Aaron M. Ucko pushed to branch upstream at Debian Med / ncbi-vdb
Commits: 1234be86 by Aaron M. Ucko at 2025-04-02T21:06:48-04:00 New upstream version 3.2.1+dfsg - - - - - 285 changed files: - CHANGES.md - build/Makefile.env - build/Makefile.vers - build/common.cmake - interfaces/insdc/sra.h - interfaces/insdc/sra.vschema - interfaces/kdb/consistency-check.h - interfaces/kdb/database.h - interfaces/kdb/kdb-priv.h - interfaces/kdb/manager.h - interfaces/vdb/page-map-priv.h → interfaces/kdb/page-map-priv.h - libs/vdb/page-map.h → interfaces/kdb/page-map.h - interfaces/kfc/ctx.h - interfaces/kfg/kfg-priv.h - interfaces/klib/vdb_release_version.h - interfaces/ncbi/vdb-blast.h - − interfaces/search/grep.h - − interfaces/search/nucstrstr.h - − interfaces/search/ref-variation.h - interfaces/vdb/manager.h - interfaces/vdb/table.h - interfaces/vdb/vdb-priv.h - interfaces/vfs/manager.h - interfaces/vfs/path-priv.h - interfaces/vfs/path.h - libs/CMakeLists.txt - libs/axf/align-ref-name.c - libs/axf/cigar.c - libs/axf/get-sam-flags.c - libs/axf/ref-preserve_qual.c - libs/axf/ref-restore-read.c - libs/axf/refseq.c - libs/axf/restore-read.c - libs/axf/seq-restore-linkage-group.c - libs/axf/wgs.c - libs/axf/wgs.h - libs/blast/blast-mgr.c - libs/cloud/aws-auth.c - libs/cloud/aws.c - libs/cloud/cloud.c - libs/cloud/gcp.c - libs/kapp/args.c - libs/kapp/main.c - libs/kdb/CMakeLists.txt - + libs/kdb/ColumnBlob.hpp - + libs/kdb/RColumnBlob.cpp - libs/kdb/wcolumnblob.c → libs/kdb/WColumnBlob.cpp - libs/kdb/btree.c - interfaces/search/smith-waterman.h → libs/kdb/coldata.c - interfaces/search/extern.h → libs/kdb/coldata.h - libs/kdb/column-cc.c - libs/kdb/columnblob-base.c → libs/kdb/columnblob-base.cpp - libs/kdb/database-base.c - libs/kdb/database-cc.c - libs/kdb/dbmgr-cmn.c - libs/kdb/index-base.c - libs/kdb/index-cmn.c - libs/kdb/index-cmn.h - libs/kdb/kdb-cmn.c - libs/kdb/kdb-cmn.h - libs/kdb/libkdb.vers.h - libs/kdb/manager-base.c - libs/kdb/manager-base.h - libs/vdb/page-map.c → libs/kdb/page-map.c - libs/kdb/rcoldata.c - libs/kdb/rcoldata.h - libs/kdb/rcolidx.c - libs/kdb/rcolidx2.c - libs/kdb/rcolumn.c - − libs/kdb/rcolumnblob.c - libs/kdb/rcolumnblob.h - libs/kdb/rdatabase.c - libs/kdb/rdbmgr.c - libs/kdb/rdbmgr.h - libs/kdb/rindex.c - libs/kdb/rmeta.c - libs/kdb/rtable.c - libs/kdb/rtrieidx-v2.c - libs/kdb/table-base.c - libs/kdb/table-cc.c - libs/kdb/wcoldata.c - libs/kdb/wcoldata.h - libs/kdb/wcolumn.c - libs/kdb/wcolumnblob.h - libs/kdb/wdatabase.c - libs/kdb/wdbmgr.c - libs/kdb/widxblk.c - libs/kdb/windex.c - libs/kdb/wkdb.c - libs/kdb/wmeta.c - libs/kdb/wtable.c - libs/kdb/wtrieidx-v1.c - libs/kdb/wtrieidx-v2.c - libs/kdbtext/api-manager.cpp - libs/kdbtext/column.cpp - libs/kdbtext/column.hpp - libs/kdbtext/columnblob.cpp - libs/kdbtext/columnblob.hpp - libs/kdbtext/manager.cpp - libs/kfg/kfg-priv.h - libs/kfg/ngc.c - libs/kfs/arc.c - libs/kfs/cacheteefile3.c - libs/kfs/unix/sysdll.c - libs/kns/http-file.c - libs/kns/http-priv.h - libs/kns/http-request.c - libs/kns/manager.c - libs/krypto/CMakeLists.txt - libs/krypto/aes-byte.c - libs/krypto/aes-priv.h - libs/krypto/aes_core.c - libs/ncbi-vdb/CMakeLists.txt - libs/ncbi-vdb/libncbi-vdb.vers - − libs/search/CMakeLists.txt - − libs/search/Makefile - − libs/search/agrep-dp.c - − libs/search/agrep-myers.c - − libs/search/agrep-myersunltd.c - − libs/search/agrep-wumanber.c - − libs/search/fgrep-aho.c - − libs/search/fgrep-boyermoore.c - − libs/search/fgrep-dumb.c - − libs/search/nucstrstr.c - − libs/search/search-priv.h - − libs/search/search.c - − libs/search/sw-search.c - libs/sra/reader-cmn.c - libs/sra/reader-fastq.c - libs/sra/reader-illumina.c - libs/sra/reader-sff.c - libs/sra/sracache.c - libs/sra/sratbl-cmn.c - libs/sra/wsratbl.c - libs/sraxf/dna-from-color.c - libs/sraxf/dynamic-454-read-descriptor.c - libs/sraxf/extract-coordinates.c - libs/sraxf/extract-name_coord.c - libs/sraxf/extract-name_fmt.c - libs/sraxf/extract-spot_name.c - libs/sraxf/format-spot-name.c - libs/sraxf/fpcodec.c - libs/sraxf/index_lookup.c - libs/sraxf/make-position.c - libs/sraxf/normalize.c - libs/sraxf/process-position.c - libs/sraxf/qual4_decode.c - libs/sraxf/qual4_encode.c - libs/sraxf/read-desc.c - libs/sraxf/read-seg-from-readn.c - libs/sraxf/rewrite-spot-name.c - libs/sraxf/rna-flag-common.c - libs/sraxf/set-rna-flag.c - libs/sraxf/spot-check.c - libs/sraxf/stats.c - libs/sraxf/syn_quality.c - libs/sraxf/tokenize-spot_name-454.c - libs/sraxf/tokenize-spot_name-abi.c - libs/sraxf/tokenize-spot_name-generic-fastq.c - libs/sraxf/tokenize-spot_name-helicos.c - libs/sraxf/tokenize-spot_name-illumina.c - libs/sraxf/tokenize-spot_name-ion-torrent.c - libs/sraxf/use-rna-flag.c - libs/sraxf/v0-decompress-local.h - libs/sraxf/v0-decompress.c - libs/sraxf/varloc.c - libs/vdb/CMakeLists.txt - libs/vdb/blob.c - libs/vdb/bytecode.c - libs/vdb/column-cmn.c - libs/vdb/compare.c - libs/vdb/cursor-table.c - libs/vdb/database-cmn.c - libs/vdb/database-depend.c - libs/vdb/dbmgr-cmn.c - libs/vdb/delta_average.c - libs/vdb/index_lookup.c - libs/vdb/index_project.c - libs/vdb/libvdb.vers.h - libs/vdb/linker-int.c - libs/vdb/linker-priv.h - libs/vdb/merge.c - libs/vdb/prod-cmn.c - libs/vdb/redimension.c - libs/vdb/split.c - libs/vdb/transpose.c - libs/vdb/wcolumn.c - libs/vdb/wcursor.c - libs/vdb/wphys.c - libs/vfs/manager.c - libs/vfs/names4-response.c - libs/vfs/path-priv.h - libs/vfs/path.c - libs/vfs/remote-services.c - libs/vfs/resolver-priv.h - libs/vfs/resolver.c - libs/vfs/sdl-response.c - libs/vfs/services-cache.c - libs/vfs/services-priv.h - libs/vfs/services.c - libs/vfs/srv-response.c - py_vdb/L1-manager.py - py_vdb/L10-fastq.py - py_vdb/L11-table_copy.py - py_vdb/L2-table_read.py - py_vdb/L3-table_write.py - py_vdb/L4-database_read.py - py_vdb/L5-database_write.py - py_vdb/L6-meta_read.py - py_vdb/L7-table-rnd-write.py - py_vdb/L8-import-csv.py - py_vdb/L9-index_usage.py - + py_vdb/find_ncbi_vdb.py - py_vdb/vdb.py - test/CMakeLists.txt - test/kdb/CMakeLists.txt - test/kdb/kdb.hpp - test/kdb/remote_open_test.cpp - test/vdb/test-pagemap.cpp → test/kdb/test-pagemap.cpp - + test/kdb/test-rblob.cpp - test/kdb/test-rcolumn.cpp - test/kdb/test-rdatabase.cpp - test/kdb/test-rtable.cpp - + test/kdb/test-wblob.cpp - test/kdb/test-wcolumn.cpp - test/kdb/test-wmanager.cpp - test/kdb/test-wtable.cpp - + test/kdb/testdb.kar - libs/search/.gitignore → test/kdb/testdb/tbl/SEQUENCE/col/READ/data - + test/kdb/testdb/tbl/SEQUENCE/col/READ/idx - + test/kdb/testdb/tbl/SEQUENCE/col/READ/idx0 - test/kdbtext/test-blob.cpp - test/kdbtext/test-column.cpp - test/kfg/kfgtest.cpp - test/kns/CMakeLists.txt - test/kns/knstest.cpp - test/kns/test-connect.cpp - test/kns/test-http-request.cpp - + test/kns/test-opt-bitmap.cpp - test/kns/test-proxy-with-scheme.cpp - test/kns/test-proxy-with-scheme.sh - test/kns/test-proxy-with-scheme_failure.cpp - test/ktst/CMakeLists.txt - + test/ktst/tsan.suppressions - test/schema/CMakeLists.txt - test/schema/test-schema-diff.sh - − test/schema/test_VDB-5250.py - − test/schema/test_VDB-5251.py - test/schema/wb-test-schema-ast.cpp - − test/search/CMakeLists.txt - − test/search/Makefile - − test/search/PerfCounter.h - − test/search/agrep-main.c - − test/search/search-vdb.cpp - − test/search/search-vdb.h - − test/search/test-agrep.cpp - test/vdb/CMakeLists.txt - test/vdb/WVDB_Fixture.hpp - test/vdb/test-VDB-4156.cpp - libs/search/debug.h → test/vdb/test-VDBManagerGetObjVersion.cpp - + test/vdb/test-linker.cpp - test/vdb/test-textvdb.cpp - test/vdb/test-vdb.cpp - test/vdb/test-view.cpp - test/vdb/test-wvdb.cpp - test/vfs/CMakeLists.txt - + test/vfs/SRR045450/SRR045450.sra - + test/vfs/SRR599578/SRR599578.sralite - test/vfs/Test_VFS_resolver_dflt.cpp - + test/vfs/data/SRR053325.sra - + test/vfs/data/SRR600096.sralite - test/vfs/test-json-response.cpp - test/vfs/test-resolver-with-log.cpp - test/vfs/test-sdl-response.cpp - + test/vfs/test-vfs-resolve.cpp - libs/kdb/columnblob-base.h → test/vfs/test-vpath-open-read-update.cpp - + test/vfs/test-vpath-open-read-update.h - + test/vfs/test-vpath-open-read.cpp - + test/vfs/test-vpath-open-read.h - + test/vfs/test-vpath-open-update-read.cpp - + test/vfs/test-vpath-open-update-read.h - + test/vfs/test-vpath-open-update-update.cpp - + test/vfs/test-vpath-open-update-update.h - + test/vfs/test-vpath-open.hpp - test/vfs/test_VFS_cache_sdl.cpp The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/commit/1234be86b48699a7f07b259ae285ac2a953c0ae9 -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/commit/1234be86b48699a7f07b259ae285ac2a953c0ae9 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
