[med-svn] [Git][med-team/ncbi-blastplus][master] 10 commits: New upstream version 2.17.0+ds

[Aaron M. Ucko (@ucko)]

Aaron M. Ucko pushed to branch master at Debian Med / ncbi-blastplus


Commits:
66447a51 by Aaron M. Ucko at 2025-09-27T20:39:42-04:00
New upstream version 2.17.0+ds
- - - - -
8162eb8e by Aaron M. Ucko at 2025-09-27T20:41:55-04:00
Merge tag 'upstream/2.17.0+ds'

Upstream version 2.17.0(+ds).

- - - - -
81bb56c0 by Aaron M. Ucko at 2025-09-27T21:18:47-04:00
debian/patches: Update for new release, mostly formally.

* debian/patches/series: Comment out support_mbedtls3, allow_pcre2,
  and fix_bm_for_gcc15, all incorporated upstream.
* debian/patches/system_mbedtls_only: Drop code changes (incorporated
  upstream) and port Makefile.connssl.lib's changes.

- - - - -
257a79c7 by Aaron M. Ucko at 2025-09-27T21:19:22-04:00
debian/control: Require SSE 4.2 on x86 per upstream.

- - - - -
ecfca8e2 by Aaron M. Ucko at 2025-09-27T22:23:33-04:00
debian/rules: Explicitly supply VDB_LIBDIR to configure

... to avoid a bad interaction that led to spurious runpath entries in
binaries linked against VDB.

- - - - -
0d922f64 by Aaron M. Ucko at 2025-09-27T22:26:46-04:00
Override embedded-library zlib for libzcf.so

... which is Cloudflare's fork.

- - - - -
f24eb42e by Aaron M. Ucko at 2025-09-28T16:30:17-04:00
debian/copyright: Update with more help from lrc.

* Cover zlib_cloudflare alongside (unused) zlib, accounting for the
  fork's additional copyright holders and years.
* Cover (unused) PCRE2's sljit subtree; factor out BSD-2-clause for it.
* Stop mentioning the retired extra copy of lmdb++.h.
* Enumerate cityhash and farmhash explicitly to allow for *-only
  wildcarding without pulling in murmurhash.

- - - - -
f1b51374 by Aaron M. Ucko at 2025-09-28T22:49:24-04:00
d/control: Reformat via "cme fix dpkg-control" (routine-update).

* Format potentially multi-valued entries as

  Key:
   value1,
   value2,
   ...

  rather then

  Key: value1,
       value2,
       ...

* Move Standards-Version up to between Source and Maintainer.

- - - - -
7ede11a8 by Aaron M. Ucko at 2025-09-28T23:06:21-04:00
debian/copyright: Clean up whitespace (routine-update).

Namely, a few hard tabs and a trailing space.

- - - - -
7c3ad37c by Aaron M. Ucko at 2025-09-28T23:09:00-04:00
Finalize ncbi-blast+ 2.17.0+ds-1 for unstable.

- - - - -


1959 changed files:

- + c++/compilers/.gitignore
- 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
- + c++/compilers/vs2022/Makefile.wxWidgets.app.msvc
- + c++/compilers/vs2022/build.sh
- + c++/compilers/vs2022/build_exec.bat
- + c++/compilers/vs2022/build_util.sh
- + c++/compilers/vs2022/check.sh
- + c++/compilers/vs2022/configure.bat
- + c++/compilers/vs2022/datatool.bat
- + c++/compilers/vs2022/dll/build/UtilityProjects/_CONFIGURE_.vcxproj
- + c++/compilers/vs2022/dll/build/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj
- + c++/compilers/vs2022/dll/build/UtilityProjects/configure._
- + c++/compilers/vs2022/dll/build/UtilityProjects/configure_dialog._
- + c++/compilers/vs2022/dll/build/all.bat
- + c++/compilers/vs2022/dll/build/all_gbench.bat
- + c++/compilers/vs2022/dll/build/all_gui.bat
- + c++/compilers/vs2022/dll/build/all_ncbi.bat
- + c++/compilers/vs2022/dll/build/gbench/UtilityProjects/_CONFIGURE_.vcxproj
- + c++/compilers/vs2022/dll/build/gbench/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj
- + c++/compilers/vs2022/dll/build/gbench/UtilityProjects/configure._
- + c++/compilers/vs2022/dll/build/gbench/UtilityProjects/configure_dialog._
- + c++/compilers/vs2022/dll/build/gbench/configure_prebuild.bat
- + c++/compilers/vs2022/dll/build/gbench/gbench_install/gbench-install.vcxproj
- + c++/compilers/vs2022/dll/build/gbench/ncbi_gbench.sln
- + c++/compilers/vs2022/dll/build/gui/UtilityProjects/_CONFIGURE_.vcxproj
- + c++/compilers/vs2022/dll/build/gui/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj
- + c++/compilers/vs2022/dll/build/gui/UtilityProjects/configure._
- + c++/compilers/vs2022/dll/build/gui/UtilityProjects/configure_dialog._
- + c++/compilers/vs2022/dll/build/gui/ncbi_gui_dll.sln
- + c++/compilers/vs2022/dll/build/internal/gbench/gbench_install_internal/gbench-install-internal.vcxproj
- + c++/compilers/vs2022/dll/build/ncbi_cpp_dll.sln
- + c++/compilers/vs2022/dll/dll_main.cpp
- + c++/compilers/vs2022/dll/third_party_dll_install.mak
- + c++/compilers/vs2022/dll/third_party_dll_install.vcxproj
- + c++/compilers/vs2022/dll/third_party_msvcdll_install.vcxproj
- + c++/compilers/vs2022/install.sh
- + c++/compilers/vs2022/lock_ptb_config.bat
- + c++/compilers/vs2022/make.bat
- + c++/compilers/vs2022/make_ncbi.bat
- + c++/compilers/vs2022/msvcvars.bat
- + c++/compilers/vs2022/ncbi.rc
- + c++/compilers/vs2022/ncbilogo.ico
- + c++/compilers/vs2022/protoc.bat
- + c++/compilers/vs2022/ptb.bat
- + c++/compilers/vs2022/retry.sh
- + c++/compilers/vs2022/static/build/UtilityProjects/PTB.sln
- + c++/compilers/vs2022/static/build/UtilityProjects/_CONFIGURE_.vcxproj
- + c++/compilers/vs2022/static/build/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj
- + c++/compilers/vs2022/static/build/UtilityProjects/configure._
- + c++/compilers/vs2022/static/build/UtilityProjects/configure_dialog._
- + c++/compilers/vs2022/static/build/all.bat
- + c++/compilers/vs2022/static/build/all_gui.bat
- + c++/compilers/vs2022/static/build/all_ncbi.bat
- + c++/compilers/vs2022/static/build/build-system/project_tree_builder/msbuild/msbuild_dataobj.lib.vcxproj
- + c++/compilers/vs2022/static/build/build-system/project_tree_builder/project_tree_builder.exe.vcxproj
- + c++/compilers/vs2022/static/build/corelib/xncbi.lib.vcxproj
- + c++/compilers/vs2022/static/build/gui/UtilityProjects/_CONFIGURE_.vcxproj
- + c++/compilers/vs2022/static/build/gui/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj
- + c++/compilers/vs2022/static/build/gui/UtilityProjects/configure._
- + c++/compilers/vs2022/static/build/gui/UtilityProjects/configure_dialog._
- + c++/compilers/vs2022/static/build/gui/ncbi_gui.sln
- + c++/compilers/vs2022/static/build/ncbi_cpp.sln
- + c++/compilers/vs2022/static/build/serial/datatool/datatool.exe.vcxproj
- + c++/compilers/vs2022/static/build/serial/xser.lib.vcxproj
- + c++/compilers/vs2022/static/build/util/regexp/regexp.lib.vcxproj
- + c++/compilers/vs2022/static/build/util/xregexp/xregexp.lib.vcxproj
- + c++/compilers/vs2022/static/build/util/xutil.lib.vcxproj
- + c++/compilers/vs2022/static/third_party_msvcstatic_install.vcxproj
- + c++/compilers/vs2022/static/third_party_static_install.mak
- + c++/compilers/vs2022/static/third_party_static_install.vcxproj
- + c++/compilers/vs2022/third_party_install.meta.mk
- + c++/compilers/vs2022/user/build/UtilityProjects/_CONFIGURE_.vcxproj
- + c++/compilers/vs2022/user/build/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj
- + c++/compilers/vs2022/user/build/UtilityProjects/configure._
- + c++/compilers/vs2022/user/build/UtilityProjects/configure_dialog._
- + c++/compilers/vs2022/user/build/ncbi_user.sln
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- − 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/lmdb++.h
- 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
- + c++/include/objtools/data_loaders/genbank/impl/psg_cache.hpp
- + c++/include/objtools/data_loaders/genbank/impl/psg_cdd.hpp
- + c++/include/objtools/data_loaders/genbank/impl/psg_evloop.hpp
- c++/include/objtools/data_loaders/genbank/impl/psg_loader_impl.hpp
- + c++/include/objtools/data_loaders/genbank/impl/psg_processor.hpp
- + c++/include/objtools/data_loaders/genbank/impl/psg_processors.hpp
- 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
- 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
- c++/include/util/bitset/bmblocks.h
- c++/include/util/bitset/bmbmatrix.h
- c++/include/util/bitset/bmbuffer.h
- c++/include/util/bitset/bmconst.h
- c++/include/util/bitset/bmdbg.h
- c++/include/util/bitset/bmdef.h
- c++/include/util/bitset/bmfunc.h
- c++/include/util/bitset/bmserial.h
- c++/include/util/bitset/bmsparsevec.h
- c++/include/util/bitset/bmsparsevec_algo.h
- c++/include/util/bitset/bmsparsevec_compr.h
- c++/include/util/bitset/bmsparsevec_serial.h
- c++/include/util/bitset/bmsse4.h
- c++/include/util/bitset/bmstrsparsevec.h
- c++/include/util/bitset/bmutil.h
- c++/include/util/bitset/encoding.h
- c++/include/util/compile_time.hpp
- c++/include/util/compress/bzip2.hpp
- c++/include/util/compress/bzip2/bzlib.h
- c++/include/util/compress/lzo.hpp
- c++/include/util/compress/stream_util.hpp
- c++/include/util/compress/tar.hpp
- c++/include/util/compress/zlib.hpp
- c++/include/util/compress/zlib/zconf.h
- + c++/include/util/compress/zlib_cloudflare.hpp
- + c++/include/util/compress/zlib_cloudflare/zconf_cf.h
- + c++/include/util/compress/zlib_cloudflare/zlib_cf.h
- + c++/include/util/compress/zlib_cloudflare/zutil_cf.h
- c++/include/util/compress/zstd.hpp
- c++/include/util/error_codes.hpp
- c++/include/util/format_guess.hpp
- c++/include/util/impl/compile_time_bits.hpp
- − c++/include/util/impl/ct_bitset_cxx14.hpp
- c++/include/util/impl/ct_bitset_cxx17.hpp
- − c++/include/util/impl/ct_string_cxx14.hpp
- c++/include/util/impl/ctsort_cxx14.hpp
- c++/include/util/impl/generated_fsm.hpp
- + c++/include/util/incr_time.hpp
- c++/include/util/impl/const_tuple.hpp → c++/include/util/memory_streambuf.hpp
- c++/include/util/multi_writer.hpp
- c++/include/util/range_coll.hpp
- c++/include/util/range_set.hpp
- c++/include/util/regexp/ctre/ctre-unicode.hpp
- c++/include/util/regexp/ctre/ctre.hpp
- − c++/include/util/regexp/pcre.h
- + c++/include/util/regexp/pcre2.h
- c++/include/util/regexp/pcreposix.h → c++/include/util/regexp/pcre2posix.h
- − c++/include/util/regexp/pcrecpp.h
- − c++/include/util/regexp/pcrecpparg.h
- c++/include/util/stream_source.hpp
- c++/include/util/xregexp/regexp.hpp
- c++/scripts/common/add_vdb.sh
- c++/scripts/common/check/check_exec.sh
- c++/scripts/common/check/check_exec_test.sh
- c++/scripts/common/check/check_make_cfg.sh
- c++/scripts/common/check/check_make_unix.sh
- c++/scripts/common/check/check_make_unix_cmake.sh
- c++/scripts/common/check/check_run.sh
- + c++/scripts/common/check/inspxe-suppressions/3rd_party.sup
- + c++/scripts/common/check/inspxe-suppressions/_inspxe_run.bat
- + c++/scripts/common/check/inspxe-suppressions/_inspxe_run_2024.bat
- c++/scripts/common/check/inspxe-suppressions/_vs.sup
- + c++/scripts/common/check/inspxe-suppressions/_vs2022_i2019.sup
- + c++/scripts/common/check/inspxe-suppressions/_vs2022_i2024.sup
- + c++/scripts/common/check/inspxe-suppressions/algo.sup
- c++/scripts/common/check/inspxe-suppressions/connect.sup
- c++/scripts/common/check/inspxe-suppressions/corelib.sup
- c++/scripts/common/check/inspxe-suppressions/dbapi.sup
- c++/scripts/common/check/inspxe-suppressions/misc.sup
- + c++/scripts/common/check/inspxe-suppressions/objtools.sup
- c++/scripts/common/check/inspxe-suppressions/util.sup
- c++/scripts/common/check/inspxe.sh
- c++/scripts/common/check/retry_db_load.sh
- c++/scripts/common/check/valgrind.supp
- c++/scripts/common/common.sh
- + c++/scripts/common/cxx-p2-add-api-sample
- c++/scripts/common/impl/create_flat_submakefile.awk
- c++/scripts/common/impl/create_flat_submakefile.sh
- c++/scripts/common/impl/install.sh
- c++/scripts/common/impl/ncbicxx_build_info.py
- c++/scripts/common/impl/python-config.py
- c++/scripts/common/new_cmake_project.bat
- c++/scripts/common/new_cmake_project.sh
- + c++/scripts/common/new_conan_project.bat
- + c++/scripts/common/new_conan_project.sh
- c++/scripts/projects/blast/Manifest
- c++/scripts/projects/blast/components.link
- c++/scripts/projects/blast/post_build/rpm/ncbi-blast.spec
- c++/scripts/projects/cobalt/Manifest
- c++/scripts/projects/cobalt/components.link
- c++/scripts/projects/corelib/Manifest
- c++/scripts/projects/datatool/Manifest
- c++/scripts/projects/gumbel_params/Manifest
- c++/scripts/projects/igblast/Manifest
- c++/scripts/projects/igblast/README
- c++/scripts/projects/igblast/components.link
- c++/scripts/projects/igblast/post_build/rpm/ncbi-igblast.spec
- c++/scripts/projects/magicblast/Manifest
- c++/scripts/projects/magicblast/components.link
- c++/scripts/projects/ncbi_applog/Manifest
- + c++/scripts/projects/ncbi_gpipe_deps.lst
- c++/scripts/projects/ncbi_panfs/Manifest
- c++/scripts/projects/netcache/Manifest
- c++/scripts/projects/netschedule/Manifest
- c++/scripts/projects/netschedule/components.link
- c++/scripts/projects/netstorage/Manifest
- c++/scripts/projects/netstorage_gc/Manifest
- c++/scripts/projects/perl_diag/Manifest
- c++/scripts/projects/project_tree_builder/Manifest
- c++/scripts/projects/psg_client/Manifest
- c++/scripts/projects/psg_client/components.link
- c++/scripts/projects/public/Manifest
- c++/scripts/projects/pubseq_gateway/Manifest
- c++/scripts/projects/pubseq_gateway/components.link
- c++/scripts/projects/pubseq_gateway/project.lst
- c++/scripts/projects/python_ncbi_dbapi/ChangeLog
- c++/scripts/projects/python_ncbi_dbapi/Manifest
- c++/scripts/projects/python_ncbi_dbapi/components.link
- c++/scripts/projects/python_ncbi_dbapi/post_build/post_build.py
- c++/scripts/projects/quickblastp/Manifest
- c++/scripts/projects/rmblastn/Manifest
- c++/scripts/projects/test_ccpp_read/Manifest
- c++/scripts/projects/xmlwrapp/Manifest
- c++/scripts/projects/xmlwrapp/project.lst
- c++/src/CMakeLists.txt
- c++/src/Makefile.in
- c++/src/algo/blast/Makefile.blast_macros.mk
- c++/src/algo/blast/Makefile.in
- c++/src/algo/blast/api/Makefile.xblast.lib
- c++/src/algo/blast/api/blast_dbindex.cpp
- c++/src/algo/blast/api/blast_node.cpp
- c++/src/algo/blast/api/blast_options_cxx.cpp
- c++/src/algo/blast/api/blast_options_handle.cpp
- c++/src/algo/blast/api/blast_options_local_priv.hpp
- c++/src/algo/blast/api/blast_seqalign.cpp
- c++/src/algo/blast/api/blast_usage_report.cpp
- c++/src/algo/blast/api/cdd_pssm_input.cpp
- c++/src/algo/blast/api/deltablast.cpp
- c++/src/algo/blast/api/effsearchspace_calc.cpp
- c++/src/algo/blast/api/local_blast.cpp
- c++/src/algo/blast/api/magicblast.cpp
- c++/src/algo/blast/api/prelim_search_runner.hpp
- c++/src/algo/blast/api/prelim_stage.cpp
- c++/src/algo/blast/api/remote_blast.cpp
- c++/src/algo/blast/api/rpsblast_local.cpp
- c++/src/algo/blast/api/seqsrc_query_factory.cpp
- c++/src/algo/blast/blastinput/CMakeLists.blastinput.lib.txt
- c++/src/algo/blast/blastinput/Makefile.blastinput.lib
- c++/src/algo/blast/blastinput/Makefile.in
- c++/src/algo/blast/blastinput/blast_args.cpp
- c++/src/algo/blast/blastinput/blast_fasta_input.cpp
- c++/src/algo/blast/blastinput/blast_input_aux.cpp
- c++/src/algo/blast/blastinput/blastx_args.cpp
- c++/src/algo/blast/blastinput/cmdline_flags.cpp
- c++/src/algo/blast/blastinput/unit_test/CMakeLists.blastinput_unit_test.app.txt
- c++/src/algo/blast/blastinput/unit_test/Makefile.blastinput_unit_test.app
- c++/src/algo/blast/blastinput/unit_test/blastinput_unit_test.ini
- c++/src/algo/blast/core/Makefile.blast.lib
- c++/src/algo/blast/core/blast_aascan.c
- c++/src/algo/blast/core/blast_engine.c
- c++/src/algo/blast/core/blast_filter.c
- c++/src/algo/blast/core/blast_gapalign.c
- c++/src/algo/blast/core/blast_gapalign_priv.h
- c++/src/algo/blast/core/blast_hits.c
- c++/src/algo/blast/core/blast_hspstream.c
- c++/src/algo/blast/core/blast_kappa.c
- c++/src/algo/blast/core/blast_message.c
- c++/src/algo/blast/core/blast_nalookup.c
- c++/src/algo/blast/core/blast_nascan.c
- c++/src/algo/blast/core/blast_options.c
- c++/src/algo/blast/core/blast_parameters.c
- c++/src/algo/blast/core/blast_setup.c
- c++/src/algo/blast/core/blast_stat.c
- c++/src/algo/blast/core/blast_sw.c
- c++/src/algo/blast/core/blast_traceback.c
- c++/src/algo/blast/core/blast_util.c
- c++/src/algo/blast/core/jumper.c
- c++/src/algo/blast/core/na_ungapped.c
- c++/src/algo/blast/core/phi_gapalign.c
- c++/src/algo/blast/core/phi_lookup.c
- c++/src/algo/blast/dbindex/dbindex_factory.cpp
- c++/src/algo/blast/dbindex/dbindex_search.cpp
- c++/src/algo/blast/format/Makefile.xblastformat.lib
- c++/src/algo/blast/format/blast_format.cpp
- c++/src/algo/blast/format/blastfmtutil.cpp
- c++/src/algo/blast/format/blastxml_format.cpp
- c++/src/algo/blast/format/vecscreen_run.cpp
- c++/src/algo/blast/igblast/Makefile.igblast.lib
- c++/src/algo/blast/proteinkmer/Makefile.in
- c++/src/algo/blast/proteinkmer/Makefile.proteinkmer.lib
- c++/src/algo/blast/proteinkmer/blastkmer.cpp
- c++/src/algo/blast/proteinkmer/blastkmerindex.cpp
- c++/src/algo/blast/proteinkmer/blastkmerutils.cpp
- c++/src/algo/blast/proteinkmer/kblastapi.cpp
- c++/src/algo/blast/proteinkmer/unit_test/Makefile.proteinkmer_unit_test.app
- c++/src/algo/blast/unit_tests/api/CMakeLists.blast_unit_test.app.txt
- c++/src/algo/blast/unit_tests/api/CMakeLists.blastdiag_unit_test.app.txt
- c++/src/algo/blast/unit_tests/api/CMakeLists.gapinfo_unit_test.app.txt
- c++/src/algo/blast/unit_tests/api/CMakeLists.hspfilter_besthit_unit_test.app.txt
- c++/src/algo/blast/unit_tests/api/CMakeLists.hspfilter_culling_unit_test.app.txt
- c++/src/algo/blast/unit_tests/api/CMakeLists.stat_unit_test.app.txt
- c++/src/algo/blast/unit_tests/api/CMakeLists.tracebacksearch_unit_test.app.txt
- c++/src/algo/blast/unit_tests/api/CMakeLists.txt
- c++/src/algo/blast/unit_tests/api/Makefile.aalookup_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.aascan_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.bl2seq_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.blast_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.blast_unit_test_util.lib
- c++/src/algo/blast/unit_tests/api/Makefile.blastdiag_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.blastengine_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.blastextend_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.blastfilter_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.blasthits_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.blastoptions_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.blastsetup_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.delta_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.gapinfo_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.gencode_singleton_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.hspfilter_besthit_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.hspfilter_culling_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.hspstream_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.linkhsp_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.magicblast_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.msa2pssm_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.ntlookup_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.ntscan_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.optionshandle_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.phiblast_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.prelimsearch_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.psibl2seq_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.psiblast_iteration_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.psiblast_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.pssmcreate_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.pssmenginefreqratios_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.querydata_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.queryinfo_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.redoalignment_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.remote_blast_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.rmblast_blasthits_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.rmblast_traceback_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.rps_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.scoreblk_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.search_strategy_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.seqalign_util.lib
- c++/src/algo/blast/unit_tests/api/Makefile.seqinfosrc_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.seqsrc_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.setupfactory_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.split_query_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.stat_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.subj_ranges_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.traceback_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.tracebacksearch_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.uniform_search_unit_test.app
- c++/src/algo/blast/unit_tests/api/Makefile.version_reference_unit_test.app
- c++/src/algo/blast/unit_tests/api/bl2seq_unit_test.ini
- c++/src/algo/blast/unit_tests/api/blast_test_util.hpp
- c++/src/algo/blast/unit_tests/api/blast_unit_test.cpp
- c++/src/algo/blast/unit_tests/api/blastdiag_unit_test.cpp
- c++/src/algo/blast/unit_tests/api/blastengine_unit_test.ini
- c++/src/algo/blast/unit_tests/api/blastextend_unit_test.cpp
- c++/src/algo/blast/unit_tests/api/blastfilter_unit_test.ini
- c++/src/algo/blast/unit_tests/api/blastoptions_unit_test.cpp
- c++/src/algo/blast/unit_tests/api/blastsetup_unit_test.ini
- c++/src/algo/blast/unit_tests/api/ensure_enough_corelib.hpp
- c++/src/algo/blast/unit_tests/api/gencode_singleton_unit_test.cpp
- c++/src/algo/blast/unit_tests/api/hspfilter_besthit_unit_test.cpp
- c++/src/algo/blast/unit_tests/api/hspfilter_culling_unit_test.cpp
- c++/src/algo/blast/unit_tests/api/magicblast_unit_test.cpp
- c++/src/algo/blast/unit_tests/api/mockseqsrc1_unit_test.cpp
- c++/src/algo/blast/unit_tests/api/mockseqsrc2_unit_test.cpp
- c++/src/algo/blast/unit_tests/api/msa2pssm_unit_test.cpp
- c++/src/algo/blast/unit_tests/api/ntlookup_unit_test.cpp
- c++/src/algo/blast/unit_tests/api/phiblast_unit_test.cpp
- c++/src/algo/blast/unit_tests/api/prelimsearch_unit_test.ini
- c++/src/algo/blast/unit_tests/api/psiblast_iteration_unit_test.cpp
- c++/src/algo/blast/unit_tests/api/pssm_test_util.cpp
- c++/src/algo/blast/unit_tests/api/pssmcreate_cdd_unit_test.cpp
- c++/src/algo/blast/unit_tests/api/redoalignment_unit_test.ini
- c++/src/algo/blast/unit_tests/api/remote_blast_unit_test.cpp
- c++/src/algo/blast/unit_tests/api/seqsrc_mock.cpp
- c++/src/algo/blast/unit_tests/api/stat_unit_test.cpp
- c++/src/algo/blast/unit_tests/api/subj_ranges_unit_test.cpp
- c++/src/algo/blast/unit_tests/api/subj_ranges_unit_test.ini
- c++/src/algo/blast/unit_tests/api/test_objmgr.cpp
- c++/src/algo/blast/unit_tests/api/test_objmgr.hpp
- c++/src/algo/blast/unit_tests/api/traceback_unit_test.ini
- c++/src/algo/blast/unit_tests/api/tracebacksearch_unit_test.cpp
- c++/src/algo/blast/unit_tests/api/uniform_search_unit_test.ini
- c++/src/algo/blast/unit_tests/api/version_reference_unit_test.cpp
- c++/src/algo/blast/unit_tests/blast_format/CMakeLists.blast_format_unit_test.app.txt
- c++/src/algo/blast/unit_tests/blast_format/Makefile.blast_format_unit_test.app
- c++/src/algo/blast/unit_tests/blast_format/blast_format_unit_test.cpp
- c++/src/algo/blast/unit_tests/blast_format/blast_format_unit_test.ini
- c++/src/algo/blast/unit_tests/blastdb/Makefile.bdbloader_unit_test.app
- c++/src/algo/blast/unit_tests/blastdb/bdbloader_unit_test.cpp
- + c++/src/algo/blast/unit_tests/blastdb/bdbloader_unit_test.ini
- c++/src/algo/blast/unit_tests/seqdb_reader/CMakeLists.seqdb_lmdb_unit_test.app.txt
- c++/src/algo/blast/unit_tests/seqdb_reader/CMakeLists.seqdb_tax4blast_unit_test.app.txt
- c++/src/algo/blast/unit_tests/seqdb_reader/CMakeLists.seqdb_unit_test.app.txt
- c++/src/algo/blast/unit_tests/seqdb_reader/CMakeLists.txt
- c++/src/algo/blast/unit_tests/seqdb_reader/Makefile.in
- c++/src/algo/blast/unit_tests/seqdb_reader/Makefile.seqdb_lmdb_unit_test.app
- c++/src/algo/blast/unit_tests/seqdb_reader/Makefile.seqdb_tax4blast_unit_test.app
- c++/src/algo/blast/unit_tests/seqdb_reader/Makefile.seqdb_unit_test.app
- c++/src/algo/blast/unit_tests/seqdb_reader/data/restart.pal
- c++/src/algo/blast/unit_tests/seqdb_reader/seqdb_unit_test.cpp
- c++/src/algo/blast/unit_tests/seqdb_reader/seqdb_unit_test.ini
- c++/src/algo/blast/vdb/blastn_vdb_args.cpp
- c++/src/algo/blast/vdb/common_priv.h
- c++/src/algo/blast/vdb/vdb2blast_util.cpp
- c++/src/algo/blast/vdb/vdb_priv.c
- c++/src/algo/blast/vdb/vdb_priv.h
- c++/src/algo/blast/vdb/vdbalias.cpp
- c++/src/algo/blast/vdb/vdbblast_local.cpp
- c++/src/app/CMakeLists.txt
- c++/src/app/blast/CMakeLists.blast_app_util.lib.txt
- c++/src/app/blast/CMakeLists.blastn.app.txt
- c++/src/app/blast/CMakeLists.blastp.app.txt
- c++/src/app/blast/CMakeLists.blastx.app.txt
- c++/src/app/blast/CMakeLists.deltablast.app.txt
- c++/src/app/blast/CMakeLists.psiblast.app.txt
- c++/src/app/blast/CMakeLists.rpsblast.app.txt
- c++/src/app/blast/CMakeLists.rpstblastn.app.txt
- c++/src/app/blast/CMakeLists.seedtop.app.txt
- c++/src/app/blast/CMakeLists.tblastn.app.txt
- c++/src/app/blast/CMakeLists.tblastx.app.txt
- c++/src/app/blast/CMakeLists.txt
- c++/src/app/blast/Makefile.blast_app_util.lib
- c++/src/app/blast/Makefile.blast_formatter.app
- c++/src/app/blast/Makefile.blastn.app
- c++/src/app/blast/Makefile.blastp.app
- c++/src/app/blast/Makefile.blastx.app
- c++/src/app/blast/Makefile.cleanup-blastdb-volumes.app
- c++/src/app/blast/Makefile.get_species_taxids.app
- c++/src/app/blast/Makefile.in
- c++/src/app/blast/Makefile.legacy_blast.app
- c++/src/app/blast/Makefile.psiblast.app
- c++/src/app/blast/Makefile.rpsblast.app
- c++/src/app/blast/Makefile.rpstblastn.app
- c++/src/app/blast/Makefile.seedtop.app
- c++/src/app/blast/Makefile.tblastn.app
- c++/src/app/blast/Makefile.tblastx.app
- c++/src/app/blast/Makefile.update_blastdb.app
- c++/src/app/blast/blast_app_util.cpp
- c++/src/app/blast/blast_app_util.hpp
- c++/src/app/blast/blastn_app.cpp
- c++/src/app/blast/blastp_app.cpp
- c++/src/app/blast/blastx_app.cpp
- c++/src/app/blast/tblastn_app.cpp
- c++/src/app/blast/update_blastdb.pl
- c++/src/app/blastdb/CMakeLists.blastdbcmd.app.txt
- c++/src/app/blastdb/Makefile.blastdb_aliastool.app
- c++/src/app/blastdb/Makefile.blastdb_convert.app
- c++/src/app/blastdb/Makefile.blastdb_path.app
- c++/src/app/blastdb/Makefile.blastdbcp.app
- c++/src/app/blastdb/Makefile.makeblastdb.app
- c++/src/app/blastdb/Makefile.makeprofiledb.app
- c++/src/app/blastdb/blastdbcmd.cpp
- c++/src/app/blastdb/blastdbcp.cpp
- c++/src/app/blastdb/makeblastdb.cpp
- c++/src/app/blastdb/makeprofiledb.cpp
- c++/src/app/blastvdb/Makefile.blast_formatter_vdb.app
- c++/src/app/blastvdb/Makefile.blast_vdb_cmd.app
- c++/src/app/blastvdb/Makefile.blastn_vdb.app
- c++/src/app/blastvdb/Makefile.tblastn_vdb.app
- c++/src/app/blastvdb/blast_vdb_cmd.cpp
- c++/src/app/blastvdb/blastn_vdb.cpp
- c++/src/app/blastvdb/tblastn_vdb.cpp
- c++/src/app/winmasker/Makefile.winmasker.app
- c++/src/build-system/Makefile.compress_tests
- c++/src/build-system/Makefile.dll.in
- c++/src/build-system/Makefile.flat_tuneups
- c++/src/build-system/Makefile.meta.gmake=yes
- c++/src/build-system/Makefile.meta_f
- c++/src/build-system/Makefile.mk.in
- c++/src/build-system/Makefile.mk.in.msvc
- c++/src/build-system/Makefile.mk.in.xcode
- c++/src/build-system/Makefile.xcode.tmpl
- c++/src/build-system/NEWS
- c++/src/build-system/cmake/CMake.NCBIComponents.cmake
- c++/src/build-system/cmake/CMake.NCBIComponentsCheck.cmake
- c++/src/build-system/cmake/CMake.NCBIComponentsMSVC.cmake
- c++/src/build-system/cmake/CMake.NCBIComponentsPackage.cmake
- c++/src/build-system/cmake/CMake.NCBIComponentsUNIXex.cmake
- c++/src/build-system/cmake/CMake.NCBIComponentsXCODE.cmake
- c++/src/build-system/cmake/CMake.NCBIpkg.codegen.cmake
- c++/src/build-system/cmake/CMake.NCBIpkg.conan.cmake
- c++/src/build-system/cmake/CMake.NCBIpkg.setup.cmake
- c++/src/build-system/cmake/CMake.NCBIptb.cmake
- c++/src/build-system/cmake/CMake.NCBIptb.ctest.cmake
- c++/src/build-system/cmake/CMake.NCBIptb.datatool.cmake
- c++/src/build-system/cmake/CMake.NCBIptb.definitions.cmake
- c++/src/build-system/cmake/CMake.NCBIptb.grpc.cmake
- c++/src/build-system/cmake/CMake.NCBIptb.install.cmake
- c++/src/build-system/cmake/CMake.NCBIptb.legacy.cmake
- c++/src/build-system/cmake/CMake.NCBIptb.ncbi.cmake
- c++/src/build-system/cmake/CMake.NCBIptb.ntest.cmake
- c++/src/build-system/cmake/CMake.NCBItoolkit.cmake
- c++/src/build-system/cmake/CMakeChecks.basic-checks.cmake
- c++/src/build-system/cmake/CMakeChecks.boost.cmake
- c++/src/build-system/cmake/CMakeChecks.cmake
- c++/src/build-system/cmake/CMakeChecks.compiler.cmake
- c++/src/build-system/cmake/CMakeChecks.final-message.cmake
- c++/src/build-system/cmake/CMakeChecks.srcid.cmake
- c++/src/build-system/cmake/CMakeMacros.cmake
- c++/src/build-system/cmake/TestDriver.cmake
- c++/src/build-system/cmake/cmClang.sh
- c++/src/build-system/cmake/cmICC.sh
- c++/src/build-system/cmake/cmake-cfg-unix.sh
- c++/src/build-system/cmake/cmake-cfg-vs.bat
- c++/src/build-system/cmake/cmake-cfg-xcode.sh
- c++/src/build-system/cmake/cmake_configure_ext_gpipe.sh
- − c++/src/build-system/cmake/conanfile.MSVC.txt
- − c++/src/build-system/cmake/conanfile.UNIX.txt
- − c++/src/build-system/cmake/conanfile.XCODE.txt
- c++/src/build-system/cmake/conanfile.py
- c++/src/build-system/cmake/config.cmake.h.in
- + c++/src/build-system/cmake/test-atomic64.cpp
- c++/src/build-system/cmake/toolchains/aarch64-darwin-clang.cmake
- c++/src/build-system/cmake/toolchains/aarch64-darwin-clang.cmake.in
- c++/src/build-system/cmake/toolchains/aarch64-linux-gcc.cmake
- c++/src/build-system/cmake/toolchains/aarch64-linux-gcc.cmake.in
- c++/src/build-system/cmake/toolchains/amd64-windows-msvc-192.cmake
- c++/src/build-system/cmake/toolchains/amd64-windows-msvc.cmake
- + c++/src/build-system/cmake/toolchains/arm64-darwin-clang.cmake.in
- c++/src/build-system/cmake/toolchains/cmkTool.sh
- c++/src/build-system/cmake/toolchains/x86_64-darwin-clang.cmake
- c++/src/build-system/cmake/toolchains/x86_64-darwin-clang.cmake.in
- c++/src/build-system/cmake/toolchains/x86_64-linux-clang-1600.cmake
- c++/src/build-system/cmake/toolchains/x86_64-linux-clang.cmake.in
- c++/src/build-system/cmake/toolchains/x86_64-linux-gcc-1220.cmake
- c++/src/build-system/cmake/toolchains/x86_64-linux-gcc-1320.cmake
- c++/src/build-system/cmake/toolchains/x86_64-linux-gcc-730.cmake
- c++/src/build-system/cmake/toolchains/x86_64-linux-gcc.cmake.in
- c++/src/build-system/cmake/toolchains/x86_64-linux-icc-210.cmake
- + c++/src/build-system/cmake/toolchains/x86_64-linux-icc-240.cmake
- c++/src/build-system/cmake/toolchains/x86_64-linux-icc.cmake.in
- c++/src/build-system/config.h.in
- c++/src/build-system/config.site.ex
- c++/src/build-system/config.site.ncbi
- c++/src/build-system/configure
- c++/src/build-system/configure.ac
- c++/src/build-system/datatool_version.txt
- c++/src/build-system/helpers/Makefile.run_with_lock.app
- c++/src/build-system/helpers/run_with_lock.c
- c++/src/build-system/install.sh.in
- c++/src/build-system/library_relations.txt
- c++/src/build-system/ncbi_package_version
- c++/src/build-system/project_tree_builder.ini
- c++/src/build-system/project_tree_builder/mac_prj_generator.cpp
- c++/src/build-system/project_tree_builder/proj_builder_app.cpp
- c++/src/build-system/project_tree_builder/proj_tree_builder.cpp
- c++/src/build-system/ptb_version.txt
- c++/src/build-system/relocate.sh.in
- c++/src/cgi/CMakeLists.cgi.lib.txt
- + c++/src/cgi/CMakeLists.fcgi_st.lib.txt
- c++/src/cgi/CMakeLists.txt
- c++/src/cgi/cgiapp.cpp
- c++/src/cgi/cgictx.cpp
- c++/src/cgi/fcgi_run.cpp
- c++/src/cgi/fcgiapp_mt.cpp
- + c++/src/cgi/fcgiapp_st.cpp
- c++/src/cgi/ncbicgi.cpp
- c++/src/connect/CMakeLists.txt
- + c++/src/connect/CMakeLists.xconnsftp.lib.txt
- c++/src/connect/Makefile.connect.lib
- c++/src/connect/Makefile.connect.lib.unix
- c++/src/connect/Makefile.connssl.lib
- c++/src/connect/Makefile.connssl.lib.unix
- c++/src/connect/Makefile.in
- + c++/src/connect/Makefile.xconnsftp.lib
- + c++/src/connect/Makefile.xconnsftp.mk
- c++/src/connect/connect_misc.cpp
- c++/src/connect/connect_misc_impl.hpp
- c++/src/connect/connection_pool.cpp
- c++/src/connect/ext/ncbi_dblb_svcmapper.cpp
- c++/src/connect/ext/ncbi_localnet.c
- c++/src/connect/mbedtls/aes.c
- + c++/src/connect/mbedtls/aesce.c
- + c++/src/connect/mbedtls/aesce.h
- c++/src/connect/mbedtls/aesni.c
- c++/src/connect/mbedtls/mbedtls/aesni.h → c++/src/connect/mbedtls/aesni.h
- + c++/src/connect/mbedtls/alignment.h
- − c++/src/connect/mbedtls/arc4.c
- c++/src/connect/mbedtls/aria.c
- c++/src/connect/mbedtls/asn1parse.c
- c++/src/connect/mbedtls/asn1write.c
- c++/src/connect/mbedtls/base64.c
- + c++/src/connect/mbedtls/base64_internal.h
- c++/src/connect/mbedtls/bignum.c
- + c++/src/connect/mbedtls/bignum_core.c
- + c++/src/connect/mbedtls/bignum_core.h
- + c++/src/connect/mbedtls/bignum_core_invasive.h
- c++/src/connect/mbedtls/bignum_internal.h
- + c++/src/connect/mbedtls/bignum_mod.c
- + c++/src/connect/mbedtls/bignum_mod.h
- + c++/src/connect/mbedtls/bignum_mod_raw.c
- + c++/src/connect/mbedtls/bignum_mod_raw.h
- + c++/src/connect/mbedtls/bignum_mod_raw_invasive.h
- + c++/src/connect/mbedtls/block_cipher.c
- + c++/src/connect/mbedtls/block_cipher_internal.h
- − c++/src/connect/mbedtls/blowfish.c
- c++/src/connect/mbedtls/mbedtls/bn_mul.h → c++/src/connect/mbedtls/bn_mul.h
- c++/src/connect/mbedtls/camellia.c
- c++/src/connect/mbedtls/ccm.c
- − c++/src/connect/mbedtls/certs.c
- c++/src/connect/mbedtls/chacha20.c
- c++/src/connect/mbedtls/chachapoly.c
- c++/src/connect/mbedtls/check_crypto_config.h
- c++/src/connect/mbedtls/cipher.c
- c++/src/connect/mbedtls/cipher_wrap.c
- c++/src/connect/mbedtls/mbedtls/cipher_internal.h → c++/src/connect/mbedtls/cipher_wrap.h
- c++/src/connect/mbedtls/cmac.c
- c++/src/connect/mbedtls/common.h
- c++/src/connect/mbedtls/constant_time.c
- + c++/src/connect/mbedtls/constant_time_impl.h
- c++/src/connect/mbedtls/constant_time_internal.h
- − c++/src/connect/mbedtls/constant_time_invasive.h
- + c++/src/connect/mbedtls/ctr.h
- c++/src/connect/mbedtls/ctr_drbg.c
- c++/src/connect/mbedtls/debug.c
- + c++/src/connect/mbedtls/debug_internal.h
- c++/src/connect/mbedtls/des.c
- c++/src/connect/mbedtls/dhm.c
- c++/src/connect/mbedtls/ecdh.c
- c++/src/connect/mbedtls/ecdsa.c
- c++/src/connect/mbedtls/ecjpake.c
- c++/src/connect/mbedtls/ecp.c
- c++/src/connect/mbedtls/ecp_curves.c
- + c++/src/connect/mbedtls/ecp_curves_new.c
- c++/src/connect/mbedtls/mbedtls/ecp_internal.h → c++/src/connect/mbedtls/ecp_internal_alt.h
- c++/src/connect/mbedtls/ecp_invasive.h
- c++/src/connect/mbedtls/entropy.c
- c++/src/connect/mbedtls/entropy_poll.c
- c++/src/connect/mbedtls/mbedtls/entropy_poll.h → c++/src/connect/mbedtls/entropy_poll.h
- c++/src/connect/mbedtls/error.c
- c++/src/connect/mbedtls/gcm.c
- − c++/src/connect/mbedtls/havege.c
- c++/src/connect/mbedtls/hmac_drbg.c
- + c++/src/connect/mbedtls/lmots.c
- + c++/src/connect/mbedtls/lmots.h
- + c++/src/connect/mbedtls/lms.c
- c++/src/connect/mbedtls/mbedtls/aes.h
- − c++/src/connect/mbedtls/mbedtls/arc4.h
- c++/src/connect/mbedtls/mbedtls/aria.h
- c++/src/connect/mbedtls/mbedtls/asn1.h
- c++/src/connect/mbedtls/mbedtls/asn1write.h
- c++/src/connect/mbedtls/mbedtls/base64.h
- c++/src/connect/mbedtls/mbedtls/bignum.h
- + c++/src/connect/mbedtls/mbedtls/block_cipher.h
- − c++/src/connect/mbedtls/mbedtls/blowfish.h
- + c++/src/connect/mbedtls/mbedtls/build_info.h
- c++/src/connect/mbedtls/mbedtls/camellia.h
- c++/src/connect/mbedtls/mbedtls/ccm.h
- − c++/src/connect/mbedtls/mbedtls/certs.h
- c++/src/connect/mbedtls/mbedtls/chacha20.h
- c++/src/connect/mbedtls/mbedtls/chachapoly.h
- c++/src/connect/mbedtls/mbedtls/check_config.h
- c++/src/connect/mbedtls/mbedtls/cipher.h
- c++/src/connect/mbedtls/mbedtls/cmac.h
- − c++/src/connect/mbedtls/mbedtls/compat-1.3.h
- + c++/src/connect/mbedtls/mbedtls/compat-2.x.h
- + c++/src/connect/mbedtls/mbedtls/config_adjust_legacy_crypto.h
- + c++/src/connect/mbedtls/mbedtls/config_adjust_legacy_from_psa.h
- + c++/src/connect/mbedtls/mbedtls/config_adjust_psa_from_legacy.h
- + c++/src/connect/mbedtls/mbedtls/config_adjust_psa_superset_legacy.h
- + c++/src/connect/mbedtls/mbedtls/config_adjust_ssl.h
- + c++/src/connect/mbedtls/mbedtls/config_adjust_x509.h
- c++/src/connect/mbedtls/mbedtls/config_psa.h
- c++/src/connect/mbedtls/mbedtls/constant_time.h
- c++/src/connect/mbedtls/mbedtls/ctr_drbg.h
- c++/src/connect/mbedtls/mbedtls/debug.h
- c++/src/connect/mbedtls/mbedtls/des.h
- c++/src/connect/mbedtls/mbedtls/dhm.h
- c++/src/connect/mbedtls/mbedtls/ecdh.h
- c++/src/connect/mbedtls/mbedtls/ecdsa.h
- c++/src/connect/mbedtls/mbedtls/ecjpake.h
- c++/src/connect/mbedtls/mbedtls/ecp.h
- c++/src/connect/mbedtls/mbedtls/entropy.h
- c++/src/connect/mbedtls/mbedtls/error.h
- c++/src/connect/mbedtls/mbedtls/gcm.h
- − c++/src/connect/mbedtls/mbedtls/havege.h
- c++/src/connect/mbedtls/mbedtls/hkdf.h
- c++/src/connect/mbedtls/mbedtls/hmac_drbg.h
- + c++/src/connect/mbedtls/mbedtls/lms.h
- c++/src/connect/mbedtls/mbedtls/config.h → c++/src/connect/mbedtls/mbedtls/mbedtls_config.h
- c++/src/connect/mbedtls/mbedtls/md.h
- − c++/src/connect/mbedtls/mbedtls/md2.h
- − c++/src/connect/mbedtls/mbedtls/md4.h
- c++/src/connect/mbedtls/mbedtls/md5.h
- c++/src/connect/mbedtls/mbedtls/memory_buffer_alloc.h
- c++/src/connect/mbedtls/mbedtls/ncbicxx_rename_mbedtls.h
- − c++/src/connect/mbedtls/mbedtls/net.h
- c++/src/connect/mbedtls/mbedtls/net_sockets.h
- c++/src/connect/mbedtls/mbedtls/nist_kw.h
- c++/src/connect/mbedtls/mbedtls/oid.h
- c++/src/connect/mbedtls/mbedtls/pem.h
- c++/src/connect/mbedtls/mbedtls/pk.h
- − c++/src/connect/mbedtls/mbedtls/pkcs11.h
- c++/src/connect/mbedtls/mbedtls/pkcs12.h
- c++/src/connect/mbedtls/mbedtls/pkcs5.h
- + c++/src/connect/mbedtls/mbedtls/pkcs7.h
- c++/src/connect/mbedtls/mbedtls/platform.h
- c++/src/connect/mbedtls/mbedtls/platform_time.h
- c++/src/connect/mbedtls/mbedtls/platform_util.h
- c++/src/connect/mbedtls/mbedtls/poly1305.h
- + c++/src/connect/mbedtls/mbedtls/private_access.h
- c++/src/connect/mbedtls/mbedtls/psa_util.h
- c++/src/connect/mbedtls/mbedtls/ripemd160.h
- c++/src/connect/mbedtls/mbedtls/rsa.h
- c++/src/connect/mbedtls/mbedtls/sha1.h
- c++/src/connect/mbedtls/mbedtls/sha256.h
- + c++/src/connect/mbedtls/mbedtls/sha3.h
- c++/src/connect/mbedtls/mbedtls/sha512.h
- c++/src/connect/mbedtls/mbedtls/ssl.h
- c++/src/connect/mbedtls/mbedtls/ssl_cache.h
- c++/src/connect/mbedtls/mbedtls/ssl_ciphersuites.h
- c++/src/connect/mbedtls/mbedtls/ssl_cookie.h
- c++/src/connect/mbedtls/mbedtls/ssl_ticket.h
- c++/src/connect/mbedtls/mbedtls/threading.h
- c++/src/connect/mbedtls/mbedtls/timing.h
- c++/src/connect/mbedtls/mbedtls/version.h
- c++/src/connect/mbedtls/mbedtls/x509.h
- c++/src/connect/mbedtls/mbedtls/x509_crl.h
- c++/src/connect/mbedtls/mbedtls/x509_crt.h
- c++/src/connect/mbedtls/mbedtls/x509_csr.h
- − c++/src/connect/mbedtls/mbedtls/xtea.h
- c++/src/connect/mbedtls/mbedtls_md5.c
- c++/src/connect/mbedtls/md.c
- − c++/src/connect/mbedtls/md2.c
- − c++/src/connect/mbedtls/md4.c
- + c++/src/connect/mbedtls/md_psa.h
- c++/src/connect/mbedtls/mbedtls/md_internal.h → c++/src/connect/mbedtls/md_wrap.h
- c++/src/connect/mbedtls/memory_buffer_alloc.c
- c++/src/connect/mbedtls/mps_common.h
- c++/src/connect/mbedtls/mps_reader.c
- c++/src/connect/mbedtls/mps_trace.c
- c++/src/connect/mbedtls/net_sockets.c
- c++/src/connect/mbedtls/nist_kw.c
- c++/src/connect/mbedtls/oid.c
- c++/src/connect/mbedtls/padlock.c
- c++/src/connect/mbedtls/mbedtls/padlock.h → c++/src/connect/mbedtls/padlock.h
- c++/src/connect/mbedtls/pem.c
- c++/src/connect/mbedtls/pk.c
- + c++/src/connect/mbedtls/pk_ecc.c
- + c++/src/connect/mbedtls/pk_internal.h
- c++/src/connect/mbedtls/pk_wrap.c
- c++/src/connect/mbedtls/mbedtls/pk_internal.h → c++/src/connect/mbedtls/pk_wrap.h
- − c++/src/connect/mbedtls/pkcs11.c
- c++/src/connect/mbedtls/pkcs12.c
- c++/src/connect/mbedtls/pkcs5.c
- + c++/src/connect/mbedtls/pkcs7.c
- c++/src/connect/mbedtls/pkparse.c
- c++/src/connect/mbedtls/pkwrite.c
- + c++/src/connect/mbedtls/pkwrite.h
- c++/src/connect/mbedtls/platform.c
- c++/src/connect/mbedtls/platform_util.c
- c++/src/connect/mbedtls/poly1305.c
- + c++/src/connect/mbedtls/psa/build_info.h
- c++/src/connect/mbedtls/psa/crypto.h
- + c++/src/connect/mbedtls/psa/crypto_adjust_auto_enabled.h
- + c++/src/connect/mbedtls/psa/crypto_adjust_config_dependencies.h
- + c++/src/connect/mbedtls/psa/crypto_adjust_config_key_pair_types.h
- + c++/src/connect/mbedtls/psa/crypto_adjust_config_synonyms.h
- c++/src/connect/mbedtls/psa/crypto_builtin_composites.h
- + c++/src/connect/mbedtls/psa/crypto_builtin_key_derivation.h
- c++/src/connect/mbedtls/psa/crypto_builtin_primitives.h
- c++/src/connect/mbedtls/psa/crypto_compat.h
- c++/src/connect/mbedtls/psa/crypto_config.h
- c++/src/connect/mbedtls/psa/crypto_driver_contexts_composites.h
- + c++/src/connect/mbedtls/psa/crypto_driver_contexts_key_derivation.h
- c++/src/connect/mbedtls/psa/crypto_driver_contexts_primitives.h
- c++/src/connect/mbedtls/psa/crypto_extra.h
- + c++/src/connect/mbedtls/psa/crypto_legacy.h
- c++/src/connect/mbedtls/psa/crypto_platform.h
- c++/src/connect/mbedtls/psa/crypto_se_driver.h
- c++/src/connect/mbedtls/psa/crypto_sizes.h
- c++/src/connect/mbedtls/psa/crypto_struct.h
- c++/src/connect/mbedtls/psa/crypto_types.h
- c++/src/connect/mbedtls/psa/crypto_values.h
- c++/src/connect/mbedtls/psa_crypto.c
- c++/src/connect/mbedtls/psa_crypto_aead.c
- c++/src/connect/mbedtls/psa_crypto_aead.h
- c++/src/connect/mbedtls/psa_crypto_cipher.c
- c++/src/connect/mbedtls/psa_crypto_cipher.h
- c++/src/connect/mbedtls/psa_crypto_client.c
- c++/src/connect/mbedtls/psa_crypto_core.h
- + c++/src/connect/mbedtls/psa_crypto_core_common.h
- − c++/src/connect/mbedtls/psa_crypto_driver_wrappers.c
- c++/src/connect/mbedtls/psa_crypto_driver_wrappers.h
- + c++/src/connect/mbedtls/psa_crypto_driver_wrappers_no_static.c
- + c++/src/connect/mbedtls/psa_crypto_driver_wrappers_no_static.h
- c++/src/connect/mbedtls/psa_crypto_ecp.c
- c++/src/connect/mbedtls/psa_crypto_ecp.h
- + c++/src/connect/mbedtls/psa_crypto_ffdh.c
- + c++/src/connect/mbedtls/psa_crypto_ffdh.h
- c++/src/connect/mbedtls/psa_crypto_hash.c
- c++/src/connect/mbedtls/psa_crypto_hash.h
- c++/src/connect/mbedtls/psa_crypto_invasive.h
- c++/src/connect/mbedtls/psa_crypto_mac.c
- + c++/src/connect/mbedtls/psa_crypto_pake.c
- + c++/src/connect/mbedtls/psa_crypto_pake.h
- c++/src/connect/mbedtls/psa_crypto_random_impl.h
- c++/src/connect/mbedtls/psa_crypto_rsa.c
- c++/src/connect/mbedtls/psa_crypto_rsa.h
- c++/src/connect/mbedtls/psa_crypto_se.c
- c++/src/connect/mbedtls/psa_crypto_se.h
- c++/src/connect/mbedtls/psa_crypto_slot_management.c
- c++/src/connect/mbedtls/psa_crypto_slot_management.h
- c++/src/connect/mbedtls/psa_crypto_storage.c
- c++/src/connect/mbedtls/psa_crypto_storage.h
- c++/src/connect/mbedtls/psa_its_file.c
- + c++/src/connect/mbedtls/psa_util.c
- + c++/src/connect/mbedtls/psa_util_internal.h
- c++/src/connect/mbedtls/ripemd160.c
- c++/src/connect/mbedtls/rsa.c
- c++/src/connect/mbedtls/rsa_internal.c → c++/src/connect/mbedtls/rsa_alt_helpers.c
- c++/src/connect/mbedtls/mbedtls/rsa_internal.h → c++/src/connect/mbedtls/rsa_alt_helpers.h
- + c++/src/connect/mbedtls/rsa_internal.h
- c++/src/connect/mbedtls/sha1.c
- c++/src/connect/mbedtls/sha256.c
- + c++/src/connect/mbedtls/sha3.c
- c++/src/connect/mbedtls/sha512.c
- c++/src/connect/mbedtls/ssl_cache.c
- c++/src/connect/mbedtls/ssl_ciphersuites.c
- + c++/src/connect/mbedtls/ssl_ciphersuites_internal.h
- + c++/src/connect/mbedtls/ssl_client.c
- + c++/src/connect/mbedtls/ssl_client.h
- c++/src/connect/mbedtls/ssl_cookie.c
- + c++/src/connect/mbedtls/ssl_debug_helpers.h
- + c++/src/connect/mbedtls/ssl_debug_helpers_generated.c
- c++/src/connect/mbedtls/mbedtls/ssl_internal.h → c++/src/connect/mbedtls/ssl_misc.h
- c++/src/connect/mbedtls/ssl_msg.c
- c++/src/connect/mbedtls/ssl_ticket.c
- c++/src/connect/mbedtls/ssl_tls.c
- c++/src/connect/mbedtls/ssl_cli.c → c++/src/connect/mbedtls/ssl_tls12_client.c
- c++/src/connect/mbedtls/ssl_srv.c → c++/src/connect/mbedtls/ssl_tls12_server.c
- + c++/src/connect/mbedtls/ssl_tls13_client.c
- + c++/src/connect/mbedtls/ssl_tls13_generic.c
- + c++/src/connect/mbedtls/ssl_tls13_invasive.h
- c++/src/connect/mbedtls/ssl_tls13_keys.c
- c++/src/connect/mbedtls/ssl_tls13_keys.h
- + c++/src/connect/mbedtls/ssl_tls13_server.c
- c++/src/connect/mbedtls/threading.c
- c++/src/connect/mbedtls/timing.c
- c++/src/connect/mbedtls/version_features.c
- c++/src/connect/mbedtls/x509.c
- c++/src/connect/mbedtls/x509_create.c
- c++/src/connect/mbedtls/x509_crl.c
- c++/src/connect/mbedtls/x509_crt.c
- c++/src/connect/mbedtls/x509_csr.c
- + c++/src/connect/mbedtls/x509_internal.h
- + c++/src/connect/mbedtls/x509write.c
- c++/src/connect/mbedtls/x509write_crt.c
- c++/src/connect/mbedtls/x509write_csr.c
- − c++/src/connect/mbedtls/xtea.c
- c++/src/connect/ncbi_base64.c
- c++/src/connect/ncbi_comm.h
- c++/src/connect/ncbi_conn_stream.cpp
- c++/src/connect/ncbi_conn_streambuf.cpp
- c++/src/connect/ncbi_conn_test.cpp
- c++/src/connect/ncbi_connection.c
- c++/src/connect/ncbi_connector.c
- c++/src/connect/ncbi_connutil.c
- c++/src/connect/ncbi_core_cxx.cpp
- c++/src/connect/ncbi_dispd.c
- c++/src/connect/ncbi_ftp_connector.c
- c++/src/connect/ncbi_gnutls.c
- c++/src/connect/ncbi_heapmgr.c
- c++/src/connect/ncbi_http2_session.cpp
- c++/src/connect/ncbi_http2_session_impl.hpp
- c++/src/connect/ncbi_http_connector.c
- c++/src/connect/ncbi_http_session.cpp
- c++/src/connect/ncbi_ipv6.c
- c++/src/connect/ncbi_lbdns.c
- c++/src/connect/ncbi_lbsmd.c
- c++/src/connect/ncbi_linkerd.c
- c++/src/connect/ncbi_localip.c
- c++/src/connect/ncbi_mbedtls.c
- c++/src/connect/ncbi_namedpipe.cpp
- c++/src/connect/ncbi_namerd.c
- c++/src/connect/ncbi_once.h
- c++/src/connect/ncbi_pipe.cpp
- c++/src/connect/ncbi_priv.c
- c++/src/connect/ncbi_priv.h
- c++/src/connect/ncbi_sendmail.c
- c++/src/connect/ncbi_service.c
- c++/src/connect/ncbi_service_connector.c
- c++/src/connect/ncbi_service_cxx.cpp
- c++/src/connect/ncbi_servicep.h
- + c++/src/connect/ncbi_sftp.cpp
- + c++/src/connect/ncbi_sftp_impl.hpp
- c++/src/connect/ncbi_socket.c
- c++/src/connect/ncbi_socketp.h
- c++/src/connect/ncbi_strerror.c
- c++/src/connect/ncbi_tls.c
- c++/src/connect/ncbi_usage_report.cpp
- c++/src/connect/ncbi_userhost.cpp
- c++/src/connect/ncbi_util.c
- c++/src/connect/ncbi_uv_nghttp2.cpp
- c++/src/connect/server.cpp
- c++/src/connect/server_monitor.cpp
- c++/src/connect/services/grid_rw_impl.cpp
- c++/src/connect/services/grid_worker.cpp
- c++/src/connect/services/json_over_uttp.cpp
- c++/src/connect/services/netservice_api.cpp
- c++/src/connect/services/netservice_params.cpp
- c++/src/connect/services/netstorageobjectloc.cpp
- c++/src/connect/services/srv_connections.cpp
- c++/src/connect/services/srv_connections_impl.hpp
- c++/src/connect/threaded_server.cpp
- c++/src/corelib/CMakeLists.corelib.lib.txt
- c++/src/corelib/CMakeLists.txt
- c++/src/corelib/Makefile.corelib.lib
- c++/src/corelib/Makefile.in
- c++/src/corelib/Makefile.test_mt.lib
- c++/src/corelib/env_reg.cpp
- c++/src/corelib/metareg.cpp
- c++/src/corelib/ncbi_base64.c
- c++/src/corelib/ncbi_cookies.cpp
- c++/src/corelib/ncbi_dbsvcmapper.cpp
- c++/src/corelib/ncbi_pool_balancer.cpp
- c++/src/corelib/ncbi_stack.cpp
- c++/src/corelib/ncbi_stack_libbackward.cpp
- c++/src/corelib/ncbi_system.cpp
- c++/include/objects/mla/Error_val.hpp → c++/src/corelib/ncbi_test.cpp
- c++/src/corelib/ncbi_url.cpp
- c++/src/corelib/ncbiapp.cpp
- c++/src/corelib/ncbiargs.cpp
- c++/src/corelib/ncbicfg.c.in
- c++/src/corelib/ncbidiag.cpp
- c++/src/corelib/ncbienv.cpp
- c++/src/corelib/ncbifile.cpp
- c++/src/corelib/ncbistr.cpp
- c++/src/corelib/ncbithr.cpp
- c++/src/corelib/ncbitime.cpp
- c++/src/corelib/request_ctx.cpp
- c++/src/corelib/request_status.cpp
- c++/src/corelib/rwstreambuf.cpp
- c++/src/corelib/test_boost.cpp
- c++/src/corelib/test_mt.cpp
- c++/src/corelib/version.cpp
- c++/src/dbapi/blobstream.cpp
- c++/src/dbapi/conn_impl.cpp
- c++/src/dbapi/conn_impl.hpp
- c++/src/dbapi/cursor_impl.cpp
- c++/src/dbapi/dbapi.cpp
- c++/src/dbapi/driver/CMakeLists.txt
- c++/src/dbapi/driver/Makefile.in
- c++/src/dbapi/driver/dbapi_conn_factory.cpp
- c++/src/dbapi/driver/dbapi_impl_connection.cpp
- c++/src/dbapi/driver/dbapi_impl_context.cpp
- c++/src/dbapi/driver/dbapi_pool_balancer.cpp
- c++/src/dbapi/driver/dbapi_svc_mapper.cpp
- c++/src/dbapi/driver/interfaces.cpp
- c++/src/dbapi/driver/odbc/connection.cpp
- c++/src/dbapi/driver/odbc/result.cpp
- c++/src/dbapi/driver/public.cpp
- c++/src/dbapi/rs_impl.cpp
- c++/src/dbapi/rw_impl.cpp
- c++/src/html/html.cpp
- c++/src/html/page.cpp
- c++/src/objects/CMakeLists.txt
- c++/src/objects/Makefile.in
- c++/src/objects/Makefile.sources
- c++/src/objects/blast/names.cpp
- c++/src/objects/entrez2/CMakeLists.entrez2cli.lib.txt
- c++/src/objects/entrezgene/Entrezgene.cpp
- c++/src/objects/gbproj/ProjectItem.cpp
- c++/src/objects/general/Dbtag.cpp
- c++/src/objects/general/Dbtag.inc
- c++/src/objects/general/User_field.cpp
- c++/src/objects/general/uoconv.cpp
- c++/src/objects/genomecoll/CMakeLists.gencoll_client.asn.txt
- c++/src/objects/id1/CMakeLists.id1cli.lib.txt
- c++/src/objects/id2/CMakeLists.id2cli.lib.txt
- c++/src/objects/id2/ID2_Request_Packet.cpp
- c++/src/objects/macro/CMakeLists.macro.asn.txt
- c++/src/objects/macro/String_constraint.cpp
- c++/src/objects/macro/macro.asn
- − c++/src/objects/mla/.cvsignore.extra
- − c++/src/objects/mla/CMakeLists.mla.asn.txt
- − c++/src/objects/mla/CMakeLists.mlacli.lib.txt
- − c++/src/objects/mla/CMakeLists.txt
- − c++/src/objects/mla/Makefile.mla.lib
- − c++/src/objects/mla/Makefile.mlacli.lib
- − c++/src/objects/mla/mla.asn
- − c++/src/objects/mla/mla.def
- − c++/src/objects/mla/mla.module
- c++/src/objects/nt_sources.sh
- c++/src/objects/pub/Pub.cpp
- c++/src/objects/remap/CMakeLists.remapcli.lib.txt
- c++/src/objects/remap/remap_client.cpp
- c++/src/objects/seq/Linkage_evidence.cpp
- c++/src/objects/seq/seq_align_mapper_base.cpp
- c++/src/objects/seq/seq_id_tree.cpp
- c++/src/objects/seq/seq_id_tree.hpp
- c++/src/objects/seq/so_map.cpp
- c++/src/objects/seqalign/Dense_seg.cpp
- c++/src/objects/seqalign/Seq_align.cpp
- c++/src/objects/seqalign/Spliced_seg.cpp
- c++/src/objects/seqfeat/BioSource.cpp
- c++/src/objects/seqfeat/Gb_qual.cpp
- c++/src/objects/seqfeat/OrgMod.cpp
- c++/src/objects/seqfeat/RNA_ref.cpp
- c++/src/objects/seqfeat/SeqFeatData.cpp
- c++/src/objects/seqfeat/SubSource.cpp
- c++/src/objects/seqfeat/ecnum_ambiguous.inc
- c++/src/objects/seqfeat/ecnum_deleted.inc
- c++/src/objects/seqfeat/ecnum_replaced.inc
- c++/src/objects/seqfeat/ecnum_replaced.txt
- c++/src/objects/seqfeat/ecnum_specific.inc
- c++/src/objects/seqfeat/ecnum_specific.txt
- c++/src/objects/seqfeat/institution_codes.inc
- c++/src/objects/seqfeat/institution_codes.txt
- c++/src/objects/seqloc/Seq_id.cpp
- c++/src/objects/seqloc/accguide.txt
- c++/src/objects/seqloc/accguide2.inc
- c++/src/objects/seqloc/accguide2.txt
- c++/src/objects/taxon1/local_taxon.cpp
- c++/src/objects/trackmgr/CMakeLists.trackmgrcli.lib.txt
- c++/src/objects/valerr/ValidErrItem.cpp
- c++/src/objects/valerr/ValidError.cpp
- c++/src/objects/valid/validrules.inc
- c++/src/objmgr/CMakeLists.objmgr.lib.txt
- c++/src/objmgr/Makefile.objmgr.lib
- c++/src/objmgr/annot_collector.cpp
- c++/src/objmgr/bioseq_base_info.cpp
- + c++/src/objmgr/bioseq_sort.cpp
- c++/src/objmgr/data_loader.cpp
- c++/src/objmgr/data_source.cpp
- c++/src/objmgr/scope.cpp
- c++/src/objmgr/scope_impl.cpp
- c++/src/objmgr/scope_info.cpp
- c++/src/objmgr/seq_id_sort.cpp
- c++/src/objmgr/seq_map.cpp
- c++/src/objmgr/seq_vector.cpp
- c++/src/objmgr/split/id_range.cpp
- c++/src/objmgr/tse_assigner.cpp
- c++/src/objmgr/tse_handle.cpp
- c++/src/objmgr/tse_split_info.cpp
- c++/src/objmgr/util/autodef.cpp
- c++/src/objmgr/util/autodef_options.cpp
- c++/src/objmgr/util/create_defline.cpp
- c++/src/objmgr/util/objutil.cpp
- c++/src/objmgr/util/seq_loc_util.cpp
- c++/src/objmgr/util/seqtitle.cpp
- c++/src/objmgr/util/sequence.cpp
- c++/src/objmgr/util/weight.cpp
- c++/src/objtools/CMakeLists.txt
- c++/src/objtools/Makefile.in
- c++/src/objtools/align_format/CMakeLists.align_format.lib.txt
- c++/src/objtools/align_format/Makefile.align_format.lib
- c++/src/objtools/align_format/align_format_util.cpp
- c++/src/objtools/align_format/format_flags.cpp
- c++/src/objtools/align_format/showalign.cpp
- c++/src/objtools/align_format/showdefline.cpp
- c++/src/objtools/align_format/tabular.cpp
- c++/src/objtools/align_format/taxFormat.cpp
- c++/src/objtools/align_format/unit_test/CMakeLists.align_format_unit_test.app.txt
- c++/src/objtools/align_format/unit_test/Makefile.align_format_unit_test.app
- c++/src/objtools/align_format/unit_test/align_format_unit_test.ini
- c++/src/objtools/align_format/unit_test/data/large_gi.asn
- c++/src/objtools/align_format/unit_test/data/nucl_32b_gi.ndb
- c++/src/objtools/align_format/unit_test/data/nucl_32b_gi.nin
- c++/src/objtools/align_format/unit_test/data/nucl_32b_gi.ntf
- c++/src/objtools/align_format/unit_test/tabularinof_unit_test.cpp
- c++/src/objtools/align_format/vectorscreen.cpp
- c++/src/objtools/alnmgr/aln_builders.cpp
- c++/src/objtools/alnmgr/aln_generators.cpp
- c++/src/objtools/alnmgr/alnmap.cpp
- c++/src/objtools/alnmgr/alnmatch.cpp
- c++/src/objtools/alnmgr/alnmerger.cpp
- c++/src/objtools/alnmgr/alnseq.cpp
- c++/src/objtools/alnmgr/alntext.cpp
- c++/src/objtools/alnmgr/alnvec.cpp
- c++/src/objtools/alnmgr/alnvec_iterator.cpp
- c++/src/objtools/alnmgr/score_builder_base.cpp
- c++/src/objtools/alnmgr/sparse_aln.cpp
- c++/src/objtools/blast/CMakeLists.txt
- c++/src/objtools/blast/Makefile.in
- c++/src/objtools/blast/blastdb_format/blastdb_dataextract.cpp
- c++/src/objtools/blast/blastdb_format/seq_formatter.cpp
- c++/src/objtools/blast/blastdb_format/unit_test/CMakeLists.blastdb_format_unit_test.app.txt
- c++/src/objtools/blast/blastdb_format/unit_test/Makefile.blastdb_format_unit_test.app
- + c++/src/objtools/blast/blastdb_format/unit_test/blastdb_format_unit_test.ini
- c++/src/objtools/blast/blastdb_format/unit_test/seq_writer_unit_test.cpp
- − c++/src/objtools/blast/gene_info_reader/CMakeLists.gene_info.lib.txt
- − c++/src/objtools/blast/gene_info_reader/CMakeLists.txt
- − c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
- − c++/src/objtools/blast/gene_info_reader/Makefile.in
- − c++/src/objtools/blast/gene_info_reader/demo/CMakeLists.gene_info_reader.app.txt
- − c++/src/objtools/blast/gene_info_reader/demo/CMakeLists.txt
- − c++/src/objtools/blast/gene_info_reader/demo/Makefile.gene_info_reader.app
- − c++/src/objtools/blast/gene_info_reader/demo/Makefile.in
- − c++/src/objtools/blast/gene_info_reader/demo/gene_info_reader_app.cpp
- − c++/src/objtools/blast/gene_info_reader/file_utils.cpp
- − c++/src/objtools/blast/gene_info_reader/gene_info.cpp
- − c++/src/objtools/blast/gene_info_reader/gene_info_reader.cpp
- − c++/src/objtools/blast/gene_info_reader/unit_test/CMakeLists.gene_info_unit_test.app.txt
- − c++/src/objtools/blast/gene_info_reader/unit_test/CMakeLists.txt
- − c++/src/objtools/blast/gene_info_reader/unit_test/Makefile.gene_info_unit_test.app
- − c++/src/objtools/blast/gene_info_reader/unit_test/Makefile.in
- − c++/src/objtools/blast/gene_info_reader/unit_test/data/geneinfo.dat
- − c++/src/objtools/blast/gene_info_reader/unit_test/data/geneinfo.g2i
- − c++/src/objtools/blast/gene_info_reader/unit_test/data/geneinfo.g2o
- − c++/src/objtools/blast/gene_info_reader/unit_test/data/geneinfo.i2g
- − c++/src/objtools/blast/gene_info_reader/unit_test/data/geneinfo.i2o
- − c++/src/objtools/blast/gene_info_reader/unit_test/gene_info_test.cpp
- − c++/src/objtools/blast/gene_info_reader/unit_test/gene_info_unit_test.ini
- c++/src/objtools/blast/seqdb_reader/CMakeLists.seqdb.lib.txt
- c++/src/objtools/blast/seqdb_reader/Makefile.in
- c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
- c++/src/objtools/blast/seqdb_reader/demo/CMakeLists.tax4blast.app.txt
- c++/src/objtools/blast/seqdb_reader/demo/CMakeLists.txt
- c++/src/objtools/blast/seqdb_reader/demo/Makefile.in
- c++/src/objtools/blast/seqdb_reader/demo/Makefile.seqdb_demo.app
- c++/src/objtools/blast/seqdb_reader/demo/Makefile.tax4blast.app
- c++/src/objtools/blast/seqdb_reader/demo/tax4blast.cpp
- c++/src/objtools/blast/seqdb_reader/seqdb.cpp
- c++/src/objtools/blast/seqdb_reader/seqdb_lmdb.cpp
- c++/src/objtools/blast/seqdb_reader/seqdbalias.cpp
- c++/src/objtools/blast/seqdb_reader/seqdbblob.cpp
- c++/src/objtools/blast/seqdb_reader/seqdbcommon.cpp
- c++/src/objtools/blast/seqdb_reader/seqdbfile.cpp
- c++/src/objtools/blast/seqdb_reader/seqdbgilistset.cpp
- c++/src/objtools/blast/seqdb_reader/seqdbimpl.cpp
- c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
- c++/src/objtools/blast/seqdb_reader/seqdbisam.cpp
- c++/src/objtools/blast/seqdb_reader/seqdboidlist.cpp
- c++/src/objtools/blast/seqdb_reader/seqdboidlist.hpp
- c++/src/objtools/blast/seqdb_reader/seqdbtax.cpp
- c++/src/objtools/blast/seqdb_reader/seqdbvol.cpp
- c++/src/objtools/blast/seqdb_reader/tax4blastsqlite.cpp
- c++/src/objtools/blast/seqdb_reader/test/CMakeLists.seqdb_perf.app.txt
- c++/src/objtools/blast/seqdb_reader/test/Makefile.seqdb_perf.app
- c++/src/objtools/blast/seqdb_writer/build-alias-index
- c++/src/objtools/blast/seqdb_writer/build_db.cpp
- c++/src/objtools/blast/seqdb_writer/seqidlist_writer.cpp
- c++/src/objtools/blast/seqdb_writer/unit_test/CMakeLists.writedb_lmdb_unit_test.app.txt
- c++/src/objtools/blast/seqdb_writer/unit_test/CMakeLists.writedb_unit_test.app.txt
- c++/src/objtools/blast/seqdb_writer/unit_test/Makefile.writedb_lmdb_unit_test.app
- c++/src/objtools/blast/seqdb_writer/unit_test/Makefile.writedb_unit_test.app
- + c++/src/objtools/blast/seqdb_writer/unit_test/data/test_vol.00.phr
- + c++/src/objtools/blast/seqdb_writer/unit_test/data/test_vol.00.pin
- + c++/src/objtools/blast/seqdb_writer/unit_test/data/test_vol.00.pog
- + c++/src/objtools/blast/seqdb_writer/unit_test/data/test_vol.00.ppd
- + c++/src/objtools/blast/seqdb_writer/unit_test/data/test_vol.00.ppi
- + c++/src/objtools/blast/seqdb_writer/unit_test/data/test_vol.00.psd
- + c++/src/objtools/blast/seqdb_writer/unit_test/data/test_vol.00.psi
- + c++/src/objtools/blast/seqdb_writer/unit_test/data/test_vol.00.psq
- + c++/src/objtools/blast/seqdb_writer/unit_test/data/test_vol.01.phr
- + c++/src/objtools/blast/seqdb_writer/unit_test/data/test_vol.01.pin
- + c++/src/objtools/blast/seqdb_writer/unit_test/data/test_vol.01.pog
- + c++/src/objtools/blast/seqdb_writer/unit_test/data/test_vol.01.ppd
- + c++/src/objtools/blast/seqdb_writer/unit_test/data/test_vol.01.ppi
- + c++/src/objtools/blast/seqdb_writer/unit_test/data/test_vol.01.psd
- + c++/src/objtools/blast/seqdb_writer/unit_test/data/test_vol.01.psi
- + c++/src/objtools/blast/seqdb_writer/unit_test/data/test_vol.01.psq
- + c++/src/objtools/blast/seqdb_writer/unit_test/data/test_vol.02.phr
- + c++/src/objtools/blast/seqdb_writer/unit_test/data/test_vol.02.pin
- + c++/src/objtools/blast/seqdb_writer/unit_test/data/test_vol.02.pog
- + c++/src/objtools/blast/seqdb_writer/unit_test/data/test_vol.02.ppd
- + c++/src/objtools/blast/seqdb_writer/unit_test/data/test_vol.02.ppi
- + c++/src/objtools/blast/seqdb_writer/unit_test/data/test_vol.02.psd
- + c++/src/objtools/blast/seqdb_writer/unit_test/data/test_vol.02.psi
- + c++/src/objtools/blast/seqdb_writer/unit_test/data/test_vol.02.psq
- c++/src/objtools/blast/seqdb_writer/unit_test/writedb_unit_test.cpp
- c++/src/objtools/blast/seqdb_writer/unit_test/writedb_unit_test.ini
- c++/src/objtools/blast/seqdb_writer/writedb.cpp
- c++/src/objtools/blast/seqdb_writer/writedb_impl.cpp
- c++/src/objtools/blast/seqdb_writer/writedb_impl.hpp
- c++/src/objtools/blast/services/Makefile.blast_services.lib
- c++/src/objtools/blast/services/unit_test/Makefile.blast_services_unit_test.app
- c++/src/objtools/cleanup/CMakeLists.cleanup.lib.txt
- c++/src/objtools/cleanup/Makefile.cleanup.lib
- c++/src/objtools/cleanup/autogenerated_cleanup.cpp
- c++/src/objtools/cleanup/autogenerated_cleanup.hpp
- c++/src/objtools/cleanup/autogenerated_extended_cleanup.cpp
- c++/src/objtools/cleanup/capitalization_string.cpp
- c++/src/objtools/cleanup/cleanup.cpp
- c++/src/objtools/cleanup/cleanup_pub.cpp
- c++/src/objtools/cleanup/cleanup_utils.cpp
- c++/src/objtools/cleanup/cleanup_utils.hpp
- c++/src/objtools/cleanup/fix_feature_id.cpp
- c++/src/objtools/cleanup/influenza_set.cpp
- c++/src/objtools/cleanup/newcleanupp.cpp
- c++/src/objtools/cleanup/newcleanupp.hpp
- c++/src/objtools/data_loaders/blastdb/bdbloader_rmt.cpp
- c++/src/objtools/data_loaders/blastdb/remote_blastdb_adapter.hpp
- c++/src/objtools/data_loaders/genbank/CMakeLists.ncbi_xloader_genbank.lib.txt
- c++/src/objtools/data_loaders/genbank/CMakeLists.ncbi_xreader.lib.txt
- c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
- c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
- c++/src/objtools/data_loaders/genbank/blob_id.cpp
- c++/src/objtools/data_loaders/genbank/dispatcher.cpp
- c++/src/objtools/data_loaders/genbank/gbloader.cpp
- c++/src/objtools/data_loaders/genbank/gbnative.cpp
- c++/src/objtools/data_loaders/genbank/gicache/reader_gicache.cpp
- c++/src/objtools/data_loaders/genbank/id1/reader_id1.cpp
- c++/src/objtools/data_loaders/genbank/info_cache.cpp
- c++/src/objtools/data_loaders/genbank/processors.cpp
- + c++/src/objtools/data_loaders/genbank/psg_blob_processor.cpp
- + c++/src/objtools/data_loaders/genbank/psg_cache.cpp
- + c++/src/objtools/data_loaders/genbank/psg_cdd.cpp
- + c++/src/objtools/data_loaders/genbank/psg_evloop.cpp
- c++/src/objtools/data_loaders/genbank/psg_loader.cpp
- c++/src/objtools/data_loaders/genbank/psg_loader_impl.cpp
- + c++/src/objtools/data_loaders/genbank/psg_processor.cpp
- + c++/src/objtools/data_loaders/genbank/psg_processors.cpp
- c++/src/objtools/data_loaders/genbank/reader.cpp
- c++/src/objtools/data_loaders/genbank/reader_id2_base.cpp
- c++/src/objtools/data_loaders/genbank/request_result.cpp
- c++/src/objtools/edit/CMakeLists.edit.lib.txt
- c++/src/objtools/edit/Makefile.edit.lib
- c++/src/objtools/edit/dblink_field.cpp
- c++/src/objtools/edit/eutils_updater.cpp
- c++/src/objtools/edit/feattable_edit.cpp
- c++/src/objtools/edit/gaps_edit.cpp
- c++/src/objtools/edit/mail_report.cpp
- c++/src/objtools/edit/pub_fix.cpp
- c++/src/objtools/edit/pub_fix_aux.hpp
- c++/src/objtools/edit/remote_updater.cpp
- c++/src/objtools/edit/seq_entry_edit.cpp
- c++/src/objtools/edit/text_object_description.cpp
- c++/src/objtools/eutils/api/efetch.cpp
- c++/src/objtools/eutils/api/eutils.cpp
- c++/src/objtools/eutils/efetch/CMakeLists.efetch.lib.txt
- c++/src/objtools/eutils/efetch/Makefile.in
- c++/src/objtools/eutils/efetch/PubmedArticle.cpp
- c++/src/objtools/eutils/efetch/PubmedBookArticle.cpp
- c++/src/objtools/eutils/efetch/efetch.xsd
- c++/src/objtools/format/CMakeLists.txt
- c++/src/objtools/format/CMakeLists.xformat.lib.txt
- c++/src/objtools/format/Makefile.in
- c++/src/objtools/format/Makefile.xformat.lib
- c++/src/objtools/format/alignment_item.cpp
- c++/src/objtools/format/cigar_formatter.cpp
- c++/src/objtools/format/comment_item.cpp
- c++/src/objtools/format/dbsource_item.cpp
- c++/src/objtools/format/defline_item.cpp
- c++/src/objtools/format/embl_formatter.cpp
- c++/src/objtools/format/feature_item.cpp
- c++/src/objtools/format/flat_file_config.cpp
- c++/src/objtools/format/flat_file_generator.cpp
- c++/src/objtools/format/flat_file_html.cpp
- c++/src/objtools/format/flat_seqloc.cpp
- c++/src/objtools/format/gather_items.cpp
- c++/src/objtools/format/gbseq_formatter.cpp
- c++/src/objtools/format/genbank_formatter.cpp
- c++/src/objtools/format/genbank_gather.cpp
- c++/src/objtools/format/gene_finder.cpp
- c++/src/objtools/format/genome_project_item.cpp
- c++/src/objtools/format/inst_info_map.cpp
- c++/src/objtools/format/item_formatter.cpp
- c++/src/objtools/format/keywords_item.cpp
- c++/src/objtools/format/locus_item.cpp
- c++/src/objtools/format/qualifiers.cpp
- c++/src/objtools/format/reference_item.cpp
- c++/src/objtools/format/source_item.cpp
- c++/src/objtools/logging/message.cpp
- c++/src/objtools/pubseq_gateway/CMakeLists.txt
- c++/src/objtools/pubseq_gateway/Makefile.in
- c++/src/objtools/pubseq_gateway/client/CMakeLists.psg_client.lib.txt
- c++/src/objtools/pubseq_gateway/client/Makefile.psg_client_macros.mk
- c++/src/objtools/pubseq_gateway/client/psg_client.cpp
- c++/src/objtools/pubseq_gateway/client/psg_client_impl.hpp
- c++/src/objtools/pubseq_gateway/client/psg_client_transport.cpp
- c++/src/objtools/pubseq_gateway/client/psg_client_transport.hpp
- c++/src/objtools/pubseq_gateway/client/test/test_psg_client_impl.cpp
- c++/src/objtools/readers/agp_util.cpp
- c++/src/objtools/readers/agp_validate_reader.cpp
- c++/src/objtools/readers/aln_formatguess.cpp
- c++/src/objtools/readers/aln_reader.cpp
- c++/src/objtools/readers/alnread.cpp
- c++/src/objtools/readers/bed_column_data.cpp
- c++/src/objtools/readers/bed_reader.cpp
- c++/src/objtools/readers/descr_mod_apply.cpp
- c++/src/objtools/readers/fasta.cpp
- c++/src/objtools/readers/fasta_reader_utils.cpp
- c++/src/objtools/readers/feature_mod_apply.cpp
- c++/src/objtools/readers/gff2_data.cpp
- c++/src/objtools/readers/gff2_reader.cpp
- c++/src/objtools/readers/gff3_location_merger.cpp
- c++/src/objtools/readers/gff3_reader.cpp
- c++/src/objtools/readers/glimmer_reader.cpp
- c++/src/objtools/readers/gtf_location_merger.cpp
- c++/src/objtools/readers/gtf_location_merger.hpp
- c++/src/objtools/readers/gtf_reader.cpp
- c++/src/objtools/readers/gvf_reader.cpp
- c++/src/objtools/readers/idmapper_config.cpp
- c++/src/objtools/readers/idmapper_gcassembly.cpp
- c++/src/objtools/readers/line_error.cpp
- c++/src/objtools/readers/mod_reader.cpp
- c++/src/objtools/readers/mod_to_enum.cpp
- c++/src/objtools/readers/reader_base.cpp
- c++/src/objtools/readers/readfeat.cpp
- c++/src/objtools/readers/rm_reader.cpp
- c++/src/objtools/readers/source_mod_parser.cpp
- c++/src/objtools/readers/struct_cmt_reader.cpp
- c++/src/objtools/readers/vcf_reader.cpp
- c++/src/objtools/readers/wiggle_reader.cpp
- c++/src/serial/datatool/aliasstr.cpp
- c++/src/serial/datatool/choicestr.cpp
- c++/src/serial/datatool/datatool.hpp
- c++/src/serial/datatool/enumtype.cpp
- c++/src/serial/datatool/mcontainer.cpp
- c++/src/serial/datatool/mcontainer.hpp
- c++/src/serial/datatool/xsdlexer.cpp
- c++/src/serial/datatool/xsdparser.cpp
- c++/src/serial/grpc_integration/CMakeLists.grpc_integration.lib.txt
- c++/src/serial/grpc_integration/grpc_integration.cpp
- c++/src/serial/memberlist.cpp
- c++/src/serial/objistr.cpp
- c++/src/serial/objistrxml.cpp
- c++/src/serial/objostr.cpp
- c++/src/serial/objostrasn.cpp
- c++/src/serial/objostrasnb.cpp
- c++/src/serial/objostrxml.cpp
- c++/src/serial/stdtypes.cpp
- c++/src/sra/data_loaders/bam/bamloader_impl.cpp
- c++/src/sra/data_loaders/bam/test/CMakeLists.test_bam_loader.app.txt
- c++/src/sra/data_loaders/bam/test/Makefile.test_bam_loader.app
- c++/src/sra/data_loaders/bam/test/test_bam_loader.cpp
- c++/src/sra/data_loaders/csra/csraloader.cpp
- c++/src/sra/data_loaders/csra/csraloader_impl.cpp
- c++/src/sra/data_loaders/csra/test/CMakeLists.txt
- c++/src/sra/data_loaders/csra/test/Makefile.test_csra_loader.app
- c++/src/sra/data_loaders/csra/test/Makefile.test_csra_loader_mt.app
- c++/src/sra/data_loaders/csra/test/Makefile.test_sra.app
- c++/src/sra/data_loaders/csra/test/test_csra_loader.cpp
- c++/src/sra/data_loaders/csra/test/test_csra_loader_mt.cpp
- c++/src/sra/data_loaders/snp/snploader.cpp
- c++/src/sra/data_loaders/snp/snploader_impl.cpp
- c++/src/sra/data_loaders/sra/test/CMakeLists.test_sra_loader.app.txt
- c++/src/sra/data_loaders/sra/test/Makefile.test_sra_loader.app
- c++/src/sra/data_loaders/vdbgraph/test/CMakeLists.test_vdbgraph_loader.app.txt
- c++/src/sra/data_loaders/vdbgraph/test/Makefile.test_vdbgraph_loader.app
- c++/src/sra/data_loaders/vdbgraph/test/test_vdbgraph_loader.cpp
- + c++/src/sra/data_loaders/vdbgraph/test/test_vdbgraph_loader.ini
- c++/src/sra/data_loaders/vdbgraph/vdbgraphloader_impl.cpp
- c++/src/sra/data_loaders/wgs/wgsloader.cpp
- c++/src/sra/data_loaders/wgs/wgsloader_impl.cpp
- c++/src/sra/readers/bam/bamgraph.cpp
- c++/src/sra/readers/bam/bamindex.cpp
- c++/src/sra/readers/bam/bamread.cpp
- c++/src/sra/readers/bam/bgzf.cpp
- c++/src/sra/readers/bam/vdbfile.cpp
- c++/src/sra/readers/sra/CMakeLists.sraread.lib.txt
- c++/src/sra/readers/sra/Makefile.sraread.lib
- c++/src/sra/readers/sra/csraread.cpp
- c++/src/sra/readers/sra/graphread.cpp
- c++/src/sra/readers/sra/snpread.cpp
- c++/src/sra/readers/sra/snpread_packed.cpp
- c++/src/sra/readers/sra/sraread.cpp
- c++/src/sra/readers/sra/vdbcache.cpp
- c++/src/sra/readers/sra/vdbread.cpp
- c++/src/sra/readers/sra/wgsread.cpp
- c++/src/sra/readers/sra/wgsresolver_impl.cpp
- c++/src/util/CMakeLists.util.lib.txt
- c++/src/util/Makefile.util.lib
- c++/src/util/bytesrc.cpp
- c++/src/util/cache_async.cpp
- c++/src/util/checksum/cityhash/city.cc
- c++/src/util/checksum/farmhash/farmhash.cc
- c++/src/util/compress/CMakeLists.txt
- c++/src/util/compress/Makefile.in
- c++/src/util/compress/api/CMakeLists.compress.lib.txt
- c++/src/util/compress/api/Makefile.compress.lib
- c++/src/util/compress/api/Makefile.in
- c++/src/util/compress/api/archive.cpp
- c++/src/util/compress/api/bzip2.cpp
- c++/src/util/compress/api/lzo.cpp
- c++/src/util/compress/api/stream_util.cpp
- c++/src/util/compress/api/tar.cpp
- c++/src/util/compress/api/zlib.cpp
- + c++/src/util/compress/api/zlib_cloudflare.cpp
- c++/src/util/compress/api/zstd.cpp
- c++/src/util/compress/bzip2/CHANGES
- c++/src/util/compress/bzip2/LICENSE
- c++/src/util/compress/bzip2/README
- c++/src/util/compress/bzip2/README.COMPILATION.PROBLEMS
- − c++/src/util/compress/bzip2/README.XML.STUFF
- c++/src/util/compress/bzip2/blocksort.c
- c++/src/util/compress/bzip2/bzdiff
- c++/src/util/compress/bzip2/bzgrep
- c++/src/util/compress/bzip2/bzip.css
- c++/src/util/compress/bzip2/bzip2.1
- c++/src/util/compress/bzip2/bzip2.c
- c++/src/util/compress/bzip2/bzip2.txt
- c++/src/util/compress/bzip2/bzip2recover.c
- c++/src/util/compress/bzip2/bzlib.c
- c++/src/util/compress/bzip2/bzlib_private.h
- c++/src/util/compress/bzip2/compress.c
- c++/src/util/compress/bzip2/crctable.c
- c++/src/util/compress/bzip2/decompress.c
- c++/src/util/compress/bzip2/huffman.c
- c++/src/util/compress/bzip2/manual.html
- c++/src/util/compress/bzip2/manual.pdf
- c++/src/util/compress/bzip2/mk251.c
- c++/src/util/compress/bzip2/randtable.c
- c++/src/util/compress/bzip2/spewG.c
- c++/src/util/compress/bzip2/unzcrash.c
- + c++/src/util/compress/zlib_cloudflare/CMakeLists.txt
- + c++/src/util/compress/zlib_cloudflare/CMakeLists.zlib_cf.lib.txt
- + c++/src/util/compress/zlib_cloudflare/ChangeLog
- + c++/src/util/compress/zlib_cloudflare/FAQ
- + c++/src/util/compress/zlib_cloudflare/INDEX
- + c++/src/util/compress/zlib_cloudflare/LICENSE
- c++/src/objects/mla/Makefile.in → c++/src/util/compress/zlib_cloudflare/Makefile.in
- + c++/src/util/compress/zlib_cloudflare/Makefile.zlib_cf.lib
- + c++/src/util/compress/zlib_cloudflare/Makefile.zlib_cf.lib.unix
- + c++/src/util/compress/zlib_cloudflare/README
- + c++/src/util/compress/zlib_cloudflare/_gitversion
- + c++/src/util/compress/zlib_cloudflare/_patch
- + c++/src/util/compress/zlib_cloudflare/_readme
- + c++/src/util/compress/zlib_cloudflare/adler32.c
- + c++/src/util/compress/zlib_cloudflare/adler32_simd.c
- + c++/src/util/compress/zlib_cloudflare/adler32_simd.h
- + c++/src/util/compress/zlib_cloudflare/chunkcopy.h
- + c++/src/util/compress/zlib_cloudflare/compress.c
- + c++/src/util/compress/zlib_cloudflare/crc32.c
- + c++/src/util/compress/zlib_cloudflare/crc32.h
- + c++/src/util/compress/zlib_cloudflare/crc32_simd.c
- + c++/src/util/compress/zlib_cloudflare/crc32_simd.h
- + c++/src/util/compress/zlib_cloudflare/deflate.c
- + c++/src/util/compress/zlib_cloudflare/deflate.h
- + c++/src/util/compress/zlib_cloudflare/gzclose.c
- + c++/src/util/compress/zlib_cloudflare/gzguts.h
- + c++/src/util/compress/zlib_cloudflare/gzlib.c
- + c++/src/util/compress/zlib_cloudflare/gzread.c
- + c++/src/util/compress/zlib_cloudflare/gzwrite.c
- + c++/src/util/compress/zlib_cloudflare/infback.c
- + c++/src/util/compress/zlib_cloudflare/inffast.c
- + c++/src/util/compress/zlib_cloudflare/inffast.h
- + c++/src/util/compress/zlib_cloudflare/inffast_chunk.c
- + c++/src/util/compress/zlib_cloudflare/inffast_chunk.h
- + c++/src/util/compress/zlib_cloudflare/inffixed.h
- + c++/src/util/compress/zlib_cloudflare/inflate.c
- + c++/src/util/compress/zlib_cloudflare/inflate.h
- + c++/src/util/compress/zlib_cloudflare/inftrees.c
- + c++/src/util/compress/zlib_cloudflare/inftrees.h
- + c++/src/util/compress/zlib_cloudflare/ncbi_z_compress.c
- + c++/src/util/compress/zlib_cloudflare/trees.c
- + c++/src/util/compress/zlib_cloudflare/trees.h
- + c++/src/util/compress/zlib_cloudflare/uncompr.c
- + c++/src/util/compress/zlib_cloudflare/zutil.c
- c++/src/util/format_guess.cpp
- c++/src/objtools/data_loaders/genbank/incr_time.cpp → c++/src/util/incr_time.cpp
- + c++/src/util/memory_streambuf.cpp
- c++/src/util/miscmath.c
- c++/src/util/multi_writer.cpp
- c++/src/util/multipattern_search.cpp
- c++/src/util/multipattern_search_impl.hpp
- c++/src/util/regexp/AUTHORS
- c++/src/util/regexp/CMakeLists.regexp.lib.txt
- c++/src/util/regexp/CMakeLists.test_pcre.app.txt
- c++/src/util/regexp/ChangeLog
- c++/src/util/regexp/HACKING
- c++/src/util/regexp/LICENCE
- c++/src/util/regexp/Makefile.regexp.lib
- c++/src/util/regexp/Makefile.test_pcre.app
- c++/src/util/regexp/NEWS
- c++/src/util/regexp/README
- c++/src/util/regexp/README.NCBI
- c++/src/util/regexp/RunTest
- c++/src/util/regexp/RunTest.bat
- c++/src/util/regexp/config.h
- + c++/src/util/regexp/config.h.generic
- + c++/src/util/regexp/pcre2_auto_possess.c
- c++/src/util/regexp/pcre_chartables.c → c++/src/util/regexp/pcre2_chartables.c
- c++/src/util/regexp/pcre_refcount.c → c++/src/util/regexp/pcre2_chkdint.c
- + c++/src/util/regexp/pcre2_compile.c
- c++/src/util/regexp/pcre_fullinfo.c → c++/src/util/regexp/pcre2_config.c
- + c++/src/util/regexp/pcre2_context.c
- + c++/src/util/regexp/pcre2_convert.c
- c++/src/util/regexp/pcre_dfa_exec.c → c++/src/util/regexp/pcre2_dfa_match.c
- + c++/src/util/regexp/pcre2_dftables.c
- + c++/src/util/regexp/pcre2_error.c
- c++/src/util/regexp/pcre_config.c → c++/src/util/regexp/pcre2_extuni.c
- + c++/src/util/regexp/pcre2_find_bracket.c
- + c++/src/util/regexp/pcre2_fuzzsupport.c
- c++/src/util/regexp/pcre_internal.h → c++/src/util/regexp/pcre2_internal.h
- + c++/src/util/regexp/pcre2_intmodedep.h
- c++/src/util/regexp/pcre_jit_compile.c → c++/src/util/regexp/pcre2_jit_compile.c
- + c++/src/util/regexp/pcre2_jit_match.c
- + c++/src/util/regexp/pcre2_jit_misc.c
- + c++/src/util/regexp/pcre2_jit_neon_inc.h
- + c++/src/util/regexp/pcre2_jit_simd_inc.h
- + c++/src/util/regexp/pcre2_jit_test.c
- c++/src/util/regexp/pcre_maketables.c → c++/src/util/regexp/pcre2_maketables.c
- + c++/src/util/regexp/pcre2_match.c
- + c++/src/util/regexp/pcre2_match_data.c
- c++/src/util/regexp/pcre_newline.c → c++/src/util/regexp/pcre2_newline.c
- c++/src/util/regexp/pcre_ord2utf8.c → c++/src/util/regexp/pcre2_ord2utf.c
- c++/src/util/regexp/pcre_byte_order.c → c++/src/util/regexp/pcre2_pattern_info.c
- c++/src/util/regexp/pcre_printint.c → c++/src/util/regexp/pcre2_printint.c
- + c++/src/util/regexp/pcre2_script_run.c
- + c++/src/util/regexp/pcre2_serialize.c
- c++/src/util/regexp/pcre_string_utils.c → c++/src/util/regexp/pcre2_string_utils.c
- c++/src/util/regexp/pcre_study.c → c++/src/util/regexp/pcre2_study.c
- + c++/src/util/regexp/pcre2_substitute.c
- + c++/src/util/regexp/pcre2_substring.c
- + c++/src/util/regexp/pcre2_tables.c
- + c++/src/util/regexp/pcre2_ucd.c
- c++/src/util/regexp/ucp.h → c++/src/util/regexp/pcre2_ucp.h
- + c++/src/util/regexp/pcre2_ucptables.c
- c++/src/util/regexp/pcre_valid_utf8.c → c++/src/util/regexp/pcre2_valid_utf.c
- c++/src/util/regexp/pcre_xclass.c → c++/src/util/regexp/pcre2_xclass.c
- c++/src/util/regexp/pcredemo.c → c++/src/util/regexp/pcre2demo.c
- c++/src/util/regexp/pcregrep.c → c++/src/util/regexp/pcre2grep.c
- c++/src/util/regexp/pcreposix.c → c++/src/util/regexp/pcre2posix.c
- + c++/src/util/regexp/pcre2posix_test.c
- + c++/src/util/regexp/pcre2test.c
- − c++/src/util/regexp/pcre_compile.c
- − c++/src/util/regexp/pcre_exec.c
- − c++/src/util/regexp/pcre_get.c
- − c++/src/util/regexp/pcre_globals.c
- − c++/src/util/regexp/pcre_jit_test.c
- − c++/src/util/regexp/pcre_printint.src
- − c++/src/util/regexp/pcre_scanner.cc
- − c++/src/util/regexp/pcre_scanner.h
- − c++/src/util/regexp/pcre_scanner_unittest.cc
- − c++/src/util/regexp/pcre_stringpiece.cc
- − c++/src/util/regexp/pcre_stringpiece_unittest.cc
- − c++/src/util/regexp/pcre_tables.c
- − c++/src/util/regexp/pcre_ucd.c
- − c++/src/util/regexp/pcre_version.c
- − c++/src/util/regexp/pcrecpp.cc
- − c++/src/util/regexp/pcrecpp.h
- − c++/src/util/regexp/pcrecpp_internal.h
- − c++/src/util/regexp/pcreposix.h
- − c++/src/util/regexp/pcretest.c
- − c++/src/util/regexp/perltest.pl
- + c++/src/util/regexp/sljit/allocator_src/sljitExecAllocatorApple.c
- + c++/src/util/regexp/sljit/allocator_src/sljitExecAllocatorCore.c
- + c++/src/util/regexp/sljit/allocator_src/sljitExecAllocatorFreeBSD.c
- + c++/src/util/regexp/sljit/allocator_src/sljitExecAllocatorPosix.c
- + c++/src/util/regexp/sljit/allocator_src/sljitExecAllocatorWindows.c
- + c++/src/util/regexp/sljit/allocator_src/sljitProtExecAllocatorNetBSD.c
- + c++/src/util/regexp/sljit/allocator_src/sljitProtExecAllocatorPosix.c
- + c++/src/util/regexp/sljit/allocator_src/sljitWXExecAllocatorPosix.c
- + c++/src/util/regexp/sljit/allocator_src/sljitWXExecAllocatorWindows.c
- + c++/src/util/regexp/sljit/sljitConfig.h
- + c++/src/util/regexp/sljit/sljitConfigCPU.h
- + c++/src/util/regexp/sljit/sljitConfigInternal.h
- + c++/src/util/regexp/sljit/sljitLir.c
- + c++/src/util/regexp/sljit/sljitLir.h
- + c++/src/util/regexp/sljit/sljitNativeARM_32.c
- + c++/src/util/regexp/sljit/sljitNativeARM_64.c
- + c++/src/util/regexp/sljit/sljitNativeARM_T2_32.c
- + c++/src/util/regexp/sljit/sljitNativeLOONGARCH_64.c
- + c++/src/util/regexp/sljit/sljitNativeMIPS_32.c
- + c++/src/util/regexp/sljit/sljitNativeMIPS_64.c
- + c++/src/util/regexp/sljit/sljitNativeMIPS_common.c
- + c++/src/util/regexp/sljit/sljitNativePPC_32.c
- + c++/src/util/regexp/sljit/sljitNativePPC_64.c
- + c++/src/util/regexp/sljit/sljitNativePPC_common.c
- + c++/src/util/regexp/sljit/sljitNativeRISCV_32.c
- + c++/src/util/regexp/sljit/sljitNativeRISCV_64.c
- + c++/src/util/regexp/sljit/sljitNativeRISCV_common.c
- + c++/src/util/regexp/sljit/sljitNativeS390X.c
- + c++/src/util/regexp/sljit/sljitNativeX86_32.c
- + c++/src/util/regexp/sljit/sljitNativeX86_64.c
- + c++/src/util/regexp/sljit/sljitNativeX86_common.c
- + c++/src/util/regexp/sljit/sljitSerialize.c
- + c++/src/util/regexp/sljit/sljitUtils.c
- c++/src/util/regexp/testdata/grepinput
- c++/src/util/regexp/testdata/grepinput8
- + c++/src/util/regexp/testdata/grepinputC.bz2
- + c++/src/util/regexp/testdata/grepinputC.gz
- + c++/src/util/regexp/testdata/grepinputM
- c++/src/util/regexp/testdata/grepinputv
- + c++/src/util/regexp/testdata/grepnot.bz2
- c++/src/util/regexp/testdata/grepoutput
- c++/src/util/regexp/testdata/grepoutput8
- + c++/src/util/regexp/testdata/grepoutputC
- + c++/src/util/regexp/testdata/grepoutputCN
- + c++/src/util/regexp/testdata/grepoutputCNU
- + c++/src/util/regexp/testdata/grepoutputCU
- + c++/src/util/regexp/testdata/grepoutputCbz2
- + c++/src/util/regexp/testdata/grepoutputCgz
- c++/src/util/regexp/testdata/grepoutputN
- + c++/src/util/regexp/testdata/grepoutputUN
- c++/src/util/regexp/testdata/greppatN4
- − c++/src/util/regexp/testdata/saved16
- − c++/src/util/regexp/testdata/saved16BE-1
- − c++/src/util/regexp/testdata/saved16BE-2
- − c++/src/util/regexp/testdata/saved16LE-1
- − c++/src/util/regexp/testdata/saved16LE-2
- − c++/src/util/regexp/testdata/saved32
- − c++/src/util/regexp/testdata/saved32BE-1
- − c++/src/util/regexp/testdata/saved32BE-2
- − c++/src/util/regexp/testdata/saved32LE-1
- − c++/src/util/regexp/testdata/saved32LE-2
- − c++/src/util/regexp/testdata/saved8
- + c++/src/util/regexp/testdata/testbtables
- c++/src/util/regexp/testdata/testinput1
- c++/src/util/regexp/testdata/testinput10
- c++/src/util/regexp/testdata/testinput11
- c++/src/util/regexp/testdata/testinput12
- c++/src/util/regexp/testdata/testinput13
- c++/src/util/regexp/testdata/testinput14
- c++/src/util/regexp/testdata/testinput15
- c++/src/util/regexp/testdata/testinput16
- c++/src/util/regexp/testdata/testinput17
- c++/src/util/regexp/testdata/testinput18
- c++/src/util/regexp/testdata/testinput19
- c++/src/util/regexp/testdata/testinput2
- c++/src/util/regexp/testdata/testinput20
- c++/src/util/regexp/testdata/testinput21
- c++/src/util/regexp/testdata/testinput22
- c++/src/util/regexp/testdata/testinput23
- c++/src/util/regexp/testdata/testinput24
- c++/src/util/regexp/testdata/testinput25
- c++/src/util/regexp/testdata/testinput26
- c++/src/util/regexp/testdata/testinput3
- c++/src/util/regexp/testdata/testinput4
- c++/src/util/regexp/testdata/testinput5
- c++/src/util/regexp/testdata/testinput6
- c++/src/util/regexp/testdata/testinput7
- c++/src/util/regexp/testdata/testinput8
- c++/src/util/regexp/testdata/testinput9
- c++/src/util/regexp/testdata/testinputEBC
- + c++/src/util/regexp/testdata/testinputheap
- c++/src/util/regexp/testdata/testoutput1
- c++/src/util/regexp/testdata/testoutput10
- c++/src/util/regexp/testdata/testoutput11-16
- c++/src/util/regexp/testdata/testoutput11-32
- − c++/src/util/regexp/testdata/testoutput12
- + c++/src/util/regexp/testdata/testoutput12-16
- + c++/src/util/regexp/testdata/testoutput12-32
- c++/src/util/regexp/testdata/testoutput13
- − c++/src/util/regexp/testdata/testoutput14
- + c++/src/util/regexp/testdata/testoutput14-16
- + c++/src/util/regexp/testdata/testoutput14-32
- + c++/src/util/regexp/testdata/testoutput14-8
- c++/src/util/regexp/testdata/testoutput15
- c++/src/util/regexp/testdata/testoutput16
- c++/src/util/regexp/testdata/testoutput17
- + c++/src/util/regexp/testdata/testoutput18
- − c++/src/util/regexp/testdata/testoutput18-16
- − c++/src/util/regexp/testdata/testoutput18-32
- c++/src/util/regexp/testdata/testoutput19
- c++/src/util/regexp/testdata/testoutput2
- c++/src/util/regexp/testdata/testoutput20
- + c++/src/util/regexp/testdata/testoutput21
- − c++/src/util/regexp/testdata/testoutput21-16
- − c++/src/util/regexp/testdata/testoutput21-32
- c++/src/util/regexp/testdata/testoutput22-16
- c++/src/util/regexp/testdata/testoutput22-32
- + c++/src/util/regexp/testdata/testoutput22-8
- c++/src/util/regexp/testdata/testoutput23
- c++/src/util/regexp/testdata/testoutput24
- c++/src/util/regexp/testdata/testoutput25
- c++/src/util/regexp/testdata/testoutput26
- c++/src/util/regexp/testdata/testoutput3
- c++/src/util/regexp/testdata/testoutput3A
- c++/src/util/regexp/testdata/testoutput3B
- c++/src/util/regexp/testdata/testoutput4
- c++/src/util/regexp/testdata/testoutput5
- c++/src/util/regexp/testdata/testoutput6
- c++/src/util/regexp/testdata/testoutput7
- − c++/src/util/regexp/testdata/testoutput8
- + c++/src/util/regexp/testdata/testoutput8-16-2
- + c++/src/util/regexp/testdata/testoutput8-16-3
- + c++/src/util/regexp/testdata/testoutput8-16-4
- + c++/src/util/regexp/testdata/testoutput8-32-2
- + c++/src/util/regexp/testdata/testoutput8-32-3
- + c++/src/util/regexp/testdata/testoutput8-32-4
- c++/src/util/regexp/testdata/testoutput11-8 → c++/src/util/regexp/testdata/testoutput8-8-2
- + c++/src/util/regexp/testdata/testoutput8-8-3
- + c++/src/util/regexp/testdata/testoutput8-8-4
- c++/src/util/regexp/testdata/testoutput9
- c++/src/util/regexp/testdata/testoutputEBC
- + c++/src/util/regexp/testdata/testoutputheap-16
- + c++/src/util/regexp/testdata/testoutputheap-32
- + c++/src/util/regexp/testdata/testoutputheap-8
- c++/src/util/regexp/testdata/wintestinput3
- c++/src/util/regexp/testdata/wintestoutput3
- c++/src/util/strbuffer.cpp
- c++/src/util/stream_source.cpp
- c++/src/util/unicode.cpp
- c++/src/util/unicode_plans.inl
- c++/src/util/xregexp/CMakeLists.txt
- c++/src/util/xregexp/Makefile.xregexp.lib
- c++/src/util/xregexp/convert_dates_iso8601.cpp
- c++/src/util/xregexp/regexp.cpp
- debian/changelog
- debian/control
- debian/copyright
- + debian/ncbi-blast+.lintian-overrides
- debian/patches/big_endian_workaround
- debian/patches/fix_lib_deps
- debian/patches/hurd_fixes
- debian/patches/no_multiarch_rpath
- debian/patches/optin_usage_report
- debian/patches/run_perl_directly
- debian/patches/series
- debian/patches/skip_services_unit_test
- debian/patches/spelling
- debian/patches/suppress_tls_version_checks
- debian/patches/system_mbedtls_only
- debian/rules


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/77af51e35721ccda06cd4a16fd1a3497a4a217f4...7c3ad37c04e81930176dd9e0ca086004918aa7a2

-- 
View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/77af51e35721ccda06cd4a16fd1a3497a4a217f4...7c3ad37c04e81930176dd9e0ca086004918aa7a2
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20250929/e917c2a6/attachment-0001.htm>