New upstream version 2.17.0+ds
authorAaron M. Ucko <ucko@debian.org>
Sun, 28 Sep 2025 00:39:42 +0000 (20:39 -0400)
committerAaron M. Ucko <ucko@debian.org>
Sun, 28 Sep 2025 00:39:42 +0000 (20:39 -0400)
commit66447a51caa24672ca571dc7f92d822ffd3b8874
tree45d616f6236ed691022925084ebed29a292d6149
parente69e9a2f4c6f482245434666ca15379112a6cdfe
New upstream version 2.17.0+ds
1983 files changed:
c++/compilers/.gitignore [new file with mode: 0644]
c++/compilers/unix/GCC.sh
c++/compilers/unix/ICC.sh
c++/compilers/vs2019/static/build/util/regexp/regexp.lib.vcxproj
c++/compilers/vs2022/Makefile.WinMain.app.msvc [new file with mode: 0644]
c++/compilers/vs2022/Makefile.wxWidgets.app.msvc [new file with mode: 0644]
c++/compilers/vs2022/build.sh [new file with mode: 0644]
c++/compilers/vs2022/build_exec.bat [new file with mode: 0644]
c++/compilers/vs2022/build_util.sh [new file with mode: 0644]
c++/compilers/vs2022/check.sh [new file with mode: 0644]
c++/compilers/vs2022/configure.bat [new file with mode: 0644]
c++/compilers/vs2022/datatool.bat [new file with mode: 0644]
c++/compilers/vs2022/dll/build/UtilityProjects/_CONFIGURE_.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/dll/build/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/dll/build/UtilityProjects/configure._ [new file with mode: 0644]
c++/compilers/vs2022/dll/build/UtilityProjects/configure_dialog._ [new file with mode: 0644]
c++/compilers/vs2022/dll/build/all.bat [new file with mode: 0644]
c++/compilers/vs2022/dll/build/all_gbench.bat [new file with mode: 0644]
c++/compilers/vs2022/dll/build/all_gui.bat [new file with mode: 0644]
c++/compilers/vs2022/dll/build/all_ncbi.bat [new file with mode: 0644]
c++/compilers/vs2022/dll/build/gbench/UtilityProjects/_CONFIGURE_.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/dll/build/gbench/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/dll/build/gbench/UtilityProjects/configure._ [new file with mode: 0644]
c++/compilers/vs2022/dll/build/gbench/UtilityProjects/configure_dialog._ [new file with mode: 0644]
c++/compilers/vs2022/dll/build/gbench/configure_prebuild.bat [new file with mode: 0644]
c++/compilers/vs2022/dll/build/gbench/gbench_install/gbench-install.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/dll/build/gbench/ncbi_gbench.sln [new file with mode: 0644]
c++/compilers/vs2022/dll/build/gui/UtilityProjects/_CONFIGURE_.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/dll/build/gui/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/dll/build/gui/UtilityProjects/configure._ [new file with mode: 0644]
c++/compilers/vs2022/dll/build/gui/UtilityProjects/configure_dialog._ [new file with mode: 0644]
c++/compilers/vs2022/dll/build/gui/ncbi_gui_dll.sln [new file with mode: 0644]
c++/compilers/vs2022/dll/build/internal/gbench/gbench_install_internal/gbench-install-internal.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/dll/build/ncbi_cpp_dll.sln [new file with mode: 0644]
c++/compilers/vs2022/dll/dll_main.cpp [new file with mode: 0644]
c++/compilers/vs2022/dll/third_party_dll_install.mak [new file with mode: 0644]
c++/compilers/vs2022/dll/third_party_dll_install.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/dll/third_party_msvcdll_install.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/install.sh [new file with mode: 0644]
c++/compilers/vs2022/lock_ptb_config.bat [new file with mode: 0644]
c++/compilers/vs2022/make.bat [new file with mode: 0644]
c++/compilers/vs2022/make_ncbi.bat [new file with mode: 0644]
c++/compilers/vs2022/msvcvars.bat [new file with mode: 0644]
c++/compilers/vs2022/ncbi.rc [new file with mode: 0644]
c++/compilers/vs2022/ncbilogo.ico [new file with mode: 0644]
c++/compilers/vs2022/protoc.bat [new file with mode: 0644]
c++/compilers/vs2022/ptb.bat [new file with mode: 0644]
c++/compilers/vs2022/retry.sh [new file with mode: 0644]
c++/compilers/vs2022/static/build/UtilityProjects/PTB.sln [new file with mode: 0644]
c++/compilers/vs2022/static/build/UtilityProjects/_CONFIGURE_.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/static/build/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/static/build/UtilityProjects/configure._ [new file with mode: 0644]
c++/compilers/vs2022/static/build/UtilityProjects/configure_dialog._ [new file with mode: 0644]
c++/compilers/vs2022/static/build/all.bat [new file with mode: 0644]
c++/compilers/vs2022/static/build/all_gui.bat [new file with mode: 0644]
c++/compilers/vs2022/static/build/all_ncbi.bat [new file with mode: 0644]
c++/compilers/vs2022/static/build/build-system/project_tree_builder/msbuild/msbuild_dataobj.lib.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/static/build/build-system/project_tree_builder/project_tree_builder.exe.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/static/build/corelib/xncbi.lib.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/static/build/gui/UtilityProjects/_CONFIGURE_.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/static/build/gui/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/static/build/gui/UtilityProjects/configure._ [new file with mode: 0644]
c++/compilers/vs2022/static/build/gui/UtilityProjects/configure_dialog._ [new file with mode: 0644]
c++/compilers/vs2022/static/build/gui/ncbi_gui.sln [new file with mode: 0644]
c++/compilers/vs2022/static/build/ncbi_cpp.sln [new file with mode: 0644]
c++/compilers/vs2022/static/build/serial/datatool/datatool.exe.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/static/build/serial/xser.lib.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/static/build/util/regexp/regexp.lib.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/static/build/util/xregexp/xregexp.lib.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/static/build/util/xutil.lib.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/static/third_party_msvcstatic_install.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/static/third_party_static_install.mak [new file with mode: 0644]
c++/compilers/vs2022/static/third_party_static_install.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/third_party_install.meta.mk [new file with mode: 0644]
c++/compilers/vs2022/user/build/UtilityProjects/_CONFIGURE_.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/user/build/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj [new file with mode: 0644]
c++/compilers/vs2022/user/build/UtilityProjects/configure._ [new file with mode: 0644]
c++/compilers/vs2022/user/build/UtilityProjects/configure_dialog._ [new file with mode: 0644]
c++/compilers/vs2022/user/build/ncbi_user.sln [new file with mode: 0644]
c++/compilers/xcode30_prj/configure
c++/compilers/xcode30_prj/postbuild.sh
c++/compilers/xcode30_prj/static/UtilityProjects/PTB.xcodeproj/project.pbxproj
c++/include/algo/blast/api/blast_dbindex.hpp
c++/include/algo/blast/api/blast_exception.hpp
c++/include/algo/blast/api/blast_node.hpp
c++/include/algo/blast/api/blast_options.hpp
c++/include/algo/blast/api/blast_prot_options.hpp
c++/include/algo/blast/api/blast_usage_report.hpp
c++/include/algo/blast/api/cdd_pssm_input.hpp
c++/include/algo/blast/blastinput/blast_args.hpp
c++/include/algo/blast/blastinput/blast_input_aux.hpp
c++/include/algo/blast/blastinput/cmdline_flags.hpp
c++/include/algo/blast/core/blast_engine.h
c++/include/algo/blast/core/blast_gapalign.h
c++/include/algo/blast/core/blast_message.h
c++/include/algo/blast/core/blast_options.h
c++/include/algo/blast/core/blast_sw.h
c++/include/algo/blast/core/phi_gapalign.h
c++/include/algo/blast/dbindex/dbindex.hpp
c++/include/algo/blast/format/data4xmlformat.hpp
c++/include/algo/blast/igblast/igblast.hpp
c++/include/algo/blast/proteinkmer/mhfile.hpp
c++/include/algo/blast/vdb/blastn_vdb_args.hpp
c++/include/algo/blast/vdb/seqsrc_vdb.h
c++/include/algo/blast/vdb/vdb2blast_util.hpp
c++/include/algo/blast/vdb/vdbblast_local.hpp
c++/include/cgi/caf_plain.hpp
c++/include/cgi/cgi_exception.hpp
c++/include/cgi/cgiapp.hpp
c++/include/cgi/cgictx.hpp
c++/include/cgi/fcgiapp_mt.hpp
c++/include/cgi/fcgiapp_st.hpp [new file with mode: 0644]
c++/include/common/boost_skew_guard.hpp
c++/include/common/config/ncbiconf_msvc.h
c++/include/common/config/ncbiconf_xcode.h
c++/include/common/metamodules_doxygen.h
c++/include/common/ncbi_build_info.h
c++/include/common/ncbi_export.h
c++/include/common/ncbi_package_ver.h
c++/include/common/ncbi_revision.h.in
c++/include/common/ncbi_sample_api.hpp [new file with mode: 0644]
c++/include/common/ncbi_sanitizers.h
c++/include/common/ncbi_sc_version.h
c++/include/common/ncbi_source_ver.h
c++/include/common/ncbiconf_impl.h
c++/include/common/test_data_path.h
c++/include/connect/error_codes.hpp
c++/include/connect/ext/ncbi_localnet.h
c++/include/connect/impl/connect_misc.hpp
c++/include/connect/impl/ncbi_servicep.h [new file with mode: 0644]
c++/include/connect/impl/ncbi_uv_nghttp2.hpp
c++/include/connect/ncbi_base64.h
c++/include/connect/ncbi_conn_stream.hpp
c++/include/connect/ncbi_conn_test.hpp
c++/include/connect/ncbi_connector.h
c++/include/connect/ncbi_connutil.h
c++/include/connect/ncbi_core.h
c++/include/connect/ncbi_ftp_connector.h
c++/include/connect/ncbi_http_connector.h
c++/include/connect/ncbi_http_session.hpp
c++/include/connect/ncbi_pipe.hpp
c++/include/connect/ncbi_pipe_connector.hpp
c++/include/connect/ncbi_service.h
c++/include/connect/ncbi_sftp.hpp [new file with mode: 0644]
c++/include/connect/ncbi_socket.h
c++/include/connect/ncbi_socket.hpp
c++/include/connect/ncbi_tls.h
c++/include/connect/ncbi_types.h
c++/include/connect/ncbi_usage_report.hpp
c++/include/connect/ncbi_util.h
c++/include/corelib/env_reg.hpp
c++/include/corelib/hash_impl/_hash_fun.h
c++/include/corelib/impl/ncbi_dbsvcmapper.hpp
c++/include/corelib/impl/std_backport.hpp [new file with mode: 0644]
c++/include/corelib/impl/stringutf8_deprecated.inl
c++/include/corelib/ncbi_base64.h
c++/include/corelib/ncbi_base_build_ver.h
c++/include/corelib/ncbi_pool_balancer.hpp
c++/include/corelib/ncbi_system.hpp
c++/include/corelib/ncbi_test.hpp [new file with mode: 0644]
c++/include/corelib/ncbi_url.hpp
c++/include/corelib/ncbiapp_api.hpp
c++/include/corelib/ncbidbg.hpp
c++/include/corelib/ncbidiag.hpp
c++/include/corelib/ncbienv.hpp
c++/include/corelib/ncbiexec.hpp
c++/include/corelib/ncbiexpt.hpp
c++/include/corelib/ncbifile.hpp
c++/include/corelib/ncbifloat.h
c++/include/corelib/ncbimisc.hpp
c++/include/corelib/ncbistd.hpp
c++/include/corelib/ncbistr.hpp
c++/include/corelib/ncbithr.hpp
c++/include/corelib/ncbitime.hpp
c++/include/corelib/phone_home_policy.hpp [new file with mode: 0644]
c++/include/corelib/request_ctx.hpp
c++/include/corelib/request_status.hpp
c++/include/corelib/stream_utils.hpp
c++/include/corelib/tempstr.hpp
c++/include/corelib/test_mt.hpp
c++/include/corelib/version.hpp
c++/include/corelib/version_api.hpp
c++/include/dbapi/dbapi.hpp
c++/include/dbapi/driver/dbapi_conn_factory.hpp
c++/include/dbapi/driver/dbapi_svc_mapper.hpp
c++/include/dbapi/driver/drivers.hpp
c++/include/dbapi/driver/impl/dbapi_impl_connection.hpp
c++/include/dbapi/driver/impl/dbapi_impl_context.hpp
c++/include/dbapi/driver/impl/dbapi_pool_balancer.hpp
c++/include/dbapi/driver/interfaces.hpp
c++/include/dbapi/driver/odbc/interfaces.hpp
c++/include/dbapi/driver/public.hpp
c++/include/dbapi/driver/util/blobstore.hpp
c++/include/misc/jsonwrapp/jsonwrapp11.hpp
c++/include/ncbi_pch.hpp
c++/include/ncbi_source_ver.h
c++/include/ncbiconf.h
c++/include/objects/blast/names.hpp
c++/include/objects/entrezgene/Entrezgene.hpp
c++/include/objects/general/Dbtag.hpp
c++/include/objects/general/User_field.hpp
c++/include/objects/macro/String_constraint.hpp
c++/include/objects/mla/.cvsignore.extra [deleted file]
c++/include/objects/mla/Error_val.hpp [deleted file]
c++/include/objects/seq/so_map.hpp
c++/include/objects/seqalign/Spliced_seg.hpp
c++/include/objects/seqfeat/BioSource.hpp
c++/include/objects/seqfeat/OrgMod.hpp
c++/include/objects/seqfeat/SeqFeatData.hpp
c++/include/objects/seqfeat/SubSource.hpp
c++/include/objects/seqloc/Seq_id.hpp
c++/include/objects/taxon1/local_taxon.hpp
c++/include/objects/trackmgr/displaytrack_client.hpp
c++/include/objects/trackmgr/gridrpcclient.hpp
c++/include/objects/valerr/ValidErrItem.hpp
c++/include/objects/valerr/ValidError.hpp
c++/include/objmgr/data_loader.hpp
c++/include/objmgr/impl/bioseq_base_info.hpp
c++/include/objmgr/impl/bioseq_sort.hpp [new file with mode: 0644]
c++/include/objmgr/impl/data_source.hpp
c++/include/objmgr/impl/scope_impl.hpp
c++/include/objmgr/impl/scope_info.hpp
c++/include/objmgr/impl/seq_id_sort.hpp
c++/include/objmgr/impl/tse_loadlock.hpp
c++/include/objmgr/scope.hpp
c++/include/objmgr/tse_handle.hpp
c++/include/objmgr/util/create_defline.hpp
c++/include/objtools/align_format/align_format_util.hpp
c++/include/objtools/align_format/format_flags.hpp
c++/include/objtools/align_format/showalign.hpp
c++/include/objtools/align_format/tabular.hpp
c++/include/objtools/align_format/taxFormat.hpp
c++/include/objtools/align_format/vectorscreen.hpp
c++/include/objtools/alnmgr/aln_asn_reader.hpp
c++/include/objtools/alnmgr/alntext.hpp
c++/include/objtools/blast/blastdb_format/blastdb_dataextract.hpp
c++/include/objtools/blast/gene_info_reader/file_utils.hpp [deleted file]
c++/include/objtools/blast/gene_info_reader/gene_info.hpp [deleted file]
c++/include/objtools/blast/gene_info_reader/gene_info_reader.hpp [deleted file]
c++/include/objtools/blast/seqdb_reader/impl/lmdb++.h [deleted file]
c++/include/objtools/blast/seqdb_reader/impl/seqdbatlas.hpp
c++/include/objtools/blast/seqdb_reader/impl/seqdbfile.hpp
c++/include/objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp
c++/include/objtools/blast/seqdb_reader/impl/seqdbisam.hpp
c++/include/objtools/blast/seqdb_reader/impl/seqdbvol.hpp
c++/include/objtools/blast/seqdb_reader/itax4blast.hpp
c++/include/objtools/blast/seqdb_reader/seqdb.hpp
c++/include/objtools/blast/seqdb_reader/seqdbcommon.hpp
c++/include/objtools/blast/seqdb_reader/tax4blastsqlite.hpp
c++/include/objtools/blast/seqdb_writer/build_db.hpp
c++/include/objtools/blast/seqdb_writer/writedb.hpp
c++/include/objtools/cleanup/capitalization_string.hpp
c++/include/objtools/cleanup/cleanup.hpp
c++/include/objtools/cleanup/cleanup_change.hpp
c++/include/objtools/cleanup/fix_feature_id.hpp
c++/include/objtools/cleanup/influenza_set.hpp
c++/include/objtools/data_loaders/genbank/blob_id.hpp
c++/include/objtools/data_loaders/genbank/gbloader.hpp
c++/include/objtools/data_loaders/genbank/gbnative.hpp
c++/include/objtools/data_loaders/genbank/impl/dispatcher.hpp
c++/include/objtools/data_loaders/genbank/impl/incr_time.hpp
c++/include/objtools/data_loaders/genbank/impl/info_cache.hpp
c++/include/objtools/data_loaders/genbank/impl/psg_blob_processor.hpp [new file with mode: 0644]
c++/include/objtools/data_loaders/genbank/impl/psg_cache.hpp [new file with mode: 0644]
c++/include/objtools/data_loaders/genbank/impl/psg_cdd.hpp [new file with mode: 0644]
c++/include/objtools/data_loaders/genbank/impl/psg_evloop.hpp [new file with mode: 0644]
c++/include/objtools/data_loaders/genbank/impl/psg_loader_impl.hpp
c++/include/objtools/data_loaders/genbank/impl/psg_processor.hpp [new file with mode: 0644]
c++/include/objtools/data_loaders/genbank/impl/psg_processors.hpp [new file with mode: 0644]
c++/include/objtools/data_loaders/genbank/impl/reader_id2_base.hpp
c++/include/objtools/data_loaders/genbank/impl/reader_service.hpp
c++/include/objtools/data_loaders/genbank/impl/statistics.hpp
c++/include/objtools/data_loaders/genbank/psg_loader.hpp
c++/include/objtools/data_loaders/genbank/reader.hpp
c++/include/objtools/data_loaders/genbank/reader_interface.hpp
c++/include/objtools/edit/dblink_field.hpp
c++/include/objtools/edit/eutils_updater.hpp
c++/include/objtools/edit/feattable_edit.hpp
c++/include/objtools/edit/field_handler.hpp
c++/include/objtools/edit/huge_asn_loader.hpp
c++/include/objtools/edit/huge_asn_reader.hpp
c++/include/objtools/edit/huge_file.hpp
c++/include/objtools/edit/huge_file_process.hpp
c++/include/objtools/edit/pub_fix.hpp
c++/include/objtools/edit/remote_updater.hpp
c++/include/objtools/eutils/api/efetch.hpp
c++/include/objtools/eutils/api/eutils.hpp
c++/include/objtools/format/cigar_formatter.hpp
c++/include/objtools/format/embl_formatter.hpp
c++/include/objtools/format/embl_gather.hpp
c++/include/objtools/format/feature_gather.hpp
c++/include/objtools/format/flat_expt.hpp
c++/include/objtools/format/flat_file_config.hpp
c++/include/objtools/format/flat_file_generator.hpp
c++/include/objtools/format/flat_file_html.hpp
c++/include/objtools/format/format_item_ostream.hpp
c++/include/objtools/format/ftable_gather.hpp
c++/include/objtools/format/gather_items.hpp
c++/include/objtools/format/gbseq_formatter.hpp
c++/include/objtools/format/genbank_formatter.hpp
c++/include/objtools/format/genbank_gather.hpp
c++/include/objtools/format/item_formatter.hpp
c++/include/objtools/format/items/flat_seqloc.hpp
c++/include/objtools/format/items/gap_item.hpp
c++/include/objtools/format/items/source_item.hpp
c++/include/objtools/format/ostream_text_ostream.hpp
c++/include/objtools/format/text_ostream.hpp
c++/include/objtools/pubseq_gateway/client/impl/misc.hpp
c++/include/objtools/pubseq_gateway/client/psg_client.hpp
c++/include/objtools/readers/agp_util.hpp
c++/include/objtools/readers/agp_validate_reader.hpp
c++/include/objtools/readers/aln_reader.hpp
c++/include/objtools/readers/bed_reader.hpp
c++/include/objtools/readers/co_generator.hpp [new file with mode: 0644]
c++/include/objtools/readers/fasta.hpp
c++/include/objtools/readers/fasta_exception.hpp
c++/include/objtools/readers/gff2_reader.hpp
c++/include/objtools/readers/gff3_location_merger.hpp
c++/include/objtools/readers/gff3_reader.hpp
c++/include/objtools/readers/gtf_reader.hpp
c++/include/objtools/readers/gvf_reader.hpp
c++/include/objtools/readers/idmapper.hpp
c++/include/objtools/readers/line_error.hpp
c++/include/objtools/readers/message_listener.hpp
c++/include/objtools/readers/mod_reader.hpp
c++/include/objtools/readers/reader_base.hpp
c++/include/objtools/readers/readfeat.hpp
c++/include/objtools/readers/source_mod_parser.hpp
c++/include/objtools/readers/struct_cmt_reader.hpp
c++/include/objtools/readers/table_filter.hpp
c++/include/objtools/readers/wiggle_reader.hpp
c++/include/serial/impl/objistr.inl
c++/include/serial/objectiter.hpp
c++/include/serial/objistr.hpp
c++/include/serial/objostr.hpp
c++/include/serial/streamiter.hpp
c++/include/sra/data_loaders/bam/impl/bamloader_impl.hpp
c++/include/sra/data_loaders/csra/impl/csraloader_impl.hpp
c++/include/sra/data_loaders/snp/impl/snploader_impl.hpp
c++/include/sra/data_loaders/vdbgraph/impl/vdbgraphloader_impl.hpp
c++/include/sra/data_loaders/wgs/impl/wgsloader_impl.hpp
c++/include/sra/readers/bam/bamgraph.hpp
c++/include/sra/readers/bam/bamindex.hpp
c++/include/sra/readers/bam/bamread.hpp
c++/include/sra/readers/bam/cache_with_lock.hpp
c++/include/sra/readers/ncbi_traces_path.hpp
c++/include/sra/readers/sra/csraread.hpp
c++/include/sra/readers/sra/exception.hpp
c++/include/sra/readers/sra/impl/wgs-contig.h
c++/include/sra/readers/sra/snpread.hpp
c++/include/sra/readers/sra/vdbcache.hpp
c++/include/sra/readers/sra/vdbread.hpp
c++/include/sra/readers/sra/wgsread.hpp
c++/include/util/bitset/bm.h
c++/include/util/bitset/bmaggregator.h
c++/include/util/bitset/bmalgo_impl.h
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