/{klib => kfc}/rc.h (76%)
copy tools/sra-sort/caps.h => interfaces/kfc/rsrc.h (69%)
create mode 100644 interfaces/kfc/xc.h
copy libs/kdb/trieidx-priv.h => interfaces/kfc/xcdefs.h (70%)
copy interfaces/{kfs/quickmount.h => kfc/xcext.h} (64%)
copy interfaces/{os/linux/os-native.h => kfc/xcgen.h} (60%)
copy tools/util/syspass-priv.h => interfaces/klib/misc.h (88%)
delete mode 100644 interfaces/kns/KCurlRequest.h
delete mode 100644 interfaces/kns/entrez-fetcher.h
delete mode 100644 interfaces/kns/url-fetcher.h
copy tools/util/test-sra-priv.h => interfaces/ncbi/vdb-blast-priv.h (76%)
create mode 100644 interfaces/ncbi/vdb-blast.h
copy libs/{ktst => blast}/Makefile (81%)
create mode 100644 libs/blast/blast.c
create mode 100644 libs/kfs/from_to_namelist.c
copy interfaces/cc/icc/compiler.h => libs/klib/unix/misc.c (89%)
copy interfaces/cc/icc/compiler.h => libs/klib/win/misc.c (88%)
delete mode 100644 libs/kns/KCurlFile.c
delete mode 100644 libs/kns/KCurlRequest.c
delete mode 100644 libs/kns/curlhdr/curl.h
delete mode 100644 libs/kns/curlhdr/curlver.h
delete mode 100644 libs/kns/curlhdr/easy.h
delete mode 100644 libs/kns/curlhdr/multi.h
delete mode 100644 libs/kns/curlhdr/types.h
delete mode 100644 libs/kns/entrez-fetcher.c
delete mode 100644 libs/kns/kns_mgr_priv.h
copy libs/kns/{unix => linux}/sysendpoint.c (85%)
create mode 100644 libs/kns/linux/syspoll.c
rename libs/kns/{unix => mac}/sysendpoint.c (100%)
create mode 100644 libs/kns/mac/syspoll.c
create mode 100644 libs/kns/manager.c
copy libs/{kproc/win/syslock-priv.h => kns/mgr-priv.h} (81%)
rename interfaces/kns/curl-file.h => libs/kns/poll-priv.h (83%)
copy interfaces/cc/gcc/compiler.h => libs/kns/sysmgr.h (93%)
create mode 100644 libs/kns/undyinghttp.c
delete mode 100644 libs/vfs/keyring-priv.h
--
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