biology/ncbi-blast+: Update to 2.14.0

A few bug fixes, enhancements, and performance improvements

Changes: https://www.ncbi.nlm.nih.gov/books/NBK131777/

4 files changed, 827 insertions, 123 deletions

diff --git a/biology/ncbi-blast+/Makefile b/biology/ncbi-blast+/Makefile
index b24c056c6b8a..55de83407c4b 100644
--- a/biology/ncbi-blast+/Makefile
+++ b/biology/ncbi-blast+/Makefile
@@ -1,6 +1,5 @@
 PORTNAME=	ncbi-blast+
-DISTVERSION=	2.12.0
-PORTREVISION=	10
+DISTVERSION=	2.14.0
 CATEGORIES=	biology perl5 python
 MASTER_SITES=	https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \
 		https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/
@@ -8,7 +7,7 @@ DISTNAME=	ncbi-blast-${PORTVERSION}+-src
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	NCBI implementation of Basic Local Alignment Search Tool
-WWW=		http://blast.ncbi.nlm.nih.gov
+WWW=		https://blast.ncbi.nlm.nih.gov
 
 LICENSE=	PD
 LICENSE_FILE=	${WRKSRC}/scripts/projects/blast/LICENSE
@@ -29,7 +28,9 @@ LIB_DEPENDS=	libpcre.so:devel/pcre \
 		libsqlite3.so:databases/sqlite3 \
 		libuv.so:devel/libuv \
 		libnghttp2.so:www/libnghttp2 \
-		libgrpc.so:devel/grpc
+		libgrpc.so:devel/grpc \
+		libzstd.so:archivers/zstd \
+		libdw.so:devel/elfutils
 RUN_DEPENDS=	p5-List-MoreUtils>=0:lang/p5-List-MoreUtils \
 		p5-JSON>=0:converters/p5-JSON
 
diff --git a/biology/ncbi-blast+/distinfo b/biology/ncbi-blast+/distinfo
index 94e598262859..a3b7142fbb2e 100644
--- a/biology/ncbi-blast+/distinfo
+++ b/biology/ncbi-blast+/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1625068343
-SHA256 (ncbi-blast-2.12.0+-src.tar.gz) = fda3c9c9d488cad6c1880a98a236d842bcf3610e3e702af61f7a48cf0a714b88
-SIZE (ncbi-blast-2.12.0+-src.tar.gz) = 58245348
+TIMESTAMP = 1685108714
+SHA256 (ncbi-blast-2.14.0+-src.tar.gz) = bf477f1b0c3b82f0b7a7094bf003a9a83e37e3b0716c1df799060c4feab17500
+SIZE (ncbi-blast-2.14.0+-src.tar.gz) = 28200227
diff --git a/biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp b/biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp
index f15e73c87671..3ea6f61a5619 100644
--- a/biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp
+++ b/biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp
@@ -1,21 +1,21 @@
---- src/objtools/blast/seqdb_reader/test/seqdb_perf.cpp.orig	2021-01-10 02:28:53 UTC
+--- src/objtools/blast/seqdb_reader/test/seqdb_perf.cpp.orig	2021-10-14 12:36:57 UTC
 +++ src/objtools/blast/seqdb_reader/test/seqdb_perf.cpp
-@@ -137,7 +137,8 @@ CSeqDBPerfApp::x_ScanDatabase()
-     }
+@@ -138,7 +138,8 @@ CSeqDBPerfApp::x_ScanDatabase()
      LOG_POST(Info << "Will go over " << oids2iterate.size() << " sequences");
  
--#if defined(NCBI_COMPILER_GCC) && (NCBI_COMPILER_VERSION >= 900)
-+#if defined(NCBI_COMPILER_GCC) && (NCBI_COMPILER_VERSION >= 900) || \
+ #if (defined(NCBI_COMPILER_GCC) && (NCBI_COMPILER_VERSION >= 900)) || \
+-    (defined(NCBI_COMPILER_ICC) && (NCBI_COMPILER_VERSION >= 2100))
++    (defined(NCBI_COMPILER_ICC) && (NCBI_COMPILER_VERSION >= 2100)) || \
 +    defined(NCBI_COMPILER_LLVM_CLANG)
      #pragma omp parallel default(none) num_threads(m_DbHandles.size()) \
                           shared(oids2iterate,kScanUncompressed) if(m_DbHandles.size() > 1)
  #else
-@@ -208,7 +209,8 @@ CSeqDBPerfApp::x_InitApplicationData()
- 
+@@ -210,7 +211,8 @@ CSeqDBPerfApp::x_InitApplicationData()
  
      if (args["multi_threaded_creation"]) {
--#if defined(NCBI_COMPILER_GCC) && (NCBI_COMPILER_VERSION >= 900)
-+#if defined(NCBI_COMPILER_GCC) && (NCBI_COMPILER_VERSION >= 900) || \
+ #if (defined(NCBI_COMPILER_GCC) && (NCBI_COMPILER_VERSION >= 900)) || \
+-    (defined(NCBI_COMPILER_ICC) && (NCBI_COMPILER_VERSION >= 2100))
++    (defined(NCBI_COMPILER_ICC) && (NCBI_COMPILER_VERSION >= 2100)) ||
 +    defined(NCBI_COMPILER_LLVM_CLANG)
          #pragma omp parallel default(none) shared(kDbName, kNumThreads, kSeqType) num_threads(kNumThreads)
  #else
diff --git a/biology/ncbi-blast+/pkg-plist b/biology/ncbi-blast+/pkg-plist
index db5c2ec247a9..a432cd175519 100644
--- a/biology/ncbi-blast+/pkg-plist
+++ b/biology/ncbi-blast+/pkg-plist
@@ -20,6 +20,7 @@ bin/get_species_taxids.sh
 bin/legacy_blast.pl
 bin/lmdbxx_sample
 bin/makeblastdb
+bin/makeclusterdb
 bin/makembindex
 bin/makeprofiledb
 bin/project_tree_builder
@@ -30,7 +31,6 @@ bin/run_with_lock
 bin/seedtop
 bin/segmasker
 bin/seqdb_demo
-bin/seqdb_perf
 bin/tblastn
 bin/tblastx
 bin/update_blastdb.pl
@@ -211,6 +211,12 @@ 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
@@ -257,6 +263,7 @@ 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
@@ -277,6 +284,7 @@ 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_sanitizers.h
+include/ncbi-tools++/common/ncbi_sc_version.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
@@ -549,40 +557,10 @@ 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
@@ -625,13 +603,11 @@ include/ncbi-tools++/ncbi_random_macro.h
 include/ncbi-tools++/ncbi_source_ver.h
 include/ncbi-tools++/ncbiconf.h
 include/ncbi-tools++/ncbiconf_unix.h
-include/ncbi-tools++/objects/access/.cvsignore
 include/ncbi-tools++/objects/access/.gitignore
 include/ncbi-tools++/objects/access/Link_set.hpp
 include/ncbi-tools++/objects/access/Link_set_.hpp
 include/ncbi-tools++/objects/access/NCBI_Access_module.hpp
 include/ncbi-tools++/objects/access/access__.hpp
-include/ncbi-tools++/objects/biblio/.cvsignore
 include/ncbi-tools++/objects/biblio/.gitignore
 include/ncbi-tools++/objects/biblio/Affil.hpp
 include/ncbi-tools++/objects/biblio/Affil_.hpp
@@ -695,7 +671,6 @@ include/ncbi-tools++/objects/biblio/Title_.hpp
 include/ncbi-tools++/objects/biblio/biblio__.hpp
 include/ncbi-tools++/objects/biblio/biblio_macros.hpp
 include/ncbi-tools++/objects/biblio/citation_base.hpp
-include/ncbi-tools++/objects/biotree/.cvsignore
 include/ncbi-tools++/objects/biotree/.gitignore
 include/ncbi-tools++/objects/biotree/BioTreeContainer.hpp
 include/ncbi-tools++/objects/biotree/BioTreeContainer_.hpp
@@ -715,7 +690,6 @@ include/ncbi-tools++/objects/biotree/NodeSet.hpp
 include/ncbi-tools++/objects/biotree/NodeSet_.hpp
 include/ncbi-tools++/objects/biotree/Node_.hpp
 include/ncbi-tools++/objects/biotree/biotree__.hpp
-include/ncbi-tools++/objects/blast/.cvsignore
 include/ncbi-tools++/objects/blast/.gitignore
 include/ncbi-tools++/objects/blast/Blas_get_searc_resul_reply.hpp
 include/ncbi-tools++/objects/blast/Blas_get_searc_resul_reply_.hpp
@@ -846,10 +820,11 @@ include/ncbi-tools++/objects/blast/blast__.hpp
 include/ncbi-tools++/objects/blast/blastclient.hpp
 include/ncbi-tools++/objects/blast/blastclient_.hpp
 include/ncbi-tools++/objects/blast/names.hpp
-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
@@ -861,7 +836,6 @@ include/ncbi-tools++/objects/blastdb/Blast_mask_list_.hpp
 include/ncbi-tools++/objects/blastdb/NCBI_BlastDL_module.hpp
 include/ncbi-tools++/objects/blastdb/blastdb__.hpp
 include/ncbi-tools++/objects/blastdb/defline_extra.hpp
-include/ncbi-tools++/objects/blastxml/.cvsignore
 include/ncbi-tools++/objects/blastxml/.gitignore
 include/ncbi-tools++/objects/blastxml/BlastOutput.hpp
 include/ncbi-tools++/objects/blastxml/BlastOutput_.hpp
@@ -877,7 +851,6 @@ include/ncbi-tools++/objects/blastxml/Parameters_.hpp
 include/ncbi-tools++/objects/blastxml/Statistics.hpp
 include/ncbi-tools++/objects/blastxml/Statistics_.hpp
 include/ncbi-tools++/objects/blastxml/blastxml__.hpp
-include/ncbi-tools++/objects/blastxml2/.cvsignore
 include/ncbi-tools++/objects/blastxml2/.gitignore
 include/ncbi-tools++/objects/blastxml2/BlastOutput2.hpp
 include/ncbi-tools++/objects/blastxml2/BlastOutput2_.hpp
@@ -909,7 +882,6 @@ include/ncbi-tools++/objects/blastxml2/Statistics_.hpp
 include/ncbi-tools++/objects/blastxml2/Target.hpp
 include/ncbi-tools++/objects/blastxml2/Target_.hpp
 include/ncbi-tools++/objects/blastxml2/blastxml2__.hpp
-include/ncbi-tools++/objects/cdd/.cvsignore
 include/ncbi-tools++/objects/cdd/.gitignore
 include/ncbi-tools++/objects/cdd/Algorithm_type.hpp
 include/ncbi-tools++/objects/cdd/Algorithm_type_.hpp
@@ -979,7 +951,6 @@ include/ncbi-tools++/objects/cdd/Update_align_.hpp
 include/ncbi-tools++/objects/cdd/Update_comment.hpp
 include/ncbi-tools++/objects/cdd/Update_comment_.hpp
 include/ncbi-tools++/objects/cdd/cdd__.hpp
-include/ncbi-tools++/objects/cn3d/.cvsignore
 include/ncbi-tools++/objects/cn3d/.gitignore
 include/ncbi-tools++/objects/cn3d/Cn3d_GL_matrix.hpp
 include/ncbi-tools++/objects/cn3d/Cn3d_GL_matrix_.hpp
@@ -1023,7 +994,6 @@ include/ncbi-tools++/objects/cn3d/Cn3d_view_settings.hpp
 include/ncbi-tools++/objects/cn3d/Cn3d_view_settings_.hpp
 include/ncbi-tools++/objects/cn3d/NCBI_Cn3d_module.hpp
 include/ncbi-tools++/objects/cn3d/cn3d__.hpp
-include/ncbi-tools++/objects/coords/.cvsignore
 include/ncbi-tools++/objects/coords/.gitignore
 include/ncbi-tools++/objects/coords/HGVS_Coordinate.hpp
 include/ncbi-tools++/objects/coords/HGVS_Coordinate_.hpp
@@ -1036,7 +1006,6 @@ include/ncbi-tools++/objects/dbsnp/primary_track/dbsnp.pb.h
 include/ncbi-tools++/objects/dbsnp/primary_track/dbsnp_mock.grpc.pb.h
 include/ncbi-tools++/objects/dbsnp/primary_track/impl/snpptis_impl.hpp
 include/ncbi-tools++/objects/dbsnp/primary_track/snpptis.hpp
-include/ncbi-tools++/objects/docsum/.cvsignore
 include/ncbi-tools++/objects/docsum/.gitignore
 include/ncbi-tools++/objects/docsum/Assay.hpp
 include/ncbi-tools++/objects/docsum/Assay_.hpp
@@ -1064,7 +1033,6 @@ include/ncbi-tools++/objects/docsum/Rs_.hpp
 include/ncbi-tools++/objects/docsum/Ss.hpp
 include/ncbi-tools++/objects/docsum/Ss_.hpp
 include/ncbi-tools++/objects/docsum/docsum__.hpp
-include/ncbi-tools++/objects/entrez2/.cvsignore
 include/ncbi-tools++/objects/entrez2/.gitignore
 include/ncbi-tools++/objects/entrez2/E2Reply.hpp
 include/ncbi-tools++/objects/entrez2/E2Reply_.hpp
@@ -1144,7 +1112,6 @@ include/ncbi-tools++/objects/entrez2/NCBI_Entrez2_module.hpp
 include/ncbi-tools++/objects/entrez2/entrez2__.hpp
 include/ncbi-tools++/objects/entrez2/entrez2_client.hpp
 include/ncbi-tools++/objects/entrez2/entrez2_client_.hpp
-include/ncbi-tools++/objects/entrezgene/.cvsignore
 include/ncbi-tools++/objects/entrezgene/.gitignore
 include/ncbi-tools++/objects/entrezgene/Entrezgene.hpp
 include/ncbi-tools++/objects/entrezgene/Entrezgene_.hpp
@@ -1164,7 +1131,6 @@ include/ncbi-tools++/objects/entrezgene/Other_source_.hpp
 include/ncbi-tools++/objects/entrezgene/Xtra_Terms.hpp
 include/ncbi-tools++/objects/entrezgene/Xtra_Terms_.hpp
 include/ncbi-tools++/objects/entrezgene/entrezgene__.hpp
-include/ncbi-tools++/objects/featdef/.cvsignore
 include/ncbi-tools++/objects/featdef/.gitignore
 include/ncbi-tools++/objects/featdef/FeatDef.hpp
 include/ncbi-tools++/objects/featdef/FeatDefGroupSet.hpp
@@ -1180,7 +1146,6 @@ include/ncbi-tools++/objects/featdef/FeatMolType.hpp
 include/ncbi-tools++/objects/featdef/FeatMolType_.hpp
 include/ncbi-tools++/objects/featdef/NCBI_FeatDef_module.hpp
 include/ncbi-tools++/objects/featdef/featdef__.hpp
-include/ncbi-tools++/objects/gbproj/.cvsignore
 include/ncbi-tools++/objects/gbproj/.gitignore
 include/ncbi-tools++/objects/gbproj/AbstractProjectItem.hpp
 include/ncbi-tools++/objects/gbproj/AbstractProjectItem_.hpp
@@ -1212,7 +1177,6 @@ include/ncbi-tools++/objects/gbproj/ViewMemento_.hpp
 include/ncbi-tools++/objects/gbproj/gbproj__.hpp
 include/ncbi-tools++/objects/gbproj/gbproj_export.h
 include/ncbi-tools++/objects/gbproj/igbproject.hpp
-include/ncbi-tools++/objects/gbseq/.cvsignore
 include/ncbi-tools++/objects/gbseq/.gitignore
 include/ncbi-tools++/objects/gbseq/GBAltSeqData.hpp
 include/ncbi-tools++/objects/gbseq/GBAltSeqData_.hpp
@@ -1252,7 +1216,6 @@ include/ncbi-tools++/objects/gbseq/GBXref.hpp
 include/ncbi-tools++/objects/gbseq/GBXref_.hpp
 include/ncbi-tools++/objects/gbseq/NCBI_GBSeq_module.hpp
 include/ncbi-tools++/objects/gbseq/gbseq__.hpp
-include/ncbi-tools++/objects/general/.cvsignore
 include/ncbi-tools++/objects/general/.gitignore
 include/ncbi-tools++/objects/general/Date.hpp
 include/ncbi-tools++/objects/general/Date_.hpp
@@ -1277,7 +1240,6 @@ include/ncbi-tools++/objects/general/general__.hpp
 include/ncbi-tools++/objects/general/general_exception.hpp
 include/ncbi-tools++/objects/general/general_macros.hpp
 include/ncbi-tools++/objects/general/uoconv.hpp
-include/ncbi-tools++/objects/genesbyloc/.cvsignore
 include/ncbi-tools++/objects/genesbyloc/.gitignore
 include/ncbi-tools++/objects/genesbyloc/GBL_Data.hpp
 include/ncbi-tools++/objects/genesbyloc/GBL_Data_.hpp
@@ -1287,7 +1249,6 @@ include/ncbi-tools++/objects/genesbyloc/GBL_Reply.hpp
 include/ncbi-tools++/objects/genesbyloc/GBL_Reply_.hpp
 include/ncbi-tools++/objects/genesbyloc/NCBI_GenesByLoc_module.hpp
 include/ncbi-tools++/objects/genesbyloc/genesbyloc__.hpp
-include/ncbi-tools++/objects/genomecoll/.cvsignore
 include/ncbi-tools++/objects/genomecoll/.gitignore
 include/ncbi-tools++/objects/genomecoll/GCClientRequest.hpp
 include/ncbi-tools++/objects/genomecoll/GCClientRequest_.hpp
@@ -1360,7 +1321,6 @@ include/ncbi-tools++/objects/genomecoll/gencoll_client__.hpp
 include/ncbi-tools++/objects/genomecoll/genome_collection__.hpp
 include/ncbi-tools++/objects/genomecoll/genomic_collections_cli.hpp
 include/ncbi-tools++/objects/genomecoll/genomic_collections_cli_.hpp
-include/ncbi-tools++/objects/homologene/.cvsignore
 include/ncbi-tools++/objects/homologene/.gitignore
 include/ncbi-tools++/objects/homologene/HG_Alignment.hpp
 include/ncbi-tools++/objects/homologene/HG_AlignmentSet.hpp
@@ -1390,7 +1350,6 @@ include/ncbi-tools++/objects/homologene/HG_Stats.hpp
 include/ncbi-tools++/objects/homologene/HG_Stats_.hpp
 include/ncbi-tools++/objects/homologene/HomoloGene_module.hpp
 include/ncbi-tools++/objects/homologene/homologene__.hpp
-include/ncbi-tools++/objects/id1/.cvsignore
 include/ncbi-tools++/objects/id1/.gitignore
 include/ncbi-tools++/objects/id1/Entry_complexities.hpp
 include/ncbi-tools++/objects/id1/Entry_complexities_.hpp
@@ -1412,7 +1371,6 @@ include/ncbi-tools++/objects/id1/NCBI_ID1Access_module.hpp
 include/ncbi-tools++/objects/id1/id1__.hpp
 include/ncbi-tools++/objects/id1/id1_client.hpp
 include/ncbi-tools++/objects/id1/id1_client_.hpp
-include/ncbi-tools++/objects/id2/.cvsignore
 include/ncbi-tools++/objects/id2/.gitignore
 include/ncbi-tools++/objects/id2/ID2S_Reply_Get_Chunk.hpp
 include/ncbi-tools++/objects/id2/ID2S_Reply_Get_Chunk_.hpp
@@ -1474,7 +1432,6 @@ include/ncbi-tools++/objects/id2/id2_client.hpp
 include/ncbi-tools++/objects/id2/id2_client_.hpp
 include/ncbi-tools++/objects/id2/id2processor.hpp
 include/ncbi-tools++/objects/id2/id2processor_interface.hpp
-include/ncbi-tools++/objects/insdseq/.cvsignore
 include/ncbi-tools++/objects/insdseq/.gitignore
 include/ncbi-tools++/objects/insdseq/INSDAltSeqData.hpp
 include/ncbi-tools++/objects/insdseq/INSDAltSeqData_.hpp
@@ -1514,7 +1471,6 @@ include/ncbi-tools++/objects/insdseq/INSDXref.hpp
 include/ncbi-tools++/objects/insdseq/INSDXref_.hpp
 include/ncbi-tools++/objects/insdseq/INSD_INSDSeq_module.hpp
 include/ncbi-tools++/objects/insdseq/insdseq__.hpp
-include/ncbi-tools++/objects/macro/.cvsignore
 include/ncbi-tools++/objects/macro/.gitignore
 include/ncbi-tools++/objects/macro/AECRParse_action.hpp
 include/ncbi-tools++/objects/macro/AECRParse_action_.hpp
@@ -1876,7 +1832,6 @@ include/ncbi-tools++/objects/macro/Word_substitution_set_.hpp
 include/ncbi-tools++/objects/macro/Xref_type.hpp
 include/ncbi-tools++/objects/macro/Xref_type_.hpp
 include/ncbi-tools++/objects/macro/macro__.hpp
-include/ncbi-tools++/objects/medlars/.cvsignore
 include/ncbi-tools++/objects/medlars/.gitignore
 include/ncbi-tools++/objects/medlars/Medlars_entry.hpp
 include/ncbi-tools++/objects/medlars/Medlars_entry_.hpp
@@ -1884,7 +1839,6 @@ include/ncbi-tools++/objects/medlars/Medlars_record.hpp
 include/ncbi-tools++/objects/medlars/Medlars_record_.hpp
 include/ncbi-tools++/objects/medlars/NCBI_Medlars_module.hpp
 include/ncbi-tools++/objects/medlars/medlars__.hpp
-include/ncbi-tools++/objects/medline/.cvsignore
 include/ncbi-tools++/objects/medline/.gitignore
 include/ncbi-tools++/objects/medline/DocRef.hpp
 include/ncbi-tools++/objects/medline/DocRef_.hpp
@@ -1902,7 +1856,6 @@ include/ncbi-tools++/objects/medline/Medline_si.hpp
 include/ncbi-tools++/objects/medline/Medline_si_.hpp
 include/ncbi-tools++/objects/medline/NCBI_Medline_module.hpp
 include/ncbi-tools++/objects/medline/medline__.hpp
-include/ncbi-tools++/objects/mim/.cvsignore
 include/ncbi-tools++/objects/mim/.gitignore
 include/ncbi-tools++/objects/mim/Mim_allelic_variant.hpp
 include/ncbi-tools++/objects/mim/Mim_allelic_variant_.hpp
@@ -1935,7 +1888,6 @@ include/ncbi-tools++/objects/mim/mim__.hpp
 include/ncbi-tools++/objects/misc/error_codes.hpp
 include/ncbi-tools++/objects/misc/sequence_macros.hpp
 include/ncbi-tools++/objects/misc/sequence_util_macros.hpp
-include/ncbi-tools++/objects/mla/.cvsignore
 include/ncbi-tools++/objects/mla/.gitignore
 include/ncbi-tools++/objects/mla/Error_val.hpp
 include/ncbi-tools++/objects/mla/Error_val_.hpp
@@ -1953,7 +1905,6 @@ include/ncbi-tools++/objects/mla/Title_type_.hpp
 include/ncbi-tools++/objects/mla/mla__.hpp
 include/ncbi-tools++/objects/mla/mla_client.hpp
 include/ncbi-tools++/objects/mla/mla_client_.hpp
-include/ncbi-tools++/objects/mmdb1/.cvsignore
 include/ncbi-tools++/objects/mmdb1/.gitignore
 include/ncbi-tools++/objects/mmdb1/Atom.hpp
 include/ncbi-tools++/objects/mmdb1/Atom_.hpp
@@ -2016,7 +1967,6 @@ include/ncbi-tools++/objects/mmdb1/Residue_graph_pntr_.hpp
 include/ncbi-tools++/objects/mmdb1/Residue_id.hpp
 include/ncbi-tools++/objects/mmdb1/Residue_id_.hpp
 include/ncbi-tools++/objects/mmdb1/mmdb1__.hpp
-include/ncbi-tools++/objects/mmdb2/.cvsignore
 include/ncbi-tools++/objects/mmdb2/.gitignore
 include/ncbi-tools++/objects/mmdb2/Alternate_conformation_id.hpp
 include/ncbi-tools++/objects/mmdb2/Alternate_conformation_id_.hpp
@@ -2064,7 +2014,6 @@ include/ncbi-tools++/objects/mmdb2/T_mesh_.hpp
 include/ncbi-tools++/objects/mmdb2/Triangles.hpp
 include/ncbi-tools++/objects/mmdb2/Triangles_.hpp
 include/ncbi-tools++/objects/mmdb2/mmdb2__.hpp
-include/ncbi-tools++/objects/mmdb3/.cvsignore
 include/ncbi-tools++/objects/mmdb3/.gitignore
 include/ncbi-tools++/objects/mmdb3/Align_stats.hpp
 include/ncbi-tools++/objects/mmdb3/Align_stats_.hpp
@@ -2142,7 +2091,6 @@ include/ncbi-tools++/objects/mmdb3/Trans_matrix_.hpp
 include/ncbi-tools++/objects/mmdb3/Transform.hpp
 include/ncbi-tools++/objects/mmdb3/Transform_.hpp
 include/ncbi-tools++/objects/mmdb3/mmdb3__.hpp
-include/ncbi-tools++/objects/ncbimime/.cvsignore
 include/ncbi-tools++/objects/ncbimime/.gitignore
 include/ncbi-tools++/objects/ncbimime/Biostruc_align.hpp
 include/ncbi-tools++/objects/ncbimime/Biostruc_align_.hpp
@@ -2164,7 +2112,6 @@ include/ncbi-tools++/objects/ncbimime/NCBI_Mime_module.hpp
 include/ncbi-tools++/objects/ncbimime/Ncbi_mime_asn1.hpp
 include/ncbi-tools++/objects/ncbimime/Ncbi_mime_asn1_.hpp
 include/ncbi-tools++/objects/ncbimime/ncbimime__.hpp
-include/ncbi-tools++/objects/objprt/.cvsignore
 include/ncbi-tools++/objects/objprt/.gitignore
 include/ncbi-tools++/objects/objprt/NCBI_ObjPrt_module.hpp
 include/ncbi-tools++/objects/objprt/PrintForm.hpp
@@ -2188,7 +2135,6 @@ include/ncbi-tools++/objects/objprt/TemplateName_.hpp
 include/ncbi-tools++/objects/objprt/UserFormat.hpp
 include/ncbi-tools++/objects/objprt/UserFormat_.hpp
 include/ncbi-tools++/objects/objprt/objprt__.hpp
-include/ncbi-tools++/objects/omssa/.cvsignore
 include/ncbi-tools++/objects/omssa/.gitignore
 include/ncbi-tools++/objects/omssa/MSBioseq.hpp
 include/ncbi-tools++/objects/omssa/MSBioseqSet.hpp
@@ -2276,7 +2222,6 @@ include/ncbi-tools++/objects/omssa/NameValue.hpp
 include/ncbi-tools++/objects/omssa/NameValue_.hpp
 include/ncbi-tools++/objects/omssa/OMSSA_module.hpp
 include/ncbi-tools++/objects/omssa/omssa__.hpp
-include/ncbi-tools++/objects/pcassay/.cvsignore
 include/ncbi-tools++/objects/pcassay/.gitignore
 include/ncbi-tools++/objects/pcassay/NCBI_PCAssay_module.hpp
 include/ncbi-tools++/objects/pcassay/PC_AnnotatedXRef.hpp
@@ -2312,7 +2257,35 @@ 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/pcsubstance/.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/.gitignore
 include/ncbi-tools++/objects/pcsubstance/NCBI_PCSubstance_module.hpp
 include/ncbi-tools++/objects/pcsubstance/PC_AtomInt.hpp
@@ -2331,6 +2304,8 @@ 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
@@ -2353,6 +2328,8 @@ 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
@@ -2390,7 +2367,6 @@ include/ncbi-tools++/objects/pcsubstance/PC_Urn_.hpp
 include/ncbi-tools++/objects/pcsubstance/PC_XRefData.hpp
 include/ncbi-tools++/objects/pcsubstance/PC_XRefData_.hpp
 include/ncbi-tools++/objects/pcsubstance/pcsubstance__.hpp
-include/ncbi-tools++/objects/proj/.cvsignore
 include/ncbi-tools++/objects/proj/.gitignore
 include/ncbi-tools++/objects/proj/NCBI_Project_module.hpp
 include/ncbi-tools++/objects/proj/Projdesc.hpp
@@ -2404,7 +2380,6 @@ include/ncbi-tools++/objects/proj/Project_id_.hpp
 include/ncbi-tools++/objects/proj/Project_item.hpp
 include/ncbi-tools++/objects/proj/Project_item_.hpp
 include/ncbi-tools++/objects/proj/proj__.hpp
-include/ncbi-tools++/objects/pub/.cvsignore
 include/ncbi-tools++/objects/pub/.gitignore
 include/ncbi-tools++/objects/pub/NCBI_Pub_module.hpp
 include/ncbi-tools++/objects/pub/Pub.hpp
@@ -2415,7 +2390,6 @@ include/ncbi-tools++/objects/pub/Pub_set.hpp
 include/ncbi-tools++/objects/pub/Pub_set_.hpp
 include/ncbi-tools++/objects/pub/pub__.hpp
 include/ncbi-tools++/objects/pub/pub_macros.hpp
-include/ncbi-tools++/objects/pubmed/.cvsignore
 include/ncbi-tools++/objects/pubmed/.gitignore
 include/ncbi-tools++/objects/pubmed/NCBI_PubMed_module.hpp
 include/ncbi-tools++/objects/pubmed/Pubmed_entry.hpp
@@ -2423,7 +2397,6 @@ include/ncbi-tools++/objects/pubmed/Pubmed_entry_.hpp
 include/ncbi-tools++/objects/pubmed/Pubmed_url.hpp
 include/ncbi-tools++/objects/pubmed/Pubmed_url_.hpp
 include/ncbi-tools++/objects/pubmed/pubmed__.hpp
-include/ncbi-tools++/objects/remap/.cvsignore
 include/ncbi-tools++/objects/remap/.gitignore
 include/ncbi-tools++/objects/remap/NCBI_Remap_module.hpp
 include/ncbi-tools++/objects/remap/RMReply.hpp
@@ -2445,7 +2418,6 @@ include/ncbi-tools++/objects/remap/Remap_result_.hpp
 include/ncbi-tools++/objects/remap/remap__.hpp
 include/ncbi-tools++/objects/remap/remap_client.hpp
 include/ncbi-tools++/objects/remap/remap_client_.hpp
-include/ncbi-tools++/objects/scoremat/.cvsignore
 include/ncbi-tools++/objects/scoremat/.gitignore
 include/ncbi-tools++/objects/scoremat/BlockProperty.hpp
 include/ncbi-tools++/objects/scoremat/BlockProperty_.hpp
@@ -2473,7 +2445,6 @@ include/ncbi-tools++/objects/scoremat/Site_annot_.hpp
 include/ncbi-tools++/objects/scoremat/Site_annot_set.hpp
 include/ncbi-tools++/objects/scoremat/Site_annot_set_.hpp
 include/ncbi-tools++/objects/scoremat/scoremat__.hpp
-include/ncbi-tools++/objects/seq/.cvsignore
 include/ncbi-tools++/objects/seq/.gitignore
 include/ncbi-tools++/objects/seq/Align_def.hpp
 include/ncbi-tools++/objects/seq/Align_def_.hpp
@@ -2575,7 +2546,6 @@ 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_type.hpp
-include/ncbi-tools++/objects/seqalign/.cvsignore
 include/ncbi-tools++/objects/seqalign/.gitignore
 include/ncbi-tools++/objects/seqalign/Dense_diag.hpp
 include/ncbi-tools++/objects/seqalign/Dense_diag_.hpp
@@ -2617,7 +2587,6 @@ include/ncbi-tools++/objects/seqalign/Std_seg_.hpp
 include/ncbi-tools++/objects/seqalign/seqalign__.hpp
 include/ncbi-tools++/objects/seqalign/seqalign_exception.hpp
 include/ncbi-tools++/objects/seqalign/seqalign_macros.hpp
-include/ncbi-tools++/objects/seqblock/.cvsignore
 include/ncbi-tools++/objects/seqblock/.gitignore
 include/ncbi-tools++/objects/seqblock/EMBL_General_module.hpp
 include/ncbi-tools++/objects/seqblock/EMBL_block.hpp
@@ -2647,7 +2616,6 @@ include/ncbi-tools++/objects/seqblock/SP_block.hpp
 include/ncbi-tools++/objects/seqblock/SP_block_.hpp
 include/ncbi-tools++/objects/seqblock/seqblock__.hpp
 include/ncbi-tools++/objects/seqblock/seqblock_macros.hpp
-include/ncbi-tools++/objects/seqcode/.cvsignore
 include/ncbi-tools++/objects/seqcode/.gitignore
 include/ncbi-tools++/objects/seqcode/NCBI_SeqCode_module.hpp
 include/ncbi-tools++/objects/seqcode/Seq_code_set.hpp
@@ -2659,7 +2627,6 @@ include/ncbi-tools++/objects/seqcode/Seq_code_type_.hpp
 include/ncbi-tools++/objects/seqcode/Seq_map_table.hpp
 include/ncbi-tools++/objects/seqcode/Seq_map_table_.hpp
 include/ncbi-tools++/objects/seqcode/seqcode__.hpp
-include/ncbi-tools++/objects/seqedit/.cvsignore
 include/ncbi-tools++/objects/seqedit/.gitignore
 include/ncbi-tools++/objects/seqedit/NCBI_SeqEdit_module.hpp
 include/ncbi-tools++/objects/seqedit/SeqEdit_Cmd.hpp
@@ -2709,7 +2676,6 @@ include/ncbi-tools++/objects/seqedit/SeqEdit_Cmd_SetDescr_.hpp
 include/ncbi-tools++/objects/seqedit/SeqEdit_Id.hpp
 include/ncbi-tools++/objects/seqedit/SeqEdit_Id_.hpp
 include/ncbi-tools++/objects/seqedit/seqedit__.hpp
-include/ncbi-tools++/objects/seqfeat/.cvsignore
 include/ncbi-tools++/objects/seqfeat/.gitignore
 include/ncbi-tools++/objects/seqfeat/BinomialOrgName.hpp
 include/ncbi-tools++/objects/seqfeat/BinomialOrgName_.hpp
@@ -2831,7 +2797,6 @@ include/ncbi-tools++/objects/seqfeat/Variation_ref.hpp
 include/ncbi-tools++/objects/seqfeat/Variation_ref_.hpp
 include/ncbi-tools++/objects/seqfeat/seqfeat__.hpp
 include/ncbi-tools++/objects/seqfeat/seqfeat_macros.hpp
-include/ncbi-tools++/objects/seqloc/.cvsignore
 include/ncbi-tools++/objects/seqloc/.gitignore
 include/ncbi-tools++/objects/seqloc/Giimport_id.hpp
 include/ncbi-tools++/objects/seqloc/Giimport_id_.hpp
@@ -2868,7 +2833,6 @@ include/ncbi-tools++/objects/seqloc/Textseq_id.hpp
 include/ncbi-tools++/objects/seqloc/Textseq_id_.hpp
 include/ncbi-tools++/objects/seqloc/seqloc__.hpp
 include/ncbi-tools++/objects/seqloc/seqloc_macros.hpp
-include/ncbi-tools++/objects/seqres/.cvsignore
 include/ncbi-tools++/objects/seqres/.gitignore
 include/ncbi-tools++/objects/seqres/Byte_graph.hpp
 include/ncbi-tools++/objects/seqres/Byte_graph_.hpp
@@ -2880,7 +2844,6 @@ include/ncbi-tools++/objects/seqres/Real_graph_.hpp
 include/ncbi-tools++/objects/seqres/Seq_graph.hpp
 include/ncbi-tools++/objects/seqres/Seq_graph_.hpp
 include/ncbi-tools++/objects/seqres/seqres__.hpp
-include/ncbi-tools++/objects/seqset/.cvsignore
 include/ncbi-tools++/objects/seqset/.gitignore
 include/ncbi-tools++/objects/seqset/Bioseq_set.hpp
 include/ncbi-tools++/objects/seqset/Bioseq_set_.hpp
@@ -2891,7 +2854,6 @@ include/ncbi-tools++/objects/seqset/gb_release_file.hpp
 include/ncbi-tools++/objects/seqset/seqset__.hpp
 include/ncbi-tools++/objects/seqset/seqset_exception.hpp
 include/ncbi-tools++/objects/seqset/seqset_macros.hpp
-include/ncbi-tools++/objects/seqsplit/.cvsignore
 include/ncbi-tools++/objects/seqsplit/.gitignore
 include/ncbi-tools++/objects/seqsplit/ID2S_Bioseq_Ids.hpp
 include/ncbi-tools++/objects/seqsplit/ID2S_Bioseq_Ids_.hpp
@@ -2949,7 +2911,6 @@ include/ncbi-tools++/objects/seqsplit/ID2S_Split_Info.hpp
 include/ncbi-tools++/objects/seqsplit/ID2S_Split_Info_.hpp
 include/ncbi-tools++/objects/seqsplit/NCBI_Seq_split_module.hpp
 include/ncbi-tools++/objects/seqsplit/seqsplit__.hpp
-include/ncbi-tools++/objects/seqtable/.cvsignore
 include/ncbi-tools++/objects/seqtable/.gitignore
 include/ncbi-tools++/objects/seqtable/BVector_data.hpp
 include/ncbi-tools++/objects/seqtable/BVector_data_.hpp
@@ -2977,7 +2938,6 @@ include/ncbi-tools++/objects/seqtable/Seq_table_.hpp
 include/ncbi-tools++/objects/seqtable/impl/delta_cache.hpp
 include/ncbi-tools++/objects/seqtable/seq_table_exception.hpp
 include/ncbi-tools++/objects/seqtable/seqtable__.hpp
-include/ncbi-tools++/objects/seqtest/.cvsignore
 include/ncbi-tools++/objects/seqtest/.gitignore
 include/ncbi-tools++/objects/seqtest/NCBI_SeqTest_module.hpp
 include/ncbi-tools++/objects/seqtest/SeqTestResults.hpp
@@ -2987,7 +2947,6 @@ include/ncbi-tools++/objects/seqtest/Seq_test_result_.hpp
 include/ncbi-tools++/objects/seqtest/Seq_test_result_set.hpp
 include/ncbi-tools++/objects/seqtest/Seq_test_result_set_.hpp
 include/ncbi-tools++/objects/seqtest/seqtest__.hpp
-include/ncbi-tools++/objects/submit/.cvsignore
 include/ncbi-tools++/objects/submit/.gitignore
 include/ncbi-tools++/objects/submit/Contact_info.hpp
 include/ncbi-tools++/objects/submit/Contact_info_.hpp
@@ -2998,7 +2957,6 @@ include/ncbi-tools++/objects/submit/Submit_block.hpp
 include/ncbi-tools++/objects/submit/Submit_block_.hpp
 include/ncbi-tools++/objects/submit/submit__.hpp
 include/ncbi-tools++/objects/submit/submit_macros.hpp
-include/ncbi-tools++/objects/taxon1/.cvsignore
 include/ncbi-tools++/objects/taxon1/.gitignore
 include/ncbi-tools++/objects/taxon1/NCBI_Taxon1_module.hpp
 include/ncbi-tools++/objects/taxon1/Taxon1_data.hpp
@@ -3018,7 +2976,6 @@ include/ncbi-tools++/objects/taxon1/Taxon2_data_.hpp
 include/ncbi-tools++/objects/taxon1/local_taxon.hpp
 include/ncbi-tools++/objects/taxon1/taxon1.hpp
 include/ncbi-tools++/objects/taxon1/taxon1__.hpp
-include/ncbi-tools++/objects/taxon3/.cvsignore
 include/ncbi-tools++/objects/taxon3/.gitignore
 include/ncbi-tools++/objects/taxon3/NCBI_Taxon3_module.hpp
 include/ncbi-tools++/objects/taxon3/SequenceOfInt.hpp
@@ -3043,7 +3000,6 @@ include/ncbi-tools++/objects/taxon3/cached_taxon3.hpp
 include/ncbi-tools++/objects/taxon3/itaxon3.hpp
 include/ncbi-tools++/objects/taxon3/taxon3.hpp
 include/ncbi-tools++/objects/taxon3/taxon3__.hpp
-include/ncbi-tools++/objects/tinyseq/.cvsignore
 include/ncbi-tools++/objects/tinyseq/.gitignore
 include/ncbi-tools++/objects/tinyseq/NCBI_TSeq_module.hpp
 include/ncbi-tools++/objects/tinyseq/TSeq.hpp
@@ -3051,7 +3007,6 @@ include/ncbi-tools++/objects/tinyseq/TSeqSet.hpp
 include/ncbi-tools++/objects/tinyseq/TSeqSet_.hpp
 include/ncbi-tools++/objects/tinyseq/TSeq_.hpp
 include/ncbi-tools++/objects/tinyseq/tinyseq__.hpp
-include/ncbi-tools++/objects/trackmgr/.cvsignore
 include/ncbi-tools++/objects/trackmgr/.gitignore
 include/ncbi-tools++/objects/trackmgr/NCBI_TrackManager_module.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_ACL_AccessLevel.hpp
@@ -3211,7 +3166,6 @@ include/ncbi-tools++/objects/trackmgr/trackmgr_client.hpp
 include/ncbi-tools++/objects/trackmgr/trackmgr_client_.hpp
 include/ncbi-tools++/objects/trackmgr/trackmgr_export.h
 include/ncbi-tools++/objects/trackmgr/trackset_client.hpp
-include/ncbi-tools++/objects/valerr/.cvsignore
 include/ncbi-tools++/objects/valerr/.gitignore
 include/ncbi-tools++/objects/valerr/NCBI_ValErrors_module.hpp
 include/ncbi-tools++/objects/valerr/ValidErrItem.hpp
@@ -3219,7 +3173,6 @@ include/ncbi-tools++/objects/valerr/ValidErrItem_.hpp
 include/ncbi-tools++/objects/valerr/ValidError.hpp
 include/ncbi-tools++/objects/valerr/ValidError_.hpp
 include/ncbi-tools++/objects/valerr/valerr__.hpp
-include/ncbi-tools++/objects/valid/.cvsignore
 include/ncbi-tools++/objects/valid/.gitignore
 include/ncbi-tools++/objects/valid/Comment_rule.hpp
 include/ncbi-tools++/objects/valid/Comment_rule_.hpp
@@ -3239,7 +3192,6 @@ include/ncbi-tools++/objects/valid/Phrase_list_.hpp
 include/ncbi-tools++/objects/valid/Severity_level.hpp
 include/ncbi-tools++/objects/valid/Severity_level_.hpp
 include/ncbi-tools++/objects/valid/valid__.hpp
-include/ncbi-tools++/objects/variation/.cvsignore
 include/ncbi-tools++/objects/variation/.gitignore
 include/ncbi-tools++/objects/variation/NCBI_VariationPackage_module.hpp
 include/ncbi-tools++/objects/variation/VariantPlacement.hpp
@@ -3251,7 +3203,6 @@ include/ncbi-tools++/objects/variation/VariationMethod.hpp
 include/ncbi-tools++/objects/variation/VariationMethod_.hpp
 include/ncbi-tools++/objects/variation/Variation_.hpp
 include/ncbi-tools++/objects/variation/variation__.hpp
-include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/.cvsignore
 include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/.gitignore
 include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/Error.hpp
 include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/Error_.hpp
@@ -3261,7 +3212,6 @@ include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/Placement_.hpp
 include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/SearchByRsIdReply.hpp
 include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/SearchByRsIdReply_.hpp
 include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/search_by_rsid__.hpp
-include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/.cvsignore
 include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/.gitignore
 include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipData.hpp
 include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipData_.hpp
@@ -3275,7 +3225,6 @@ include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipSe
 include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipServiceReply_.hpp
 include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/NCBI_dbsnp_tooltips_module.hpp
 include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/dbsnp_tooltip_service__.hpp
-include/ncbi-tools++/objects/varrep/.cvsignore
 include/ncbi-tools++/objects/varrep/.gitignore
 include/ncbi-tools++/objects/varrep/AaInterval.hpp
 include/ncbi-tools++/objects/varrep/AaInterval_.hpp
@@ -3552,13 +3501,13 @@ 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
 include/ncbi-tools++/objtools/cleanup/cleanup_message.hpp
 include/ncbi-tools++/objtools/cleanup/cleanup_pub.hpp
 include/ncbi-tools++/objtools/cleanup/fix_feature_id.hpp
+include/ncbi-tools++/objtools/cleanup/huge_file_cleanup.hpp
 include/ncbi-tools++/objtools/data_loaders/blastdb/bdbloader.hpp
 include/ncbi-tools++/objtools/data_loaders/blastdb/bdbloader_rmt.hpp
 include/ncbi-tools++/objtools/data_loaders/blastdb/blastdb_adapter.hpp
@@ -3622,6 +3571,7 @@ include/ncbi-tools++/objtools/edit/cds_fix.hpp
 include/ncbi-tools++/objtools/edit/dblink_field.hpp
 include/ncbi-tools++/objtools/edit/edit_error.hpp
 include/ncbi-tools++/objtools/edit/edit_exception.hpp
+include/ncbi-tools++/objtools/edit/eutils_updater.hpp
 include/ncbi-tools++/objtools/edit/external_annots.hpp
 include/ncbi-tools++/objtools/edit/feattable_edit.hpp
 include/ncbi-tools++/objtools/edit/feature_propagate.hpp
@@ -3630,13 +3580,20 @@ include/ncbi-tools++/objtools/edit/gap_trim.hpp
 include/ncbi-tools++/objtools/edit/gaps_edit.hpp
 include/ncbi-tools++/objtools/edit/gb_block_field.hpp
 include/ncbi-tools++/objtools/edit/gene_utils.hpp
+include/ncbi-tools++/objtools/edit/huge_asn_loader.hpp
+include/ncbi-tools++/objtools/edit/huge_asn_macro_reader.hpp
+include/ncbi-tools++/objtools/edit/huge_asn_reader.hpp
+include/ncbi-tools++/objtools/edit/huge_file.hpp
+include/ncbi-tools++/objtools/edit/huge_file_process.hpp
 include/ncbi-tools++/objtools/edit/link_cds_mrna.hpp
 include/ncbi-tools++/objtools/edit/loc_edit.hpp
 include/ncbi-tools++/objtools/edit/mail_report.hpp
+include/ncbi-tools++/objtools/edit/mla_updater.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/pubmed_updater.hpp
 include/ncbi-tools++/objtools/edit/remote_updater.hpp
 include/ncbi-tools++/objtools/edit/rna_edit.hpp
 include/ncbi-tools++/objtools/edit/seq_edit.hpp
@@ -3658,7 +3615,705 @@ 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/efetch/.gitignore
+include/ncbi-tools++/objtools/eutils/efetch/Abs.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Abs_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Abstract.hpp
+include/ncbi-tools++/objtools/eutils/efetch/AbstractText.hpp
+include/ncbi-tools++/objtools/eutils/efetch/AbstractText_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Abstract_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/AccessionNumber.hpp
+include/ncbi-tools++/objtools/eutils/efetch/AccessionNumberList.hpp
+include/ncbi-tools++/objtools/eutils/efetch/AccessionNumberList_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/AccessionNumber_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Acronym.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Acronym_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Affiliation.hpp
+include/ncbi-tools++/objtools/eutils/efetch/AffiliationInfo.hpp
+include/ncbi-tools++/objtools/eutils/efetch/AffiliationInfo_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Affiliation_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Agency.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Agency_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/And.hpp
+include/ncbi-tools++/objtools/eutils/efetch/And_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Annotation.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Annotation_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Annotation_xml.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Annotation_xml_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Apply.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Apply_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Apply_content.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Apply_content_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Approx.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Approx_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arccos.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arccos_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arccosh.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arccosh_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arccot.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arccot_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arccoth.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arccoth_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arccsc.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arccsc_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arccsch.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arccsch_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arcsec.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arcsec_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arcsech.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arcsech_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arcsin.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arcsin_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arcsinh.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arcsinh_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arctan.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arctan_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arctanh.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arctanh_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arg.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Arg_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Article.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ArticleDate.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ArticleDate_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ArticleId.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ArticleIdList.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ArticleIdList_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ArticleId_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ArticleTitle.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ArticleTitle_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Article_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Author.hpp
+include/ncbi-tools++/objtools/eutils/efetch/AuthorList.hpp
+include/ncbi-tools++/objtools/eutils/efetch/AuthorList_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Author_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/B.hpp
+include/ncbi-tools++/objtools/eutils/efetch/B_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/BeginningDate.hpp
+include/ncbi-tools++/objtools/eutils/efetch/BeginningDate_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Bind.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Bind_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Bind_content.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Bind_content_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Book.hpp
+include/ncbi-tools++/objtools/eutils/efetch/BookDocument.hpp
+include/ncbi-tools++/objtools/eutils/efetch/BookDocumentSet.hpp
+include/ncbi-tools++/objtools/eutils/efetch/BookDocumentSet_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/BookDocument_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/BookTitle.hpp
+include/ncbi-tools++/objtools/eutils/efetch/BookTitle_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Book_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Bvar.hpp
+include/ncbi-tools++/objtools/eutils/efetch/BvarQ.hpp
+include/ncbi-tools++/objtools/eutils/efetch/BvarQ_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Bvar_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Card.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Card_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Cartesianproduct.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Cartesianproduct_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Cbytes.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Cbytes_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Ceiling.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Ceiling_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Cerror.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Cerror_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Chemical.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ChemicalList.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ChemicalList_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Chemical_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Ci.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Ci_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Ci_content.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Ci_content_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Citation.hpp
+include/ncbi-tools++/objtools/eutils/efetch/CitationSubset.hpp
+include/ncbi-tools++/objtools/eutils/efetch/CitationSubset_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Citation_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Cn.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Cn_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Cn_content.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Cn_content_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Codomain.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Codomain_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/CoiStatement.hpp
+include/ncbi-tools++/objtools/eutils/efetch/CoiStatement_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/CollectionTitle.hpp
+include/ncbi-tools++/objtools/eutils/efetch/CollectionTitle_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/CollectiveName.hpp
+include/ncbi-tools++/objtools/eutils/efetch/CollectiveName_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/CommentsCorrections.hpp
+include/ncbi-tools++/objtools/eutils/efetch/CommentsCorrectionsList.hpp
+include/ncbi-tools++/objtools/eutils/efetch/CommentsCorrectionsList_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/CommentsCorrections_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Complexes.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Complexes_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Compose.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Compose_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Condition.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Condition_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Conjugate.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Conjugate_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ContExp.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ContExp_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ContractNumber.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ContractNumber_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ContributionDate.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ContributionDate_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/CopyrightInformation.hpp
+include/ncbi-tools++/objtools/eutils/efetch/CopyrightInformation_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Cos.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Cos_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Cosh.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Cosh_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Cot.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Cot_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Coth.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Coth_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Country.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Country_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Cs.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Cs_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Csc.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Csc_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Csch.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Csch_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Csymbol.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Csymbol_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Csymbol_content.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Csymbol_content_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Curl.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Curl_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/DataBank.hpp
+include/ncbi-tools++/objtools/eutils/efetch/DataBankList.hpp
+include/ncbi-tools++/objtools/eutils/efetch/DataBankList_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/DataBankName.hpp
+include/ncbi-tools++/objtools/eutils/efetch/DataBankName_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/DataBank_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/DateCompleted.hpp
+include/ncbi-tools++/objtools/eutils/efetch/DateCompleted_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/DateRevised.hpp
+include/ncbi-tools++/objtools/eutils/efetch/DateRevised_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Day.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Day_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Declare.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Declare_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Degree.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Degree_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/DeleteCitation.hpp
+include/ncbi-tools++/objtools/eutils/efetch/DeleteCitation_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/DeleteDocument.hpp
+include/ncbi-tools++/objtools/eutils/efetch/DeleteDocument_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/DescriptorName.hpp
+include/ncbi-tools++/objtools/eutils/efetch/DescriptorName_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Determinant.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Determinant_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Diff.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Diff_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/DispFormula.hpp
+include/ncbi-tools++/objtools/eutils/efetch/DispFormula_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Divergence.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Divergence_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Divide.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Divide_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Domain.hpp
+include/ncbi-tools++/objtools/eutils/efetch/DomainQ.hpp
+include/ncbi-tools++/objtools/eutils/efetch/DomainQ_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Domain_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Domainofapplication.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Domainofapplication_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ELocationID.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ELocationID_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Edition.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Edition_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Emptyset.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Emptyset_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/EndPage.hpp
+include/ncbi-tools++/objtools/eutils/efetch/EndPage_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/EndingDate.hpp
+include/ncbi-tools++/objtools/eutils/efetch/EndingDate_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Eq.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Eq_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Equivalent.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Equivalent_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Eulergamma.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Eulergamma_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Exists.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Exists_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Exp.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Exp_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Exponentiale.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Exponentiale_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Factorial.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Factorial_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Factorof.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Factorof_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/False.hpp
+include/ncbi-tools++/objtools/eutils/efetch/False_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Floor.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Floor_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Fn.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Fn_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Forall.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Forall_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ForeName.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ForeName_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Gcd.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Gcd_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/GeneSymbol.hpp
+include/ncbi-tools++/objtools/eutils/efetch/GeneSymbolList.hpp
+include/ncbi-tools++/objtools/eutils/efetch/GeneSymbolList_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/GeneSymbol_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/GeneralNote.hpp
+include/ncbi-tools++/objtools/eutils/efetch/GeneralNote_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Geq.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Geq_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Grad.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Grad_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Grant.hpp
+include/ncbi-tools++/objtools/eutils/efetch/GrantID.hpp
+include/ncbi-tools++/objtools/eutils/efetch/GrantID_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/GrantList.hpp
+include/ncbi-tools++/objtools/eutils/efetch/GrantList_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Grant_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Gt.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Gt_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/History.hpp
+include/ncbi-tools++/objtools/eutils/efetch/History_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Hour.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Hour_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/I.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ISOAbbreviation.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ISOAbbreviation_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ISSN.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ISSNLinking.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ISSNLinking_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ISSN_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/I_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Ident.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Ident_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Identifier.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Identifier_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Image.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Image_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Imaginary.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Imaginary_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Imaginaryi.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Imaginaryi_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ImpliedMrow.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ImpliedMrow_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Implies.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Implies_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/In.hpp
+include/ncbi-tools++/objtools/eutils/efetch/In_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Infinity.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Infinity_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Initials.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Initials_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Int.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Int_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Integers.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Integers_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Intersect.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Intersect_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Interval.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Interval_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Inverse.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Inverse_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Investigator.hpp
+include/ncbi-tools++/objtools/eutils/efetch/InvestigatorList.hpp
+include/ncbi-tools++/objtools/eutils/efetch/InvestigatorList_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Investigator_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Isbn.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Isbn_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Issue.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Issue_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Item.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ItemList.hpp
+include/ncbi-tools++/objtools/eutils/efetch/ItemList_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Item_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Journal.hpp
+include/ncbi-tools++/objtools/eutils/efetch/JournalIssue.hpp
+include/ncbi-tools++/objtools/eutils/efetch/JournalIssue_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Journal_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Keyword.hpp
+include/ncbi-tools++/objtools/eutils/efetch/KeywordList.hpp
+include/ncbi-tools++/objtools/eutils/efetch/KeywordList_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Keyword_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Lambda.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Lambda_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Language.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Language_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Laplacian.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Laplacian_.hpp
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+include/ncbi-tools++/objtools/eutils/efetch/LastName_.hpp
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+include/ncbi-tools++/objtools/eutils/efetch/Uplimit_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Variance.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Variance_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Vector.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Vector_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Vectorproduct.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Vectorproduct_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/VernacularTitle.hpp
+include/ncbi-tools++/objtools/eutils/efetch/VernacularTitle_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Volume.hpp
+include/ncbi-tools++/objtools/eutils/efetch/VolumeTitle.hpp
+include/ncbi-tools++/objtools/eutils/efetch/VolumeTitle_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Volume_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Xor.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Xor_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Year.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Year_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/efetch__.hpp
+include/ncbi-tools++/objtools/eutils/efetch/efetch_module.hpp
 include/ncbi-tools++/objtools/eutils/egquery/.gitignore
 include/ncbi-tools++/objtools/eutils/egquery/EGQueryResult.hpp
 include/ncbi-tools++/objtools/eutils/egquery/EGQueryResult_.hpp
@@ -3668,7 +4323,6 @@ 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
@@ -3676,7 +4330,6 @@ 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
@@ -3694,7 +4347,6 @@ 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
@@ -3732,7 +4384,6 @@ 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
@@ -3740,7 +4391,6 @@ 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
@@ -3760,7 +4410,6 @@ 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
@@ -3768,7 +4417,6 @@ 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
@@ -3778,7 +4426,6 @@ 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
@@ -3861,9 +4508,9 @@ 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/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
@@ -3874,6 +4521,7 @@ 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
@@ -4000,6 +4648,45 @@ 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/snpread_packed.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/limited_resource_map.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
@@ -4008,6 +4695,7 @@ 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
@@ -4021,6 +4709,7 @@ 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
@@ -4056,6 +4745,7 @@ include/ncbi-tools++/util/bitset/ncbi_bitset.hpp
 include/ncbi-tools++/util/bitset/ncbi_bitset_alloc.hpp
 include/ncbi-tools++/util/bitset/ncbi_bitset_util.hpp
 include/ncbi-tools++/util/bitset/readme
+include/ncbi-tools++/util/bitset/sse2neon.h
 include/ncbi-tools++/util/buffer_writer.hpp
 include/ncbi-tools++/util/bytesrc.hpp
 include/ncbi-tools++/util/cache/cache_async.hpp
@@ -4079,6 +4769,7 @@ include/ncbi-tools++/util/compress/zlib.hpp
 include/ncbi-tools++/util/compress/zlib/zconf.h
 include/ncbi-tools++/util/compress/zlib/zlib.h
 include/ncbi-tools++/util/compress/zlib/zutil.h
+include/ncbi-tools++/util/compress/zstd.hpp
 include/ncbi-tools++/util/creaders/alnread.h
 include/ncbi-tools++/util/creaders/creaders_export.h
 include/ncbi-tools++/util/data_histogram.hpp
@@ -4095,8 +4786,15 @@ 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_bitset_cxx14.hpp
+include/ncbi-tools++/util/impl/ct_bitset_cxx17.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/impl/generated_fsm.hpp
 include/ncbi-tools++/util/itransaction.hpp
 include/ncbi-tools++/util/itree.hpp
 include/ncbi-tools++/util/itree.inl
@@ -4113,6 +4811,7 @@ include/ncbi-tools++/util/math/matrix.hpp
 include/ncbi-tools++/util/math/miscmath.h
 include/ncbi-tools++/util/math/promote.hpp
 include/ncbi-tools++/util/md5.hpp
+include/ncbi-tools++/util/message_queue.hpp
 include/ncbi-tools++/util/miscmath.h
 include/ncbi-tools++/util/multi_writer.hpp
 include/ncbi-tools++/util/multipattern_search.hpp
@@ -4231,6 +4930,8 @@ 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++/libefetch-static.a
+lib/ncbi-tools++/libefetch.a
 lib/ncbi-tools++/libegquery-static.a
 lib/ncbi-tools++/libegquery.a
 lib/ncbi-tools++/libehistory-static.a
@@ -4342,6 +5043,8 @@ 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