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tille pushed a change to branch upstream
in repository sra-sdk.
from a84ff91 Imported Upstream version 2.3.3-4~dfsg
new f14de0e Imported Upstream version 2.3.4-2+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:
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 +
interfaces/klib/{time.h => sra-release-version.h} | 81 +-
interfaces/kns/KCurlRequest.h | 4 +
interfaces/kns/ascp.h | 9 +-
.../{cc/gcc/i386/strtol.h => kns/manager-ext.h} | 34 +-
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 +-
.../cc/vc++/stdbool.h => libs/klib/release-vers.h | 29 +-
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 ++++
.../sra-pileup/ref_regions.h | 75 +-
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/util/{syspass-priv.h => test-sra-priv.h} | 12 +-
tools/util/test-sra.c | 977 ++++++--
tools/util/test-sra.vers | 2 +-
tools/util/testld.vers | 2 +-
tools/util/txt2kdb.vers | 2 +-
tools/util/unix/{syspass.c => PrintOS.c} | 52 +-
tools/util/vdb-lock.vers | 2 +-
tools/util/vdb-passwd.vers | 2 +-
tools/util/vdb-unlock.vers | 2 +-
tools/util/{unix/syspass.c => win/PrintOS.c} | 52 +-
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 +-
.../out_redir.c => vdb-dump/vdb-dump-redir.c} | 4 +-
.../out_redir.h => vdb-dump/vdb-dump-redir.h} | 6 +-
tools/vdb-dump/vdb-dump.c | 274 +-
tools/vdb-dump/vdb-dump.vers | 2 +-
tools/vdb-validate/vdb-validate.vers | 2 +-
297 files changed, 9823 insertions(+), 4266 deletions(-)
copy interfaces/klib/{time.h => sra-release-version.h} (50%)
copy interfaces/{cc/gcc/i386/strtol.h => kns/manager-ext.h} (75%)
delete mode 100644 libs/align/libalign-access.vers
delete mode 100644 libs/align/libalign-reader.vers
delete mode 100644 libs/align/libncbi-bam.vers
delete mode 100644 libs/axf/libaxf.vers
delete mode 100644 libs/axf/libwaxf.vers
delete mode 100644 libs/ext/Makefile
delete mode 100644 libs/ext/bzip2/Makefile
delete mode 100644 libs/ext/curl/Makefile
delete mode 100644 libs/ext/zlib/Makefile
delete mode 100644 libs/kapp/libkapp.vers
delete mode 100644 libs/kapp/libload.vers
delete mode 100644 libs/kdb/libkdb.vers
delete mode 100644 libs/kdb/libwkdb.vers
delete mode 100644 libs/kfg/libkfg.vers
delete mode 100644 libs/kfs/libkdl.vers
delete mode 100644 libs/kfs/libkff.vers
delete mode 100644 libs/kfs/libkfs.vers
delete mode 100644 libs/klib/libkascii.vers
delete mode 100644 libs/klib/libklib.vers
delete mode 100644 libs/klib/libktlog.vers
delete mode 100644 libs/klib/libkutf8.vers
copy interfaces/cc/vc++/stdbool.h => libs/klib/release-vers.h (76%)
create mode 100644 libs/klib/sra-release-version.c
create mode 100644 libs/kns/kns_manager-ext.c
delete mode 100644 libs/kns/libkns.vers
delete mode 100644 libs/kns/libkurl.vers
delete mode 100644 libs/kproc/libkproc.vers
delete mode 100644 libs/kproc/libkq.vers
delete mode 100644 libs/kproc/libksproc.vers
delete mode 100644 libs/krypto/libkrypto.vers
delete mode 100644 libs/krypto/libkryptotest.vers
delete mode 100644 libs/kxml/libkxfs.vers
delete mode 100644 libs/kxml/libkxml.vers
delete mode 100644 libs/search/libksrch.vers
delete mode 100644 libs/search/libnucstrstr.vers
delete mode 100644 libs/sra/libsra-schema.vers
delete mode 100644 libs/sra/libsradb.vers
delete mode 100644 libs/sra/libsrareader.vers
delete mode 100644 libs/sra/libsraschema.vers
delete mode 100644 libs/sra/libwsra-schema.vers
delete mode 100644 libs/sra/libwsradb.vers
delete mode 100644 libs/sra/libwsraschema.vers
delete mode 100644 libs/sraxf/libsraxf.vers
delete mode 100644 libs/sraxf/libwsraxf.vers
delete mode 100644 libs/vdb/libvdb.vers
delete mode 100644 libs/vdb/libwvdb.vers
delete mode 100644 libs/vfs/libsrapath.vers
delete mode 100644 libs/vfs/libvfs.vers
delete mode 100644 libs/vxf/libvxf.vers
delete mode 100644 libs/vxf/libwvxf.vers
delete mode 100644 libs/wgsxf/libwgsxf.vers
delete mode 100644 libs/wgsxf/libwwgsxf.vers
create mode 100644 tools/bam-loader/bam-load.3.vers
create mode 100644 tools/sra-load/pacbio-loadxml.vers
create mode 100644 tools/sra-pileup/ref_regions.c
copy libs/kdb/wdatabase-priv.h => tools/sra-pileup/ref_regions.h (54%)
create mode 100644 tools/sra-pileup/ref_walker.c
create mode 100644 tools/sra-pileup/ref_walker.h
create mode 100644 tools/util/md5cp.vers
create mode 100644 tools/util/schema-replace.vers
copy tools/util/{syspass-priv.h => test-sra-priv.h} (88%)
copy tools/util/unix/{syspass.c => PrintOS.c} (58%)
copy tools/util/{unix/syspass.c => win/PrintOS.c} (55%)
create mode 100644 tools/vdb-dump/vdb-dump-fastq.c
copy tools/{sra-pileup/reref.h => vdb-dump/vdb-dump-fastq.h} (85%)
copy tools/{sra-pileup/out_redir.c => vdb-dump/vdb-dump-redir.c} (96%)
copy tools/{sra-pileup/out_redir.h => vdb-dump/vdb-dump-redir.h} (91%)
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