[med-svn] [sra-sdk] branch master updated (58c332f -> 5402fd3)
Andreas Tille
tille at debian.org
Wed Jul 30 12:22:34 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository sra-sdk.
from 58c332f lintian override for no-symbols-control-file
new e03f2ef Adapt get-orig-source target to new uscan implementation; use uversionmangle to get properly named download tarball
new 888f953 Imported Upstream version 2.3.5-2+dfsg
new d8167d7 Merge tag 'upstream/2.3.5-2+dfsg'
new 5ef56e1 Adapt patches to new upstream version
new 8dcca19 Ummm, we do not want to commit the patched files in Git ...
new 5402fd3 Upload to unstable
The 6 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 +-
debian/changelog | 8 +
debian/patches/10_portability.patch | 2 +-
debian/patches/build-with-system-libbz2-libz.patch | 2 +-
debian/patches/hardening.patch | 5 +-
debian/rules | 7 +-
debian/watch | 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/icc/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 +-
256 files changed, 19521 insertions(+), 11704 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/icc/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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