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ncbi-blast+: Update to 2.13.0

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Wed Mar 16 11:35:02 2022 -0500
Changeset:	6dba321bebbc53eafcbc601aafaaee5f4de51068

Modified Files:
	ncbi-blast+/Makefile
	ncbi-blast+/PLIST
	ncbi-blast+/distinfo

Log Message:
ncbi-blast+: Update to 2.13.0

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=6dba321bebbc53eafcbc601aafaaee5f4de51068

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 ncbi-blast+/Makefile |   3 +-
 ncbi-blast+/PLIST    | 300 ++++++++++++++++++++++++++++++++++++++++++++-------
 ncbi-blast+/distinfo |   6 +-
 3 files changed, 266 insertions(+), 43 deletions(-)

diffs:
diff --git a/ncbi-blast+/Makefile b/ncbi-blast+/Makefile
index 669ad92fcb..c381e996ff 100644
--- a/ncbi-blast+/Makefile
+++ b/ncbi-blast+/Makefile
@@ -1,6 +1,6 @@
 # $NetBSD: Makefile,v 1.11 2019/08/11 13:18:00 wiz Exp $
 
-DISTNAME=	ncbi-blast-2.11.0+-src
+DISTNAME=	ncbi-blast-2.13.0+-src
 PKGNAME=	${DISTNAME:S/+-src//:S/blast/blast+/}
 CATEGORIES=	biology
 MASTER_SITES=	https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \
@@ -29,6 +29,7 @@ REPLACE_BASH+=		src/app/blast/get_species_taxids.sh
 REPLACE_PERL=		src/app/blast/legacy_blast.pl src/app/blast/update_blastdb.pl
 REPLACE_PYTHON=		src/app/winmasker/windowmasker_2.2.22_adapter.py
 REPLACE_PYTHON+=	src/app/blast/cleanup-blastdb-volumes.py
+MKPIE_SUPPORTED=	no	# Temporary fix
 
 # The test for amq can hang, but amq is not needed so just avoid the test
 # configure chooses /usr/local/bin/ar with no flags
diff --git a/ncbi-blast+/PLIST b/ncbi-blast+/PLIST
index 5e8d3e5cdf..14c58887f2 100644
--- a/ncbi-blast+/PLIST
+++ b/ncbi-blast+/PLIST
@@ -212,6 +212,12 @@ include/ncbi-tools++/algo/blast/proteinkmer/blastkmerresults.hpp
 include/ncbi-tools++/algo/blast/proteinkmer/blastkmerutils.hpp
 include/ncbi-tools++/algo/blast/proteinkmer/kblastapi.hpp
 include/ncbi-tools++/algo/blast/proteinkmer/mhfile.hpp
+include/ncbi-tools++/algo/blast/vdb/blastn_vdb_args.hpp
+include/ncbi-tools++/algo/blast/vdb/seqsrc_vdb.h
+include/ncbi-tools++/algo/blast/vdb/tblastn_vdb_args.hpp
+include/ncbi-tools++/algo/blast/vdb/vdb2blast_util.hpp
+include/ncbi-tools++/algo/blast/vdb/vdbalias.hpp
+include/ncbi-tools++/algo/blast/vdb/vdbblast_local.hpp
 include/ncbi-tools++/algo/dustmask/sdust.tex
 include/ncbi-tools++/algo/dustmask/symdust.hpp
 include/ncbi-tools++/algo/segmask/segmask.hpp
@@ -258,6 +264,7 @@ include/ncbi-tools++/cgi/cgiapp.hpp
 include/ncbi-tools++/cgi/cgiapp_cached.hpp
 include/ncbi-tools++/cgi/cgictx.hpp
 include/ncbi-tools++/cgi/error_codes.hpp
+include/ncbi-tools++/cgi/fcgiapp_mt.hpp
 include/ncbi-tools++/cgi/impl/cgi_entry_reader.hpp
 include/ncbi-tools++/cgi/ncbicgi.hpp
 include/ncbi-tools++/cgi/ncbicgir.hpp
@@ -280,6 +287,7 @@ include/ncbi-tools++/common/ncbi_package_ver.h
 include/ncbi-tools++/common/ncbi_pch_impl.hpp
 include/ncbi-tools++/common/ncbi_revision.h
 include/ncbi-tools++/common/ncbi_revision.h.in
+include/ncbi-tools++/common/ncbi_sanitizers.h
 include/ncbi-tools++/common/ncbi_skew_guard.h
 include/ncbi-tools++/common/ncbi_source_ver.cmake_nodep
 include/ncbi-tools++/common/ncbi_source_ver.h
@@ -290,6 +298,8 @@ include/ncbi-tools++/common/test_data_path.h
 include/ncbi-tools++/connect/connect_export.h
 include/ncbi-tools++/connect/email_diag_handler.hpp
 include/ncbi-tools++/connect/error_codes.hpp
+include/ncbi-tools++/connect/impl/connect_misc.hpp
+include/ncbi-tools++/connect/impl/ncbi_uv_nghttp2.hpp
 include/ncbi-tools++/connect/impl/server_connection.hpp
 include/ncbi-tools++/connect/impl/thread_pool_for_server.hpp
 include/ncbi-tools++/connect/ncbi_base64.h
@@ -309,6 +319,7 @@ include/ncbi-tools++/connect/ncbi_ftp_connector.h
 include/ncbi-tools++/connect/ncbi_gnutls.h
 include/ncbi-tools++/connect/ncbi_heapmgr.h
 include/ncbi-tools++/connect/ncbi_host_info.h
+include/ncbi-tools++/connect/ncbi_http2_session.hpp
 include/ncbi-tools++/connect/ncbi_http_connector.h
 include/ncbi-tools++/connect/ncbi_http_session.hpp
 include/ncbi-tools++/connect/ncbi_iprange.h
@@ -427,6 +438,7 @@ include/ncbi-tools++/corelib/ncbi_message.hpp
 include/ncbi-tools++/corelib/ncbi_os_mswin.hpp
 include/ncbi-tools++/corelib/ncbi_os_unix.hpp
 include/ncbi-tools++/corelib/ncbi_param.hpp
+include/ncbi-tools++/corelib/ncbi_pool_balancer.hpp
 include/ncbi-tools++/corelib/ncbi_process.hpp
 include/ncbi-tools++/corelib/ncbi_safe_static.hpp
 include/ncbi-tools++/corelib/ncbi_signal.hpp
@@ -494,7 +506,6 @@ include/ncbi-tools++/corelib/version.hpp
 include/ncbi-tools++/corelib/version_api.hpp
 include/ncbi-tools++/db/error_codes.hpp
 include/ncbi-tools++/db/sqlite/sqlitewrapp.hpp
-include/ncbi-tools++/dbapi/cache/dbapi_blob_cache.hpp
 include/ncbi-tools++/dbapi/dbapi.hpp
 include/ncbi-tools++/dbapi/dbapi_variant_convert.hpp
 include/ncbi-tools++/dbapi/driver/dbapi_conn_factory.hpp
@@ -549,40 +560,10 @@ include/ncbi-tools++/html/page.hpp
 include/ncbi-tools++/html/pager.hpp
 include/ncbi-tools++/html/selection.hpp
 include/ncbi-tools++/html/writer_htmlenc.hpp
+include/ncbi-tools++/misc/drmaa2.hpp
 include/ncbi-tools++/misc/error_codes.hpp
 include/ncbi-tools++/misc/jsonwrapp/jsonwrapp.hpp
-include/ncbi-tools++/misc/jsonwrapp/jsonwrapp10.hpp
 include/ncbi-tools++/misc/jsonwrapp/jsonwrapp11.hpp
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/__NCBI_read_me.txt
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/allocators.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/document.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/encodedstream.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/encodings.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/error/en.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/error/error.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/filereadstream.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/filewritestream.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/biginteger.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/diyfp.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/dtoa.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/ieee754.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/itoa.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/meta.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/pow10.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/stack.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/strfunc.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/strtod.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/license.txt
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/memorybuffer.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/memorystream.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/msinttypes/inttypes.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/msinttypes/stdint.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/pointer.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/prettywriter.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/rapidjson.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/reader.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/stringbuffer.h
-include/ncbi-tools++/misc/jsonwrapp/rapidjson10/writer.h
 include/ncbi-tools++/misc/jsonwrapp/rapidjson11/__NCBI_read_me.txt
 include/ncbi-tools++/misc/jsonwrapp/rapidjson11/allocators.h
 include/ncbi-tools++/misc/jsonwrapp/rapidjson11/document.h
@@ -850,6 +831,8 @@ include/ncbi-tools++/objects/blastdb/.cvsignore
 include/ncbi-tools++/objects/blastdb/.gitignore
 include/ncbi-tools++/objects/blastdb/Blast_db_mask_info.hpp
 include/ncbi-tools++/objects/blastdb/Blast_db_mask_info_.hpp
+include/ncbi-tools++/objects/blastdb/Blast_db_metadata.hpp
+include/ncbi-tools++/objects/blastdb/Blast_db_metadata_.hpp
 include/ncbi-tools++/objects/blastdb/Blast_def_line.hpp
 include/ncbi-tools++/objects/blastdb/Blast_def_line_.hpp
 include/ncbi-tools++/objects/blastdb/Blast_def_line_set.hpp
@@ -2311,6 +2294,36 @@ include/ncbi-tools++/objects/pcassay/PC_RealMinMax_.hpp
 include/ncbi-tools++/objects/pcassay/PC_ResultType.hpp
 include/ncbi-tools++/objects/pcassay/PC_ResultType_.hpp
 include/ncbi-tools++/objects/pcassay/pcassay__.hpp
+include/ncbi-tools++/objects/pcassay2/.cvsignore
+include/ncbi-tools++/objects/pcassay2/.gitignore
+include/ncbi-tools++/objects/pcassay2/NCBI_PCAssay2_module.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AnnotatedXRef.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AnnotatedXRef_.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssayContainer.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssayContainer_.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssayDRAttr.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssayDRAttr_.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssayData.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssayData_.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssayDescription.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssayDescription_.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssayResults.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssayResults_.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssaySubmit.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssaySubmit_.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssayTargetInfo.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssayTargetInfo_.hpp
+include/ncbi-tools++/objects/pcassay2/PC_CategorizedComment.hpp
+include/ncbi-tools++/objects/pcassay2/PC_CategorizedComment_.hpp
+include/ncbi-tools++/objects/pcassay2/PC_ConcentrationAttr.hpp
+include/ncbi-tools++/objects/pcassay2/PC_ConcentrationAttr_.hpp
+include/ncbi-tools++/objects/pcassay2/PC_IntegerMinMax.hpp
+include/ncbi-tools++/objects/pcassay2/PC_IntegerMinMax_.hpp
+include/ncbi-tools++/objects/pcassay2/PC_RealMinMax.hpp
+include/ncbi-tools++/objects/pcassay2/PC_RealMinMax_.hpp
+include/ncbi-tools++/objects/pcassay2/PC_ResultType.hpp
+include/ncbi-tools++/objects/pcassay2/PC_ResultType_.hpp
+include/ncbi-tools++/objects/pcassay2/pcassay2__.hpp
 include/ncbi-tools++/objects/pcsubstance/.cvsignore
 include/ncbi-tools++/objects/pcsubstance/.gitignore
 include/ncbi-tools++/objects/pcsubstance/NCBI_PCSubstance_module.hpp
@@ -2330,6 +2343,8 @@ include/ncbi-tools++/objects/pcsubstance/PC_BondType.hpp
 include/ncbi-tools++/objects/pcsubstance/PC_BondType_.hpp
 include/ncbi-tools++/objects/pcsubstance/PC_Bonds.hpp
 include/ncbi-tools++/objects/pcsubstance/PC_Bonds_.hpp
+include/ncbi-tools++/objects/pcsubstance/PC_Bracket.hpp
+include/ncbi-tools++/objects/pcsubstance/PC_Bracket_.hpp
 include/ncbi-tools++/objects/pcsubstance/PC_Compound.hpp
 include/ncbi-tools++/objects/pcsubstance/PC_CompoundType.hpp
 include/ncbi-tools++/objects/pcsubstance/PC_CompoundType_.hpp
@@ -2352,6 +2367,8 @@ include/ncbi-tools++/objects/pcsubstance/PC_DrawAnnotations.hpp
 include/ncbi-tools++/objects/pcsubstance/PC_DrawAnnotations_.hpp
 include/ncbi-tools++/objects/pcsubstance/PC_Element.hpp
 include/ncbi-tools++/objects/pcsubstance/PC_Element_.hpp
+include/ncbi-tools++/objects/pcsubstance/PC_Group.hpp
+include/ncbi-tools++/objects/pcsubstance/PC_Group_.hpp
 include/ncbi-tools++/objects/pcsubstance/PC_ID.hpp
 include/ncbi-tools++/objects/pcsubstance/PC_ID_.hpp
 include/ncbi-tools++/objects/pcsubstance/PC_InfoData.hpp
@@ -2573,7 +2590,6 @@ include/ncbi-tools++/objects/seq/seq_macros.hpp
 include/ncbi-tools++/objects/seq/seqlocinfo.hpp
 include/ncbi-tools++/objects/seq/seqport_util.hpp
 include/ncbi-tools++/objects/seq/so_map.hpp
-include/ncbi-tools++/objects/seq/sofa_map.hpp
 include/ncbi-tools++/objects/seq/sofa_type.hpp
 include/ncbi-tools++/objects/seqalign/.cvsignore
 include/ncbi-tools++/objects/seqalign/.gitignore
@@ -3552,7 +3568,6 @@ include/ncbi-tools++/objtools/blast/seqdb_writer/writedb_general.hpp
 include/ncbi-tools++/objtools/blast/seqdb_writer/writedb_isam.hpp
 include/ncbi-tools++/objtools/blast/seqdb_writer/writedb_lmdb.hpp
 include/ncbi-tools++/objtools/blast/services/blast_services.hpp
-include/ncbi-tools++/objtools/cleanup/autogenerated_cleanup.hpp
 include/ncbi-tools++/objtools/cleanup/capitalization_string.hpp
 include/ncbi-tools++/objtools/cleanup/cleanup.hpp
 include/ncbi-tools++/objtools/cleanup/cleanup_change.hpp
@@ -3594,6 +3609,7 @@ include/ncbi-tools++/objtools/data_loaders/genbank/impl/reader_service.hpp
 include/ncbi-tools++/objtools/data_loaders/genbank/impl/request_result.hpp
 include/ncbi-tools++/objtools/data_loaders/genbank/impl/standalone_result.hpp
 include/ncbi-tools++/objtools/data_loaders/genbank/impl/statistics.hpp
+include/ncbi-tools++/objtools/data_loaders/genbank/impl/wgsmaster.hpp
 include/ncbi-tools++/objtools/data_loaders/genbank/psg_loader.hpp
 include/ncbi-tools++/objtools/data_loaders/genbank/reader.hpp
 include/ncbi-tools++/objtools/data_loaders/genbank/reader_interface.hpp
@@ -3634,6 +3650,7 @@ include/ncbi-tools++/objtools/edit/loc_edit.hpp
 include/ncbi-tools++/objtools/edit/mail_report.hpp
 include/ncbi-tools++/objtools/edit/parse_text_options.hpp
 include/ncbi-tools++/objtools/edit/promote.hpp
+include/ncbi-tools++/objtools/edit/pub_fix.hpp
 include/ncbi-tools++/objtools/edit/publication_edit.hpp
 include/ncbi-tools++/objtools/edit/remote_updater.hpp
 include/ncbi-tools++/objtools/edit/rna_edit.hpp
@@ -3646,6 +3663,142 @@ include/ncbi-tools++/objtools/edit/struc_comm_field.hpp
 include/ncbi-tools++/objtools/edit/text_desc_field.hpp
 include/ncbi-tools++/objtools/edit/text_object_description.hpp
 include/ncbi-tools++/objtools/error_codes.hpp
+include/ncbi-tools++/objtools/eutils/api/efetch.hpp
+include/ncbi-tools++/objtools/eutils/api/egquery.hpp
+include/ncbi-tools++/objtools/eutils/api/ehistory.hpp
+include/ncbi-tools++/objtools/eutils/api/einfo.hpp
+include/ncbi-tools++/objtools/eutils/api/elink.hpp
+include/ncbi-tools++/objtools/eutils/api/epost.hpp
+include/ncbi-tools++/objtools/eutils/api/esearch.hpp
+include/ncbi-tools++/objtools/eutils/api/espell.hpp
+include/ncbi-tools++/objtools/eutils/api/esummary.hpp
+include/ncbi-tools++/objtools/eutils/api/eutils.hpp
+include/ncbi-tools++/objtools/eutils/egquery/.cvsignore
+include/ncbi-tools++/objtools/eutils/egquery/.gitignore
+include/ncbi-tools++/objtools/eutils/egquery/EGQueryResult.hpp
+include/ncbi-tools++/objtools/eutils/egquery/EGQueryResult_.hpp
+include/ncbi-tools++/objtools/eutils/egquery/Result.hpp
+include/ncbi-tools++/objtools/eutils/egquery/ResultItem.hpp
+include/ncbi-tools++/objtools/eutils/egquery/ResultItem_.hpp
+include/ncbi-tools++/objtools/eutils/egquery/Result_.hpp
+include/ncbi-tools++/objtools/eutils/egquery/egquery__.hpp
+include/ncbi-tools++/objtools/eutils/egquery/egquery_module.hpp
+include/ncbi-tools++/objtools/eutils/ehistory/.cvsignore
+include/ncbi-tools++/objtools/eutils/ehistory/.gitignore
+include/ncbi-tools++/objtools/eutils/ehistory/EHistoryItem.hpp
+include/ncbi-tools++/objtools/eutils/ehistory/EHistoryItem_.hpp
+include/ncbi-tools++/objtools/eutils/ehistory/EHistoryResult.hpp
+include/ncbi-tools++/objtools/eutils/ehistory/EHistoryResult_.hpp
+include/ncbi-tools++/objtools/eutils/ehistory/ehistory__.hpp
+include/ncbi-tools++/objtools/eutils/ehistory/ehistory_module.hpp
+include/ncbi-tools++/objtools/eutils/einfo/.cvsignore
+include/ncbi-tools++/objtools/eutils/einfo/.gitignore
+include/ncbi-tools++/objtools/eutils/einfo/DbInfo.hpp
+include/ncbi-tools++/objtools/eutils/einfo/DbInfo_.hpp
+include/ncbi-tools++/objtools/eutils/einfo/DbList.hpp
+include/ncbi-tools++/objtools/eutils/einfo/DbList_.hpp
+include/ncbi-tools++/objtools/eutils/einfo/EInfoResult.hpp
+include/ncbi-tools++/objtools/eutils/einfo/EInfoResult_.hpp
+include/ncbi-tools++/objtools/eutils/einfo/Field.hpp
+include/ncbi-tools++/objtools/eutils/einfo/FieldList.hpp
+include/ncbi-tools++/objtools/eutils/einfo/FieldList_.hpp
+include/ncbi-tools++/objtools/eutils/einfo/Field_.hpp
+include/ncbi-tools++/objtools/eutils/einfo/Link.hpp
+include/ncbi-tools++/objtools/eutils/einfo/LinkList.hpp
+include/ncbi-tools++/objtools/eutils/einfo/LinkList_.hpp
+include/ncbi-tools++/objtools/eutils/einfo/Link_.hpp
+include/ncbi-tools++/objtools/eutils/einfo/einfo__.hpp
+include/ncbi-tools++/objtools/eutils/einfo/einfo_module.hpp
+include/ncbi-tools++/objtools/eutils/elink/.cvsignore
+include/ncbi-tools++/objtools/eutils/elink/.gitignore
+include/ncbi-tools++/objtools/eutils/elink/ELinkResult.hpp
+include/ncbi-tools++/objtools/eutils/elink/ELinkResult_.hpp
+include/ncbi-tools++/objtools/eutils/elink/FirstChars.hpp
+include/ncbi-tools++/objtools/eutils/elink/FirstChars_.hpp
+include/ncbi-tools++/objtools/eutils/elink/IconUrl.hpp
+include/ncbi-tools++/objtools/eutils/elink/IconUrl_.hpp
+include/ncbi-tools++/objtools/eutils/elink/Id.hpp
+include/ncbi-tools++/objtools/eutils/elink/IdCheckList.hpp
+include/ncbi-tools++/objtools/eutils/elink/IdCheckList_.hpp
+include/ncbi-tools++/objtools/eutils/elink/IdLinkSet.hpp
+include/ncbi-tools++/objtools/eutils/elink/IdLinkSet_.hpp
+include/ncbi-tools++/objtools/eutils/elink/IdList.hpp
+include/ncbi-tools++/objtools/eutils/elink/IdList_.hpp
+include/ncbi-tools++/objtools/eutils/elink/IdUrlList.hpp
+include/ncbi-tools++/objtools/eutils/elink/IdUrlList_.hpp
+include/ncbi-tools++/objtools/eutils/elink/IdUrlSet.hpp
+include/ncbi-tools++/objtools/eutils/elink/IdUrlSet_.hpp
+include/ncbi-tools++/objtools/eutils/elink/Id_.hpp
+include/ncbi-tools++/objtools/eutils/elink/Link.hpp
+include/ncbi-tools++/objtools/eutils/elink/LinkInfo.hpp
+include/ncbi-tools++/objtools/eutils/elink/LinkInfo_.hpp
+include/ncbi-tools++/objtools/eutils/elink/LinkSet.hpp
+include/ncbi-tools++/objtools/eutils/elink/LinkSetDb.hpp
+include/ncbi-tools++/objtools/eutils/elink/LinkSetDbHistory.hpp
+include/ncbi-tools++/objtools/eutils/elink/LinkSetDbHistory_.hpp
+include/ncbi-tools++/objtools/eutils/elink/LinkSetDb_.hpp
+include/ncbi-tools++/objtools/eutils/elink/LinkSet_.hpp
+include/ncbi-tools++/objtools/eutils/elink/Link_.hpp
+include/ncbi-tools++/objtools/eutils/elink/ObjUrl.hpp
+include/ncbi-tools++/objtools/eutils/elink/ObjUrl_.hpp
+include/ncbi-tools++/objtools/eutils/elink/Provider.hpp
+include/ncbi-tools++/objtools/eutils/elink/Provider_.hpp
+include/ncbi-tools++/objtools/eutils/elink/Url.hpp
+include/ncbi-tools++/objtools/eutils/elink/Url_.hpp
+include/ncbi-tools++/objtools/eutils/elink/elink__.hpp
+include/ncbi-tools++/objtools/eutils/elink/elink_module.hpp
+include/ncbi-tools++/objtools/eutils/epost/.cvsignore
+include/ncbi-tools++/objtools/eutils/epost/.gitignore
+include/ncbi-tools++/objtools/eutils/epost/EPostResult.hpp
+include/ncbi-tools++/objtools/eutils/epost/EPostResult_.hpp
+include/ncbi-tools++/objtools/eutils/epost/InvalidIdList.hpp
+include/ncbi-tools++/objtools/eutils/epost/InvalidIdList_.hpp
+include/ncbi-tools++/objtools/eutils/epost/epost__.hpp
+include/ncbi-tools++/objtools/eutils/epost/epost_module.hpp
+include/ncbi-tools++/objtools/eutils/esearch/.cvsignore
+include/ncbi-tools++/objtools/eutils/esearch/.gitignore
+include/ncbi-tools++/objtools/eutils/esearch/ESearchResult.hpp
+include/ncbi-tools++/objtools/eutils/esearch/ESearchResult_.hpp
+include/ncbi-tools++/objtools/eutils/esearch/ErrorList.hpp
+include/ncbi-tools++/objtools/eutils/esearch/ErrorList_.hpp
+include/ncbi-tools++/objtools/eutils/esearch/IdList.hpp
+include/ncbi-tools++/objtools/eutils/esearch/IdList_.hpp
+include/ncbi-tools++/objtools/eutils/esearch/TermSet.hpp
+include/ncbi-tools++/objtools/eutils/esearch/TermSet_.hpp
+include/ncbi-tools++/objtools/eutils/esearch/Translation.hpp
+include/ncbi-tools++/objtools/eutils/esearch/TranslationSet.hpp
+include/ncbi-tools++/objtools/eutils/esearch/TranslationSet_.hpp
+include/ncbi-tools++/objtools/eutils/esearch/TranslationStack.hpp
+include/ncbi-tools++/objtools/eutils/esearch/TranslationStack_.hpp
+include/ncbi-tools++/objtools/eutils/esearch/Translation_.hpp
+include/ncbi-tools++/objtools/eutils/esearch/WarningList.hpp
+include/ncbi-tools++/objtools/eutils/esearch/WarningList_.hpp
+include/ncbi-tools++/objtools/eutils/esearch/esearch__.hpp
+include/ncbi-tools++/objtools/eutils/esearch/esearch_module.hpp
+include/ncbi-tools++/objtools/eutils/espell/.cvsignore
+include/ncbi-tools++/objtools/eutils/espell/.gitignore
+include/ncbi-tools++/objtools/eutils/espell/ESpellResult.hpp
+include/ncbi-tools++/objtools/eutils/espell/ESpellResult_.hpp
+include/ncbi-tools++/objtools/eutils/espell/SpelledQuery.hpp
+include/ncbi-tools++/objtools/eutils/espell/SpelledQuery_.hpp
+include/ncbi-tools++/objtools/eutils/espell/espell__.hpp
+include/ncbi-tools++/objtools/eutils/espell/espell_module.hpp
+include/ncbi-tools++/objtools/eutils/esummary/.cvsignore
+include/ncbi-tools++/objtools/eutils/esummary/.gitignore
+include/ncbi-tools++/objtools/eutils/esummary/DocSum.hpp
+include/ncbi-tools++/objtools/eutils/esummary/DocSum_.hpp
+include/ncbi-tools++/objtools/eutils/esummary/ESummaryResult.hpp
+include/ncbi-tools++/objtools/eutils/esummary/ESummaryResult_.hpp
+include/ncbi-tools++/objtools/eutils/esummary/Item.hpp
+include/ncbi-tools++/objtools/eutils/esummary/Item_.hpp
+include/ncbi-tools++/objtools/eutils/esummary/esummary__.hpp
+include/ncbi-tools++/objtools/eutils/esummary/esummary_module.hpp
+include/ncbi-tools++/objtools/eutils/uilist/.cvsignore
+include/ncbi-tools++/objtools/eutils/uilist/.gitignore
+include/ncbi-tools++/objtools/eutils/uilist/IdList.hpp
+include/ncbi-tools++/objtools/eutils/uilist/IdList_.hpp
+include/ncbi-tools++/objtools/eutils/uilist/uilist__.hpp
+include/ncbi-tools++/objtools/eutils/uilist/uilist_module.hpp
 include/ncbi-tools++/objtools/format/cigar_formatter.hpp
 include/ncbi-tools++/objtools/format/context.hpp
 include/ncbi-tools++/objtools/format/embl_formatter.hpp
@@ -3723,10 +3876,9 @@ include/ncbi-tools++/objtools/readers/format_guess_ex.hpp
 include/ncbi-tools++/objtools/readers/getfeature.hpp
 include/ncbi-tools++/objtools/readers/gff2_data.hpp
 include/ncbi-tools++/objtools/readers/gff2_reader.hpp
+include/ncbi-tools++/objtools/readers/gff3_location_merger.hpp
 include/ncbi-tools++/objtools/readers/gff3_reader.hpp
-include/ncbi-tools++/objtools/readers/gff3_sofa.hpp
 include/ncbi-tools++/objtools/readers/gff_base_columns.hpp
-include/ncbi-tools++/objtools/readers/gff_reader.hpp
 include/ncbi-tools++/objtools/readers/glimmer_reader.hpp
 include/ncbi-tools++/objtools/readers/gtf_reader.hpp
 include/ncbi-tools++/objtools/readers/gvf_reader.hpp
@@ -3737,6 +3889,7 @@ include/ncbi-tools++/objtools/readers/message_listener.hpp
 include/ncbi-tools++/objtools/readers/microarray_reader.hpp
 include/ncbi-tools++/objtools/readers/mod_error.hpp
 include/ncbi-tools++/objtools/readers/mod_reader.hpp
+include/ncbi-tools++/objtools/readers/objhook_lambdas.hpp
 include/ncbi-tools++/objtools/readers/phrap.hpp
 include/ncbi-tools++/objtools/readers/psl_reader.hpp
 include/ncbi-tools++/objtools/readers/read_util.hpp
@@ -3863,6 +4016,43 @@ include/ncbi-tools++/serial/serializable.hpp
 include/ncbi-tools++/serial/serialutil.hpp
 include/ncbi-tools++/serial/streamiter.hpp
 include/ncbi-tools++/serial/typeinfo.hpp
+include/ncbi-tools++/sra/data_loaders/bam/bamloader.hpp
+include/ncbi-tools++/sra/data_loaders/bam/impl/bamloader_impl.hpp
+include/ncbi-tools++/sra/data_loaders/csra/csraloader.hpp
+include/ncbi-tools++/sra/data_loaders/csra/impl/csraloader_impl.hpp
+include/ncbi-tools++/sra/data_loaders/snp/id2snp.hpp
+include/ncbi-tools++/sra/data_loaders/snp/id2snp_entry.hpp
+include/ncbi-tools++/sra/data_loaders/snp/id2snp_params.h
+include/ncbi-tools++/sra/data_loaders/snp/impl/id2snp_impl.hpp
+include/ncbi-tools++/sra/data_loaders/snp/impl/snploader_impl.hpp
+include/ncbi-tools++/sra/data_loaders/snp/snploader.hpp
+include/ncbi-tools++/sra/data_loaders/sra/impl/sraloader_impl.hpp
+include/ncbi-tools++/sra/data_loaders/sra/sraloader.hpp
+include/ncbi-tools++/sra/data_loaders/vdbgraph/impl/vdbgraphloader_impl.hpp
+include/ncbi-tools++/sra/data_loaders/vdbgraph/vdbgraphloader.hpp
+include/ncbi-tools++/sra/data_loaders/wgs/impl/wgsloader_impl.hpp
+include/ncbi-tools++/sra/data_loaders/wgs/wgsloader.hpp
+include/ncbi-tools++/sra/error_codes.hpp
+include/ncbi-tools++/sra/readers/bam/bamgraph.hpp
+include/ncbi-tools++/sra/readers/bam/bamindex.hpp
+include/ncbi-tools++/sra/readers/bam/bamread.hpp
+include/ncbi-tools++/sra/readers/bam/bamread_base.hpp
+include/ncbi-tools++/sra/readers/bam/bgzf.hpp
+include/ncbi-tools++/sra/readers/bam/cache_with_lock.hpp
+include/ncbi-tools++/sra/readers/bam/vdbfile.hpp
+include/ncbi-tools++/sra/readers/ncbi_traces_path.hpp
+include/ncbi-tools++/sra/readers/sra/csraread.hpp
+include/ncbi-tools++/sra/readers/sra/exception.hpp
+include/ncbi-tools++/sra/readers/sra/graphread.hpp
+include/ncbi-tools++/sra/readers/sra/impl/wgs-contig.h
+include/ncbi-tools++/sra/readers/sra/impl/wgsresolver_impl.hpp
+include/ncbi-tools++/sra/readers/sra/kdbread.hpp
+include/ncbi-tools++/sra/readers/sra/sdk.hpp
+include/ncbi-tools++/sra/readers/sra/snpread.hpp
+include/ncbi-tools++/sra/readers/sra/sraread.hpp
+include/ncbi-tools++/sra/readers/sra/vdbread.hpp
+include/ncbi-tools++/sra/readers/sra/wgsread.hpp
+include/ncbi-tools++/sra/readers/sra/wgsresolver.hpp
 include/ncbi-tools++/util/align_range.hpp
 include/ncbi-tools++/util/align_range_coll.hpp
 include/ncbi-tools++/util/align_range_oper.hpp
@@ -3871,6 +4061,7 @@ include/ncbi-tools++/util/ascii85.hpp
 include/ncbi-tools++/util/bitset/bitset_debug.hpp
 include/ncbi-tools++/util/bitset/bitset_pool.hpp
 include/ncbi-tools++/util/bitset/bm.h
+include/ncbi-tools++/util/bitset/bm3vl.h
 include/ncbi-tools++/util/bitset/bm64.h
 include/ncbi-tools++/util/bitset/bmaggregator.h
 include/ncbi-tools++/util/bitset/bmalgo.h
@@ -3884,6 +4075,7 @@ include/ncbi-tools++/util/bitset/bmbmatrix.h
 include/ncbi-tools++/util/bitset/bmbmi1.h
 include/ncbi-tools++/util/bitset/bmbmi2.h
 include/ncbi-tools++/util/bitset/bmbuffer.h
+include/ncbi-tools++/util/bitset/bmbvimport.h
 include/ncbi-tools++/util/bitset/bmconst.h
 include/ncbi-tools++/util/bitset/bmdbg.h
 include/ncbi-tools++/util/bitset/bmdef.h
@@ -3898,12 +4090,15 @@ include/ncbi-tools++/util/bitset/bmsimd.h
 include/ncbi-tools++/util/bitset/bmsparsevec.h
 include/ncbi-tools++/util/bitset/bmsparsevec_algo.h
 include/ncbi-tools++/util/bitset/bmsparsevec_compr.h
+include/ncbi-tools++/util/bitset/bmsparsevec_parallel.h
 include/ncbi-tools++/util/bitset/bmsparsevec_serial.h
 include/ncbi-tools++/util/bitset/bmsparsevec_util.h
 include/ncbi-tools++/util/bitset/bmsse2.h
 include/ncbi-tools++/util/bitset/bmsse4.h
 include/ncbi-tools++/util/bitset/bmsse_util.h
 include/ncbi-tools++/util/bitset/bmstrsparsevec.h
+include/ncbi-tools++/util/bitset/bmtask.h
+include/ncbi-tools++/util/bitset/bmthreadpool.h
 include/ncbi-tools++/util/bitset/bmtimer.h
 include/ncbi-tools++/util/bitset/bmtrans.h
 include/ncbi-tools++/util/bitset/bmundef.h
@@ -3955,7 +4150,11 @@ include/ncbi-tools++/util/histogram_binning.hpp
 include/ncbi-tools++/util/icanceled.hpp
 include/ncbi-tools++/util/id_mux.hpp
 include/ncbi-tools++/util/impl/compile_time_bits.hpp
+include/ncbi-tools++/util/impl/const_tuple.hpp
 include/ncbi-tools++/util/impl/ct_crc32.hpp
+include/ncbi-tools++/util/impl/ct_string_cxx14.hpp
+include/ncbi-tools++/util/impl/ct_string_cxx17.hpp
+include/ncbi-tools++/util/impl/ctsort_cxx14.hpp
 include/ncbi-tools++/util/impl/floating_point_comparison.hpp
 include/ncbi-tools++/util/itransaction.hpp
 include/ncbi-tools++/util/itree.hpp
@@ -3980,6 +4179,7 @@ include/ncbi-tools++/util/mutex_pool.hpp
 include/ncbi-tools++/util/ncbi_cache.hpp
 include/ncbi-tools++/util/ncbi_table.hpp
 include/ncbi-tools++/util/ncbi_url.hpp
+include/ncbi-tools++/util/profile/rtprofile.hpp
 include/ncbi-tools++/util/random_gen.hpp
 include/ncbi-tools++/util/range.hpp
 include/ncbi-tools++/util/range_coll.hpp
@@ -4041,6 +4241,7 @@ include/ncbi-tools++/util/value_convert_policy.hpp
 include/ncbi-tools++/util/weakmap.hpp
 include/ncbi-tools++/util/weakmap.inl
 include/ncbi-tools++/util/xregexp/arg_regexp.hpp
+include/ncbi-tools++/util/xregexp/convert_dates_iso8601.hpp
 include/ncbi-tools++/util/xregexp/mask_regexp.hpp
 include/ncbi-tools++/util/xregexp/regexp.hpp
 include/ncbi-tools++/util/xregexp/regexp_template_tester.hpp
@@ -4089,12 +4290,30 @@ lib/ncbi-tools++/libdbsnp_tooltip_service-static.a
 lib/ncbi-tools++/libdbsnp_tooltip_service.a
 lib/ncbi-tools++/libdocsum-static.a
 lib/ncbi-tools++/libdocsum.a
+lib/ncbi-tools++/libegquery-static.a
+lib/ncbi-tools++/libegquery.a
+lib/ncbi-tools++/libehistory-static.a
+lib/ncbi-tools++/libehistory.a
+lib/ncbi-tools++/libeinfo-static.a
+lib/ncbi-tools++/libeinfo.a
+lib/ncbi-tools++/libelink-static.a
+lib/ncbi-tools++/libelink.a
 lib/ncbi-tools++/libentrez2-static.a
 lib/ncbi-tools++/libentrez2.a
 lib/ncbi-tools++/libentrez2cli-static.a
 lib/ncbi-tools++/libentrez2cli.a
 lib/ncbi-tools++/libentrezgene-static.a
 lib/ncbi-tools++/libentrezgene.a
+lib/ncbi-tools++/libepost-static.a
+lib/ncbi-tools++/libepost.a
+lib/ncbi-tools++/libesearch-static.a
+lib/ncbi-tools++/libesearch.a
+lib/ncbi-tools++/libespell-static.a
+lib/ncbi-tools++/libespell.a
+lib/ncbi-tools++/libesummary-static.a
+lib/ncbi-tools++/libesummary.a
+lib/ncbi-tools++/libeutils-static.a
+lib/ncbi-tools++/libeutils.a
 lib/ncbi-tools++/libfeatdef-static.a
 lib/ncbi-tools++/libfeatdef.a
 lib/ncbi-tools++/libgbproj-static.a
@@ -4147,9 +4366,6 @@ lib/ncbi-tools++/libmmdb-static.a
 lib/ncbi-tools++/libmmdb.a
 lib/ncbi-tools++/libncbi_xblobstorage_netcache-static.a
 lib/ncbi-tools++/libncbi_xblobstorage_netcache.a
-lib/ncbi-tools++/libncbi_xcache_dbapi-dll.so
-lib/ncbi-tools++/libncbi_xcache_dbapi-static.a
-lib/ncbi-tools++/libncbi_xcache_dbapi.a
 lib/ncbi-tools++/libncbi_xcache_netcache-dll.so
 lib/ncbi-tools++/libncbi_xcache_netcache-static.a
 lib/ncbi-tools++/libncbi_xcache_netcache.a
@@ -4185,6 +4401,8 @@ lib/ncbi-tools++/libomssa-static.a
 lib/ncbi-tools++/libomssa.a
 lib/ncbi-tools++/libpcassay-static.a
 lib/ncbi-tools++/libpcassay.a
+lib/ncbi-tools++/libpcassay2-static.a
+lib/ncbi-tools++/libpcassay2.a
 lib/ncbi-tools++/libpcsubstance-static.a
 lib/ncbi-tools++/libpcsubstance.a
 lib/ncbi-tools++/libproj-static.a
@@ -4243,6 +4461,10 @@ lib/ncbi-tools++/libtrackmgrcli-static.a
 lib/ncbi-tools++/libtrackmgrcli.a
 lib/ncbi-tools++/libtrackmgrgridcli-static.a
 lib/ncbi-tools++/libtrackmgrgridcli.a
+lib/ncbi-tools++/libuilist-static.a
+lib/ncbi-tools++/libuilist.a
+lib/ncbi-tools++/libutrtprof-static.a
+lib/ncbi-tools++/libutrtprof.a
 lib/ncbi-tools++/libvalerr-static.a
 lib/ncbi-tools++/libvalerr.a
 lib/ncbi-tools++/libvalid-static.a
diff --git a/ncbi-blast+/distinfo b/ncbi-blast+/distinfo
index a78ddea8cb..e3c951916e 100644
--- a/ncbi-blast+/distinfo
+++ b/ncbi-blast+/distinfo
@@ -1,8 +1,8 @@
 $NetBSD$
 
-RMD160 (ncbi-blast-2.11.0+-src.tar.gz) = a8036dca9cc85b589bbb7f7f24e47c7e0053ead6
-SHA512 (ncbi-blast-2.11.0+-src.tar.gz) = 617994a0e3a4675a5f7048f165ac405bbd6a715ece9aba115d7c26b6be446b889b817dd496a2e15673545e5b594684c83fc4edb22cb5ecca2fd6d342c3bd642e
-Size (ncbi-blast-2.11.0+-src.tar.gz) = 58493096 bytes
+BLAKE2s (ncbi-blast-2.13.0+-src.tar.gz) = a83651c7f2824def1c86a8541cf7060ed77e6d60e8f7bd0383464088591733f3
+SHA512 (ncbi-blast-2.13.0+-src.tar.gz) = 7842ba4dac3d046a23cb182c6289d88cb1173e8570fb6334c1aa88dd2e640aacad43efe1ef7d69b8fedbf9b8093b7d601ef8999812d5735a6789ab2752e97c2b
+Size (ncbi-blast-2.13.0+-src.tar.gz) = 59995353 bytes
 SHA1 (patch-compilers_xcode30__prj_configure) = b89b3be8671c6c692ba474476879ee67a76fdbe5
 SHA1 (patch-src_algo_blast_core_blast__kappa.c) = 6fcad996b3a8e5b6c2400608bff9de62ebf6927f
 SHA1 (patch-src_build-system_Makefile.in.top) = 71d5246867a8c985c1175c338fb0af664094ca01
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