New upstream version 2.15.0+ds
authorAaron M. Ucko <ucko@debian.org>
Thu, 18 Jul 2024 01:22:59 +0000 (21:22 -0400)
committerAaron M. Ucko <ucko@debian.org>
Thu, 18 Jul 2024 01:22:59 +0000 (21:22 -0400)
commit67807fe08f09dc9e351c079626e9a84559c19386
tree1873a5831bf1bb6331bbe990a4a9a0ad0a5956a0
parent12379a63cc5affadbbcd17e292a8cb410c81dd91
New upstream version 2.15.0+ds
2848 files changed:
c++/compilers/cygwin/build.sh
c++/compilers/unix/GCC.sh
c++/compilers/unix/ICC.sh
c++/compilers/unix/Xcode.sh
c++/compilers/vs2017/Makefile.WinMain.app.msvc [deleted file]
c++/compilers/vs2017/Makefile.wxWidgets.app.msvc [deleted file]
c++/compilers/vs2017/build.sh [deleted file]
c++/compilers/vs2017/build_exec.bat [deleted file]
c++/compilers/vs2017/build_util.sh [deleted file]
c++/compilers/vs2017/check.sh [deleted file]
c++/compilers/vs2017/configure.bat [deleted file]
c++/compilers/vs2017/datatool.bat [deleted file]
c++/compilers/vs2017/dll/build/UtilityProjects/_CONFIGURE_.vcxproj [deleted file]
c++/compilers/vs2017/dll/build/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj [deleted file]
c++/compilers/vs2017/dll/build/UtilityProjects/configure._ [deleted file]
c++/compilers/vs2017/dll/build/UtilityProjects/configure_dialog._ [deleted file]
c++/compilers/vs2017/dll/build/all.bat [deleted file]
c++/compilers/vs2017/dll/build/all_gbench.bat [deleted file]
c++/compilers/vs2017/dll/build/all_gui.bat [deleted file]
c++/compilers/vs2017/dll/build/all_ncbi.bat [deleted file]
c++/compilers/vs2017/dll/build/gbench/UtilityProjects/_CONFIGURE_.vcxproj [deleted file]
c++/compilers/vs2017/dll/build/gbench/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj [deleted file]
c++/compilers/vs2017/dll/build/gbench/UtilityProjects/configure._ [deleted file]
c++/compilers/vs2017/dll/build/gbench/UtilityProjects/configure_dialog._ [deleted file]
c++/compilers/vs2017/dll/build/gbench/configure_prebuild.bat [deleted file]
c++/compilers/vs2017/dll/build/gbench/gbench_install/gbench-install.vcxproj [deleted file]
c++/compilers/vs2017/dll/build/gbench/ncbi_gbench.sln [deleted file]
c++/compilers/vs2017/dll/build/gui/UtilityProjects/_CONFIGURE_.vcxproj [deleted file]
c++/compilers/vs2017/dll/build/gui/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj [deleted file]
c++/compilers/vs2017/dll/build/gui/UtilityProjects/configure._ [deleted file]
c++/compilers/vs2017/dll/build/gui/UtilityProjects/configure_dialog._ [deleted file]
c++/compilers/vs2017/dll/build/gui/ncbi_gui_dll.sln [deleted file]
c++/compilers/vs2017/dll/build/internal/gbench/gbench_install_internal/gbench-install-internal.vcxproj [deleted file]
c++/compilers/vs2017/dll/build/ncbi_cpp_dll.sln [deleted file]
c++/compilers/vs2017/dll/dll_main.cpp [deleted file]
c++/compilers/vs2017/dll/third_party_dll_install.mak [deleted file]
c++/compilers/vs2017/dll/third_party_dll_install.vcxproj [deleted file]
c++/compilers/vs2017/dll/third_party_msvcdll_install.vcxproj [deleted file]
c++/compilers/vs2017/install.sh [deleted file]
c++/compilers/vs2017/lock_ptb_config.bat [deleted file]
c++/compilers/vs2017/make.bat [deleted file]
c++/compilers/vs2017/make_ncbi.bat [deleted file]
c++/compilers/vs2017/msvcvars.bat [deleted file]
c++/compilers/vs2017/ncbi.rc [deleted file]
c++/compilers/vs2017/ncbilogo.ico [deleted file]
c++/compilers/vs2017/protoc.bat [deleted file]
c++/compilers/vs2017/ptb.bat [deleted file]
c++/compilers/vs2017/static/build/UtilityProjects/PTB.sln [deleted file]
c++/compilers/vs2017/static/build/UtilityProjects/_CONFIGURE_.vcxproj [deleted file]
c++/compilers/vs2017/static/build/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj [deleted file]
c++/compilers/vs2017/static/build/UtilityProjects/configure._ [deleted file]
c++/compilers/vs2017/static/build/UtilityProjects/configure_dialog._ [deleted file]
c++/compilers/vs2017/static/build/all.bat [deleted file]
c++/compilers/vs2017/static/build/all_gui.bat [deleted file]
c++/compilers/vs2017/static/build/all_ncbi.bat [deleted file]
c++/compilers/vs2017/static/build/build-system/project_tree_builder/msbuild/msbuild_dataobj.lib.vcxproj [deleted file]
c++/compilers/vs2017/static/build/build-system/project_tree_builder/project_tree_builder.exe.vcxproj [deleted file]
c++/compilers/vs2017/static/build/corelib/xncbi.lib.vcxproj [deleted file]
c++/compilers/vs2017/static/build/gui/UtilityProjects/_CONFIGURE_.vcxproj [deleted file]
c++/compilers/vs2017/static/build/gui/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj [deleted file]
c++/compilers/vs2017/static/build/gui/UtilityProjects/configure._ [deleted file]
c++/compilers/vs2017/static/build/gui/UtilityProjects/configure_dialog._ [deleted file]
c++/compilers/vs2017/static/build/gui/ncbi_gui.sln [deleted file]
c++/compilers/vs2017/static/build/ncbi_cpp.sln [deleted file]
c++/compilers/vs2017/static/build/serial/datatool/datatool.exe.vcxproj [deleted file]
c++/compilers/vs2017/static/build/serial/xser.lib.vcxproj [deleted file]
c++/compilers/vs2017/static/build/util/regexp/regexp.lib.vcxproj [deleted file]
c++/compilers/vs2017/static/build/util/xregexp/xregexp.lib.vcxproj [deleted file]
c++/compilers/vs2017/static/build/util/xutil.lib.vcxproj [deleted file]
c++/compilers/vs2017/static/third_party_msvcstatic_install.vcxproj [deleted file]
c++/compilers/vs2017/static/third_party_static_install.mak [deleted file]
c++/compilers/vs2017/static/third_party_static_install.vcxproj [deleted file]
c++/compilers/vs2017/third_party_install.meta.mk [deleted file]
c++/compilers/vs2017/user/build/UtilityProjects/_CONFIGURE_.vcxproj [deleted file]
c++/compilers/vs2017/user/build/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj [deleted file]
c++/compilers/vs2017/user/build/UtilityProjects/configure._ [deleted file]
c++/compilers/vs2017/user/build/UtilityProjects/configure_dialog._ [deleted file]
c++/compilers/vs2017/user/build/ncbi_user.sln [deleted file]
c++/compilers/vs2019/build.sh
c++/compilers/vs2019/build_exec.bat
c++/compilers/vs2019/check.sh
c++/compilers/vs2019/dll/build/gbench/gbench_install/gbench-install.vcxproj
c++/compilers/vs2019/dll/build/gui/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj
c++/compilers/vs2019/dll/third_party_msvcdll_install.vcxproj
c++/compilers/vs2019/install.sh
c++/compilers/vs2019/make.bat
c++/compilers/vs2019/protoc.bat
c++/compilers/vs2019/ptb.bat
c++/compilers/vs2019/retry.sh [new file with mode: 0644]
c++/compilers/vs2019/static/build/build-system/project_tree_builder/msbuild/msbuild_dataobj.lib.vcxproj
c++/compilers/vs2019/static/build/build-system/project_tree_builder/project_tree_builder.exe.vcxproj
c++/compilers/vs2019/static/build/corelib/xncbi.lib.vcxproj
c++/compilers/vs2019/static/build/serial/datatool/datatool.exe.vcxproj
c++/compilers/vs2019/static/build/serial/xser.lib.vcxproj
c++/compilers/vs2019/static/build/util/regexp/regexp.lib.vcxproj
c++/compilers/vs2019/static/build/util/xregexp/xregexp.lib.vcxproj
c++/compilers/vs2019/static/build/util/xutil.lib.vcxproj
c++/compilers/vs2019/static/third_party_msvcstatic_install.vcxproj
c++/compilers/xcode30_prj/configure
c++/compilers/xcode30_prj/datatool.sh
c++/compilers/xcode30_prj/postbuild.sh [new file with mode: 0755]
c++/compilers/xcode30_prj/ptb.sh
c++/compilers/xcode30_prj/static/UtilityProjects/PTB.xcodeproj/project.pbxproj
c++/configure
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/local_blast.hpp
c++/include/algo/blast/api/magicblast.hpp
c++/include/algo/blast/api/remote_blast.hpp
c++/include/algo/blast/api/search_strategy.hpp
c++/include/algo/blast/blastinput/blast_args.hpp
c++/include/algo/blast/blastinput/blast_input.hpp
c++/include/algo/blast/blastinput/blast_input_aux.hpp
c++/include/algo/blast/blastinput/blastn_args.hpp
c++/include/algo/blast/blastinput/blastp_args.hpp
c++/include/algo/blast/blastinput/blastx_args.hpp
c++/include/algo/blast/blastinput/cmdline_flags.hpp
c++/include/algo/blast/blastinput/rpsblast_args.hpp
c++/include/algo/blast/blastinput/rpstblastn_args.hpp
c++/include/algo/blast/blastinput/tblastn_args.hpp
c++/include/algo/blast/core/blast_aalookup.h
c++/include/algo/blast/core/blast_engine.h
c++/include/algo/blast/core/blast_message.h
c++/include/algo/blast/core/blast_options.h
c++/include/algo/blast/core/blast_util.h
c++/include/algo/blast/core/ncbi_std.h
c++/include/algo/blast/format/blast_format.hpp
c++/include/algo/blast/format/vecscreen_run.hpp
c++/include/algo/blast/igblast/igblast.hpp
c++/include/algo/blast/proteinkmer/mhfile.hpp
c++/include/algo/blast/vdb/blastn_vdb_args.hpp [new file with mode: 0644]
c++/include/algo/blast/vdb/seqsrc_vdb.h [new file with mode: 0644]
c++/include/algo/blast/vdb/tblastn_vdb_args.hpp [new file with mode: 0644]
c++/include/algo/blast/vdb/vdb2blast_util.hpp [new file with mode: 0644]
c++/include/algo/blast/vdb/vdbalias.hpp [new file with mode: 0644]
c++/include/algo/blast/vdb/vdbblast_local.hpp [new file with mode: 0644]
c++/include/algo/dustmask/symdust.hpp
c++/include/algo/winmask/seq_masker.hpp
c++/include/algo/winmask/seq_masker_istat.hpp
c++/include/algo/winmask/seq_masker_istat_factory.hpp
c++/include/algo/winmask/seq_masker_ostat.hpp
c++/include/algo/winmask/win_mask_config.hpp
c++/include/algo/winmask/win_mask_gen_counts.hpp
c++/include/algo/winmask/win_mask_util.hpp
c++/include/cgi/cgiapp.hpp
c++/include/cgi/cgiapp_cached.hpp
c++/include/cgi/cgictx.hpp
c++/include/cgi/error_codes.hpp
c++/include/cgi/fcgiapp_mt.hpp [new file with mode: 0644]
c++/include/cgi/ncbicgi.hpp
c++/include/common/config/ncbiconf_msvc.h
c++/include/common/config/ncbiconf_xcode.h
c++/include/common/ncbi_build_info.h
c++/include/common/ncbi_build_ver.cmake_nodep [new file with mode: 0644]
c++/include/common/ncbi_export.h
c++/include/common/ncbi_package_ver.h
c++/include/common/ncbi_revision.h.in
c++/include/common/ncbi_sanitizers.h
c++/include/common/ncbi_sc_version.h [new file with mode: 0644]
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_crypt.h [new file with mode: 0644]
c++/include/connect/ext/ncbi_dblb.h [new file with mode: 0644]
c++/include/connect/ext/ncbi_dblb_svcmapper.hpp [new file with mode: 0644]
c++/include/connect/ext/ncbi_ifconf.h [new file with mode: 0644]
c++/include/connect/ext/ncbi_localnet.h [new file with mode: 0644]
c++/include/connect/impl/connect_misc.hpp
c++/include/connect/impl/ncbi_uv_nghttp2.hpp
c++/include/connect/impl/server_connection.hpp
c++/include/connect/ncbi_buffer.h
c++/include/connect/ncbi_conn_stream.hpp
c++/include/connect/ncbi_conn_test.hpp
c++/include/connect/ncbi_connection.h
c++/include/connect/ncbi_connector.h
c++/include/connect/ncbi_connutil.h
c++/include/connect/ncbi_core.h
c++/include/connect/ncbi_core_cxx.hpp
c++/include/connect/ncbi_ftp_connector.h
c++/include/connect/ncbi_gnutls.h
c++/include/connect/ncbi_heapmgr.h
c++/include/connect/ncbi_http2_session.hpp
c++/include/connect/ncbi_http_session.hpp
c++/include/connect/ncbi_iprange.h
c++/include/connect/ncbi_ipv6.h
c++/include/connect/ncbi_lbos.hpp [deleted file]
c++/include/connect/ncbi_localip.h
c++/include/connect/ncbi_mbedtls.h
c++/include/connect/ncbi_monkey.hpp
c++/include/connect/ncbi_namedpipe.hpp
c++/include/connect/ncbi_pipe.hpp
c++/include/connect/ncbi_server_info.h
c++/include/connect/ncbi_service.h
c++/include/connect/ncbi_service.hpp
c++/include/connect/ncbi_service_cxx.hpp
c++/include/connect/ncbi_socket.h
c++/include/connect/ncbi_socket.hpp
c++/include/connect/ncbi_tls.h
c++/include/connect/ncbi_util.h
c++/include/connect/services/json_over_uttp.hpp
c++/include/corelib/atomic_util.hpp [new file with mode: 0644]
c++/include/corelib/ddumpable.hpp
c++/include/corelib/error_codes.hpp
c++/include/corelib/expr.hpp
c++/include/corelib/hash_impl/stlp_defs.hpp
c++/include/corelib/impl/ncbi_atomic_defs.h
c++/include/corelib/impl/ncbi_dbsvcmapper.hpp
c++/include/corelib/impl/ncbi_param_impl.hpp
c++/include/corelib/ncbi_base_build_ver.h [new file with mode: 0644]
c++/include/corelib/ncbi_config.hpp
c++/include/corelib/ncbi_cookies.hpp
c++/include/corelib/ncbi_pool_balancer.hpp
c++/include/corelib/ncbi_process.hpp
c++/include/corelib/ncbi_safe_static.hpp
c++/include/corelib/ncbi_tree.hpp
c++/include/corelib/ncbi_url.hpp
c++/include/corelib/ncbiapp_api.hpp
c++/include/corelib/ncbiargs.hpp
c++/include/corelib/ncbiatomic.h
c++/include/corelib/ncbicntr.hpp
c++/include/corelib/ncbidiag.hpp
c++/include/corelib/ncbidiag.inl
c++/include/corelib/ncbienv.hpp
c++/include/corelib/ncbiexec.hpp
c++/include/corelib/ncbiexpt.hpp
c++/include/corelib/ncbifile.hpp
c++/include/corelib/ncbimisc.hpp
c++/include/corelib/ncbimtx.hpp
c++/include/corelib/ncbimtx.inl
c++/include/corelib/ncbiobj.hpp
c++/include/corelib/ncbistl.hpp
c++/include/corelib/ncbistr.hpp
c++/include/corelib/ncbistre.hpp
c++/include/corelib/ncbisys.hpp
c++/include/corelib/ncbithr.hpp
c++/include/corelib/ncbitime.hpp
c++/include/corelib/perf_log.hpp
c++/include/corelib/plugin_manager.hpp
c++/include/corelib/request_ctx.hpp
c++/include/corelib/rwstream.hpp
c++/include/corelib/stream_utils.hpp
c++/include/corelib/tempstr.hpp
c++/include/corelib/test_boost.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_driver_conn_mgr.hpp
c++/include/dbapi/driver/dbapi_driver_convert.hpp
c++/include/dbapi/driver/dbapi_svc_mapper.hpp
c++/include/dbapi/driver/drivers.hpp
c++/include/dbapi/driver/exception.hpp
c++/include/dbapi/driver/impl/dbapi_driver_utils.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/types.hpp
c++/include/dbapi/error_codes.hpp
c++/include/dbapi/variant.hpp
c++/include/html/page.hpp
c++/include/misc/drmaa2.hpp [new file with mode: 0644]
c++/include/misc/jsonwrapp/jsonwrapp10.hpp [deleted file]
c++/include/misc/jsonwrapp/jsonwrapp11.hpp
c++/include/misc/jsonwrapp/rapidjson10/__NCBI_read_me.txt [deleted file]
c++/include/misc/jsonwrapp/rapidjson10/allocators.h [deleted file]
c++/include/misc/jsonwrapp/rapidjson10/document.h [deleted file]
c++/include/misc/jsonwrapp/rapidjson10/encodedstream.h [deleted file]
c++/include/misc/jsonwrapp/rapidjson10/encodings.h [deleted file]
c++/include/misc/jsonwrapp/rapidjson10/error/en.h [deleted file]
c++/include/misc/jsonwrapp/rapidjson10/error/error.h [deleted file]
c++/include/misc/jsonwrapp/rapidjson10/filereadstream.h [deleted file]
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c++/include/misc/jsonwrapp/rapidjson10/internal/biginteger.h [deleted file]
c++/include/misc/jsonwrapp/rapidjson10/internal/diyfp.h [deleted file]
c++/include/misc/jsonwrapp/rapidjson10/internal/dtoa.h [deleted file]
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c++/include/misc/jsonwrapp/rapidjson10/internal/itoa.h [deleted file]
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c++/include/misc/jsonwrapp/rapidjson10/internal/pow10.h [deleted file]
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c++/include/misc/jsonwrapp/rapidjson10/internal/strfunc.h [deleted file]
c++/include/misc/jsonwrapp/rapidjson10/internal/strtod.h [deleted file]
c++/include/misc/jsonwrapp/rapidjson10/license.txt [deleted file]
c++/include/misc/jsonwrapp/rapidjson10/memorybuffer.h [deleted file]
c++/include/misc/jsonwrapp/rapidjson10/memorystream.h [deleted file]
c++/include/misc/jsonwrapp/rapidjson10/msinttypes/inttypes.h [deleted file]
c++/include/misc/jsonwrapp/rapidjson10/msinttypes/stdint.h [deleted file]
c++/include/misc/jsonwrapp/rapidjson10/pointer.h [deleted file]
c++/include/misc/jsonwrapp/rapidjson10/prettywriter.h [deleted file]
c++/include/misc/jsonwrapp/rapidjson10/rapidjson.h [deleted file]
c++/include/misc/jsonwrapp/rapidjson10/reader.h [deleted file]
c++/include/misc/jsonwrapp/rapidjson10/stringbuffer.h [deleted file]
c++/include/misc/jsonwrapp/rapidjson10/writer.h [deleted file]
c++/include/misc/jsonwrapp/rapidjson11/__NCBI_read_me.txt
c++/include/misc/jsonwrapp/rapidjson11/document.h
c++/include/misc/jsonwrapp/rapidjson11/istreamasync.h [new file with mode: 0644]
c++/include/misc/jsonwrapp/rapidjson11/istreamwrapper.h
c++/include/misc/jsonwrapp/rapidjson11/schema.h
c++/include/ncbi_pch.hpp
c++/include/ncbi_source_ver.h
c++/include/ncbiconf.h
c++/include/objects/biblio/Affil.hpp
c++/include/objects/biblio/Auth_list.hpp
c++/include/objects/biblio/Author.hpp
c++/include/objects/biblio/Cit_art.hpp
c++/include/objects/biblio/Cit_book.hpp
c++/include/objects/biblio/Cit_gen.hpp
c++/include/objects/biblio/Cit_jour.hpp
c++/include/objects/biblio/Cit_let.hpp
c++/include/objects/biblio/Cit_pat.hpp
c++/include/objects/biblio/Cit_proc.hpp
c++/include/objects/biblio/Cit_sub.hpp
c++/include/objects/biblio/Id_pat.hpp
c++/include/objects/biblio/citation_base.hpp
c++/include/objects/entrez2/Entrez2_id_list.hpp
c++/include/objects/entrezgene/Entrezgene.hpp
c++/include/objects/general/Dbtag.hpp
c++/include/objects/general/Object_id.hpp
c++/include/objects/general/User_field.hpp
c++/include/objects/general/User_object.hpp
c++/include/objects/genomecoll/GC_Assembly.hpp
c++/include/objects/genomecoll/genomic_collections_cli.hpp
c++/include/objects/id1/id1_client.hpp
c++/include/objects/macro/String_constraint.hpp
c++/include/objects/macro/Suspect_rule_set.hpp
c++/include/objects/medline/Medline_entry.hpp
c++/include/objects/misc/error_codes.hpp
c++/include/objects/mla/mla_client.hpp [deleted file]
c++/include/objects/pub/Pub.hpp
c++/include/objects/pub/Pub_equiv.hpp
c++/include/objects/pub/Pub_set.hpp
c++/include/objects/seq/Seq_annot.hpp
c++/include/objects/seq/seq_align_mapper_base.hpp
c++/include/objects/seq/seq_id_handle.hpp
c++/include/objects/seq/seq_loc_mapper_base.hpp
c++/include/objects/seq/seq_loc_reverse_complementer.hpp
c++/include/objects/seqalign/Seq_align.hpp
c++/include/objects/seqalign/Spliced_seg.hpp
c++/include/objects/seqfeat/SeqFeatData.hpp
c++/include/objects/seqfeat/Seq_feat.hpp
c++/include/objects/seqfeat/SubSource.hpp
c++/include/objects/seqloc/Seq_id.hpp
c++/include/objects/seqloc/Seq_loc.hpp
c++/include/objects/seqset/gb_release_file.hpp
c++/include/objects/taxon1/local_taxon.hpp
c++/include/objects/taxon3/itaxon3.hpp
c++/include/objects/taxon3/taxon3.hpp
c++/include/objects/trackmgr/gridrpcclient.hpp
c++/include/objects/valerr/ValidErrItem.hpp
c++/include/objects/valerr/ValidError.hpp
c++/include/objmgr/annot_selector.hpp
c++/include/objmgr/data_loader.hpp
c++/include/objmgr/data_loader_factory.hpp
c++/include/objmgr/impl/annot_collector.hpp
c++/include/objmgr/impl/annot_type_index.hpp
c++/include/objmgr/impl/bioseq_base_info.hpp
c++/include/objmgr/impl/bioseq_info.hpp
c++/include/objmgr/impl/bioseq_set_info.hpp
c++/include/objmgr/impl/data_source.hpp
c++/include/objmgr/impl/edit_commands_impl.hpp
c++/include/objmgr/impl/handle_range.hpp
c++/include/objmgr/impl/handle_range_map.hpp
c++/include/objmgr/impl/prefetch_manager_impl.hpp
c++/include/objmgr/impl/priority.hpp
c++/include/objmgr/impl/scope_impl.hpp
c++/include/objmgr/impl/scope_info.hpp
c++/include/objmgr/impl/seq_annot_info.hpp
c++/include/objmgr/impl/snp_annot_info.hpp
c++/include/objmgr/impl/tse_chunk_info.hpp
c++/include/objmgr/impl/tse_info.hpp
c++/include/objmgr/impl/tse_info_object.hpp
c++/include/objmgr/impl/tse_loadlock.hpp
c++/include/objmgr/impl/tse_split_info.hpp
c++/include/objmgr/object_manager.hpp
c++/include/objmgr/objmgr_exception.hpp
c++/include/objmgr/scope.hpp
c++/include/objmgr/seq_map.hpp
c++/include/objmgr/tse_handle.hpp
c++/include/objmgr/util/autodef.hpp
c++/include/objmgr/util/autodef_feature_clause.hpp
c++/include/objmgr/util/create_defline.hpp
c++/include/objmgr/util/indexer.hpp
c++/include/objmgr/util/sequence.hpp
c++/include/objtools/align_format/align_format_util.hpp
c++/include/objtools/align_format/showalign.hpp
c++/include/objtools/align_format/showdefline.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/alnseq.hpp
c++/include/objtools/blast/blastdb_format/blastdb_dataextract.hpp
c++/include/objtools/blast/gene_info_reader/gene_info.hpp
c++/include/objtools/blast/gene_info_reader/gene_info_reader.hpp
c++/include/objtools/blast/seqdb_reader/impl/seqdb_lmdb.hpp
c++/include/objtools/blast/seqdb_reader/impl/seqdbatlas.hpp
c++/include/objtools/blast/seqdb_reader/impl/seqdbcol.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 [new file with mode: 0644]
c++/include/objtools/blast/seqdb_reader/seqdb.hpp
c++/include/objtools/blast/seqdb_reader/seqdbcommon.hpp
c++/include/objtools/blast/seqdb_reader/tax4blastsqlite.hpp [new file with mode: 0644]
c++/include/objtools/blast/seqdb_writer/build_db.hpp
c++/include/objtools/blast/seqdb_writer/taxid_set.hpp
c++/include/objtools/blast/seqdb_writer/writedb.hpp
c++/include/objtools/blast/seqdb_writer/writedb_files.hpp
c++/include/objtools/blast/seqdb_writer/writedb_isam.hpp
c++/include/objtools/cleanup/autogenerated_cleanup.hpp [deleted file]
c++/include/objtools/cleanup/cleanup.hpp
c++/include/objtools/cleanup/cleanup_change.hpp
c++/include/objtools/cleanup/cleanup_message.hpp
c++/include/objtools/cleanup/cleanup_pub.hpp
c++/include/objtools/cleanup/fix_feature_id.hpp
c++/include/objtools/cleanup/huge_file_cleanup.hpp [new file with mode: 0644]
c++/include/objtools/data_loaders/genbank/blob_id.hpp
c++/include/objtools/data_loaders/genbank/cache/reader_cache.hpp
c++/include/objtools/data_loaders/genbank/gbloader.hpp
c++/include/objtools/data_loaders/genbank/gbnative.hpp
c++/include/objtools/data_loaders/genbank/impl/info_cache.hpp
c++/include/objtools/data_loaders/genbank/impl/psg_loader_impl.hpp
c++/include/objtools/data_loaders/genbank/impl/reader_id1_base.hpp
c++/include/objtools/data_loaders/genbank/impl/reader_id2_base.hpp
c++/include/objtools/data_loaders/genbank/impl/request_result.hpp
c++/include/objtools/data_loaders/genbank/impl/statistics.hpp
c++/include/objtools/data_loaders/genbank/impl/wgsmaster.hpp
c++/include/objtools/data_loaders/genbank/psg_loader.hpp
c++/include/objtools/data_loaders/genbank/reader.hpp
c++/include/objtools/data_loaders/genbank/seqref.hpp
c++/include/objtools/edit/apply_object.hpp
c++/include/objtools/edit/autodef_with_tax.hpp
c++/include/objtools/edit/capitalization_string.hpp
c++/include/objtools/edit/cds_fix.hpp
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c++/include/objtools/edit/feature_propagate.hpp
c++/include/objtools/edit/field_handler.hpp
c++/include/objtools/edit/gap_trim.hpp
c++/include/objtools/edit/gaps_edit.hpp
c++/include/objtools/edit/gb_block_field.hpp
c++/include/objtools/edit/gene_utils.hpp
c++/include/objtools/edit/huge_asn_loader.hpp [new file with mode: 0644]
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c++/include/objtools/edit/huge_file_process.hpp [new file with mode: 0644]
c++/include/objtools/edit/loc_edit.hpp
c++/include/objtools/edit/mail_report.hpp
c++/include/objtools/edit/parse_text_options.hpp
c++/include/objtools/edit/promote.hpp
c++/include/objtools/edit/pub_fix.hpp
c++/include/objtools/edit/publication_edit.hpp
c++/include/objtools/edit/pubmed_updater.hpp [new file with mode: 0644]
c++/include/objtools/edit/remote_updater.hpp
c++/include/objtools/edit/seq_edit.hpp
c++/include/objtools/edit/seq_entry_edit.hpp
c++/include/objtools/edit/source_edit.hpp
c++/include/objtools/edit/string_constraint.hpp
c++/include/objtools/edit/struc_comm_field.hpp
c++/include/objtools/edit/text_desc_field.hpp
c++/include/objtools/error_codes.hpp
c++/include/objtools/eutils/api/eutils.hpp
c++/include/objtools/eutils/efetch/PubmedArticle.hpp [new file with mode: 0644]
c++/include/objtools/eutils/efetch/PubmedBookArticle.hpp [new file with mode: 0644]
c++/include/objtools/format/cigar_formatter.hpp
c++/include/objtools/format/context.hpp
c++/include/objtools/format/feature_gather.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 [new file with mode: 0644]
c++/include/objtools/format/format_item_ostream.hpp
c++/include/objtools/format/formatter.hpp
c++/include/objtools/format/gather_items.hpp
c++/include/objtools/format/gather_iter.hpp
c++/include/objtools/format/gbseq_formatter.hpp
c++/include/objtools/format/genbank_formatter.hpp
c++/include/objtools/format/item_formatter.hpp
c++/include/objtools/format/item_ostream.hpp
c++/include/objtools/format/items/accession_item.hpp
c++/include/objtools/format/items/alignment_item.hpp
c++/include/objtools/format/items/basecount_item.hpp
c++/include/objtools/format/items/comment_item.hpp
c++/include/objtools/format/items/contig_item.hpp
c++/include/objtools/format/items/ctrl_items.hpp
c++/include/objtools/format/items/date_item.hpp
c++/include/objtools/format/items/dbsource_item.hpp
c++/include/objtools/format/items/defline_item.hpp
c++/include/objtools/format/items/feature_item.hpp
c++/include/objtools/format/items/flat_seqloc.hpp
c++/include/objtools/format/items/gap_item.hpp
c++/include/objtools/format/items/gene_finder.hpp
c++/include/objtools/format/items/genome_project_item.hpp
c++/include/objtools/format/items/html_anchor_item.hpp
c++/include/objtools/format/items/keywords_item.hpp
c++/include/objtools/format/items/locus_item.hpp
c++/include/objtools/format/items/origin_item.hpp
c++/include/objtools/format/items/primary_item.hpp
c++/include/objtools/format/items/reference_item.hpp
c++/include/objtools/format/items/segment_item.hpp
c++/include/objtools/format/items/sequence_item.hpp
c++/include/objtools/format/items/source_item.hpp
c++/include/objtools/format/items/tsa_item.hpp
c++/include/objtools/format/items/version_item.hpp
c++/include/objtools/format/items/wgs_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_converter.hpp
c++/include/objtools/readers/agp_read.hpp
c++/include/objtools/readers/agp_seq_entry.hpp
c++/include/objtools/readers/agp_util.hpp
c++/include/objtools/readers/agp_validate_reader.hpp
c++/include/objtools/readers/aln_error_reporter.hpp
c++/include/objtools/readers/aln_formats.hpp
c++/include/objtools/readers/aln_reader.hpp
c++/include/objtools/readers/alnread.hpp
c++/include/objtools/readers/bed_reader.hpp
c++/include/objtools/readers/error_container.hpp
c++/include/objtools/readers/fasta.hpp
c++/include/objtools/readers/fasta_exception.hpp
c++/include/objtools/readers/fasta_reader_utils.hpp
c++/include/objtools/readers/featuredump.hpp
c++/include/objtools/readers/format_guess_ex.hpp
c++/include/objtools/readers/getfeature.hpp
c++/include/objtools/readers/gff2_data.hpp
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c++/include/objtools/readers/gff3_location_merger.hpp [new file with mode: 0644]
c++/include/objtools/readers/gff3_reader.hpp
c++/include/objtools/readers/gff_base_columns.hpp
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c++/include/objtools/readers/line_error.hpp
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c++/include/objtools/readers/microarray_reader.hpp
c++/include/objtools/readers/mod_error.hpp
c++/include/objtools/readers/mod_reader.hpp
c++/include/objtools/readers/objhook_lambdas.hpp [new file with mode: 0644]
c++/include/objtools/readers/psl_reader.hpp
c++/include/objtools/readers/read_util.hpp
c++/include/objtools/readers/reader_base.hpp
c++/include/objtools/readers/reader_error_codes.hpp
c++/include/objtools/readers/reader_idgen.hpp
c++/include/objtools/readers/reader_message.hpp
c++/include/objtools/readers/readfeat.hpp
c++/include/objtools/readers/rm_reader.hpp
c++/include/objtools/readers/seqid_validate.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/ucscregion_reader.hpp
c++/include/objtools/readers/vcf_reader.hpp
c++/include/objtools/readers/wiggle_reader.hpp
c++/include/objtools/seqmasks_io/mask_fasta_reader.hpp
c++/include/objtools/seqmasks_io/mask_writer_fasta.hpp
c++/include/serial/enumvalues.hpp
c++/include/serial/exception.hpp
c++/include/serial/grpc_integration/grpc_integration.hpp
c++/include/serial/grpc_integration/impl/grpc_support.hpp
c++/include/serial/impl/classinfohelper.hpp
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c++/include/serial/impl/member.hpp
c++/include/serial/impl/member.inl
c++/include/serial/impl/memberlist.hpp
c++/include/serial/impl/objistrxml.inl
c++/include/serial/impl/objstack.hpp
c++/include/serial/impl/stltypes.hpp
c++/include/serial/impl/typeref.hpp
c++/include/serial/impl/typeref.inl
c++/include/serial/iterator.hpp
c++/include/serial/objhook.hpp
c++/include/serial/objistr.hpp
c++/include/serial/objistrasn.hpp
c++/include/serial/objistrasnb.hpp
c++/include/serial/objistrjson.hpp
c++/include/serial/objistrxml.hpp
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c++/include/serial/objostrjson.hpp
c++/include/serial/rpcbase_impl.hpp
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c++/include/sra/data_loaders/bam/bamloader.hpp [new file with mode: 0644]
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c++/scripts/common/add_vdb.sh
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c++/scripts/common/impl/generate_all_objects.sh
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c++/src/db/CMakeLists.txt
c++/src/db/sqlite/CMakeLists.sqlitewrapp.lib.txt
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c++/src/dbapi/driver/CMakeLists.dbapi_driver.lib.txt
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c++/src/dbapi/driver/dbapi_impl_context.cpp
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c++/src/dbapi/driver/dbapi_svc_mapper.cpp
c++/src/dbapi/driver/exception.cpp
c++/src/dbapi/driver/ncbi_win_hook.cpp
c++/src/dbapi/driver/odbc/CMakeLists.ncbi_xdbapi_odbc.lib.txt
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c++/src/dbapi/driver/odbc/connection.cpp
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c++/src/html/htmlhelper.cpp
c++/src/html/page.cpp
c++/src/html/pager.cpp
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c++/src/objects/seq/Seq_inst.cpp
c++/src/objects/seq/seq_align_mapper_base.cpp
c++/src/objects/seq/seq_id_handle.cpp
c++/src/objects/seq/seq_id_tree.cpp
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c++/src/objects/seq/seq_loc_reverse_complementer.cpp
c++/src/objects/seq/seqport_util.cpp
c++/src/objects/seqalign/Dense_seg.cpp
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c++/src/objects/seqfeat/Genetic_code_table.cpp
c++/src/objects/seqfeat/OrgMod.cpp
c++/src/objects/seqfeat/Org_ref.cpp
c++/src/objects/seqfeat/PCRPrimerSeq.cpp
c++/src/objects/seqfeat/RNA_ref.cpp
c++/src/objects/seqfeat/SeqFeatData.cpp
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c++/src/util/compress/zlib/uncompr.c
c++/src/util/compress/zlib/zutil.c
c++/src/util/crc32_sse.cpp
c++/src/util/creaders/CMakeLists.creaders.lib.txt
c++/src/util/creaders/CMakeLists.txt
c++/src/util/creaders/Makefile.creaders.lib
c++/src/util/creaders/Makefile.creaders.lib.unix
c++/src/util/dictionary_util.cpp
c++/src/util/format_guess.cpp
c++/src/util/itree.cpp
c++/src/util/line_reader.cpp
c++/src/util/lmdb/CMakeLists.lmdb.lib.txt
c++/src/util/lmdb/CMakeLists.lmdb_test1.app.txt
c++/src/util/lmdb/CMakeLists.lmdb_test2.app.txt
c++/src/util/lmdb/CMakeLists.lmdb_test3.app.txt
c++/src/util/lmdb/CMakeLists.lmdb_test4.app.txt
c++/src/util/lmdb/CMakeLists.lmdb_test5.app.txt
c++/src/util/lmdb/CMakeLists.lmdb_test6.app.txt
c++/src/util/lmdb/CMakeLists.txt
c++/src/util/lmdbxx/CMakeLists.lmdbxx_sample.app.txt
c++/src/util/lmdbxx/CMakeLists.txt
c++/src/util/multipattern_search.cpp
c++/src/util/multipattern_search_impl.hpp
c++/src/util/mutex_pool.cpp
c++/src/util/regexp/CMakeLists.regexp.lib.txt
c++/src/util/regexp/CMakeLists.test_pcre.app.txt
c++/src/util/regexp/CMakeLists.txt
c++/src/util/scheduler.cpp
c++/src/util/sequtil/CMakeLists.sequtil.lib.txt
c++/src/util/sequtil/CMakeLists.txt
c++/src/util/strbuffer.cpp
c++/src/util/tables/CMakeLists.tables.lib.txt
c++/src/util/tables/CMakeLists.txt
c++/src/util/thread_pool.cpp
c++/src/util/thread_pool_old.cpp
c++/src/util/unicode_plans.inl
c++/src/util/unicode_to_ascii.txt
c++/src/util/util_misc.cpp
c++/src/util/xregexp/CMakeLists.txt
c++/src/util/xregexp/CMakeLists.xregexp.lib.txt
c++/src/util/xregexp/CMakeLists.xregexp_template_tester.lib.txt
c++/src/util/xregexp/Makefile.xregexp.lib
c++/src/util/xregexp/arg_regexp.cpp
c++/src/util/xregexp/convert_dates_iso8601.cpp
c++/src/util/xregexp/regexp.cpp