biology/ncbi-blast+: Upgrade to 2.7.1

Patch Makefile.in.top to cleanly support DESTDIR

Also resolves 225002, conflict with libproj

PR:             226037
Reported by:    wen
Reviewed by:    mat rene
Approved by:    jrm
Differential Revision:  https://reviews.freebsd.org/D14854

6 files changed, 409 insertions, 377 deletions

diff --git a/biology/ncbi-blast+/Makefile b/biology/ncbi-blast+/Makefile
index c2872fc29bc2..f252f08e1ac4 100644
--- a/biology/ncbi-blast+/Makefile
+++ b/biology/ncbi-blast+/Makefile
@@ -1,12 +1,10 @@
 # $FreeBSD$
 
-PORTNAME=	blast+
-PORTVERSION=	2.5.0
-PORTREVISION=	3
-CATEGORIES=	biology
-MASTER_SITES=	http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/ \
-		http://acadix.biz/Ports/distfiles/
-PKGNAMEPREFIX=	ncbi-
+PORTNAME=	ncbi-blast+
+DISTVERSION=	2.7.1
+CATEGORIES=	biology perl5 python
+MASTER_SITES=	https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \
+		https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/
 DISTNAME=	ncbi-blast-${PORTVERSION}+-src
 
 MAINTAINER=	jwb@FreeBSD.org
@@ -15,43 +13,55 @@ COMMENT=	NCBI implementation of Basic Local Alignment Search Tool
 LICENSE=	PD
 LICENSE_FILE=	${WRKSRC}/scripts/projects/blast/LICENSE
 
-LIB_DEPENDS=	libpcre.so:devel/pcre
+LIB_DEPENDS=	libpcre.so:devel/pcre \
+		liblmdb.so:databases/lmdb \
+		liblzo2.so:archivers/lzo2 \
+		libgnutls.so:security/gnutls \
+		libtspi.so:security/trousers \
+		libgmp.so:math/gmp \
+		libidn2.so:dns/libidn2 \
+		libnettle.so:security/nettle \
+		libhogweed.so:security/nettle \
+		libtasn1.so:security/libtasn1 \
+		libp11-kit.so:security/p11-kit \
+		libgcrypt.so:security/libgcrypt \
+		libgpg-error.so:security/libgpg-error \
+		libsqlite3.so:databases/sqlite3
 RUN_DEPENDS=	p5-List-MoreUtils>=0:lang/p5-List-MoreUtils
 
-WRKSRC=		${WRKDIR}/${DISTNAME}/c++
-
-GNU_CONFIGURE=	yes
-USES=		gmake shebangfix perl5 python
+USES=		compiler:openmp gmake shebangfix perl5 python
 SHEBANG_FILES=	src/app/blast/legacy_blast.pl \
 		src/app/blast/update_blastdb.pl \
 		src/app/winmasker/windowmasker_2.2.22_adapter.py
-
-MAKE_JOBS_UNSAFE=	yes
-
-# Requires openmp
-USE_GCC=	yes
 USE_LDCONFIG=	yes
+GNU_CONFIGURE=	yes
 
 # The test for amq can hang, but amq is not needed so just avoid the test
 CONFIGURE_ENV=	ncbi_cv_prog_amq_w=no
 
 # configure chooses /usr/local/bin/ar with no flags
 # FreeBSD boost port flagged by configure as untested version
-CONFIGURE_ARGS+=AR="ar cr" --without-boost
+# --libdir=${PREFIX}/lib/ncbi-tools++ doesn't respect DESTDIR, so do
+# a postinstall mv.
+CONFIGURE_ARGS+=	AR="ar cr" --without-boost --libdir=${PREFIX}/lib/ncbi-tools++
+
+WRKSRC_SUBDIR=		c++
+
+MAKE_JOBS_UNSAFE=	yes
 
 # Fix "undefined _ThreadRuneLocale" error on 10.0
 # Fix unknown options in configure
-# Add staging support to configure-generated Makefile
 post-patch:
-	${REINPLACE_CMD} \
+	@${REINPLACE_CMD} \
 		-e 's|-D_THREAD_SAFE|-D_THREAD_SAFE -D__RUNETYPE_INTERNAL|' \
 		-e '/--infodir=DIR/d' \
 		-e '/--mandir=DIR/d' \
 		${WRKSRC}/src/build-system/configure
-	${REINPLACE_CMD} -e 's|@prefix@|${STAGEDIR}@prefix@|g' \
-		${WRKSRC}/src/build-system/Makefile.in.top
 
 post-install:
-	${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/*.so
+	@${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/*/*/.cvsignore.extra
+	@${RM} -rf ${STAGEDIR}${PREFIX}/lib/X11
+	@${RMDIR} ${STAGEDIR}${PREFIX}/lib/debug
+	${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/ncbi-tools++/*.so
 
 .include <bsd.port.mk>
diff --git a/biology/ncbi-blast+/distinfo b/biology/ncbi-blast+/distinfo
index 74aa3b15dc44..f532546f648e 100644
--- a/biology/ncbi-blast+/distinfo
+++ b/biology/ncbi-blast+/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1480648908
-SHA256 (ncbi-blast-2.5.0+-src.tar.gz) = cce122a29d309127a478353856b351914232e78a9546941781ff0a4c18ec9c54
-SIZE (ncbi-blast-2.5.0+-src.tar.gz) = 19938544
+TIMESTAMP = 1518995346
+SHA256 (ncbi-blast-2.7.1+-src.tar.gz) = 10a78d3007413a6d4c983d2acbf03ef84b622b82bd9a59c6bd9fbdde9d0298ca
+SIZE (ncbi-blast-2.7.1+-src.tar.gz) = 23254824
diff --git a/biology/ncbi-blast+/files/patch-src_build-system_Makefile.in.top b/biology/ncbi-blast+/files/patch-src_build-system_Makefile.in.top
index 0ccfbe40632c..5f5d103c2082 100644
--- a/biology/ncbi-blast+/files/patch-src_build-system_Makefile.in.top
+++ b/biology/ncbi-blast+/files/patch-src_build-system_Makefile.in.top
@@ -1,11 +1,32 @@
---- src/build-system/Makefile.in.top.orig	2014-11-13 01:41:55.000000000 +0900
-+++ src/build-system/Makefile.in.top	2016-12-02 16:39:58.415910000 +0900
-@@ -51,7 +51,7 @@
+--- src/build-system/Makefile.in.top.orig	2018-03-27 03:40:40 UTC
++++ src/build-system/Makefile.in.top
+@@ -37,21 +37,21 @@ check: $(PROJECTS)
+ 	fi
+ 
+ install-toolkit:
+-	-$(RMDIR) $(pincludedir)
+-	$(INSTALL) -d $(bindir) $(libdir) $(pincludedir)
+-	$(INSTALL) $(lbindir)/* $(bindir)
+-	$(INSTALL) -m 644 $(llibdir)/*.* $(libdir)
++	-$(RMDIR) $(DESTDIR)$(pincludedir)
++	$(INSTALL) -d $(DESTDIR)$(bindir) $(DESTDIR)$(libdir) $(DESTDIR)$(pincludedir)
++	$(INSTALL) $(lbindir)/* $(DESTDIR)$(bindir)
++	$(INSTALL) -m 644 $(llibdir)/*.* $(DESTDIR)$(libdir)
+ 	if test -d $(llibdir)/ncbi; then \
+-	    cp -pPR $(llibdir)/ncbi $(libdir)/; \
++	    cp -pPR $(llibdir)/ncbi $(DESTDIR)$(libdir)/; \
+ 	fi
+-	-rm -f $(libdir)/lib*-static.a
+-	cd $(libdir)  && \
++	-rm -f $(DESTDIR)$(libdir)/lib*-static.a
++	cd $(DESTDIR)$(libdir)  && \
+ 	    for x in *.a; do \
+ 	        $(LN_S) "$$x" "`$(BASENAME) \"$$x\" .a`-static.a"; \
  	    done
- 	cd $(includedir0) && find * -name CVS -prune -o -print |\
-             cpio -pd $(pincludedir)
--	$(INSTALL) -m 644 $(incdir)/* $(pincludedir)
-+	cd $(incdir) && find * | cpio -pd $(pincludedir)
+ 	for d in $(includedir0) $(incdir); do \
+ 	    cd $$d && find * -name .svn -prune -o -print | \
+-                cpio -pd $(pincludedir) ; \
++                cpio -pd $(DESTDIR)$(pincludedir) ; \
+ 	done
  ## set up appropriate build and status directories somewhere under $(libdir)?
  
- install-gbench:
diff --git a/biology/ncbi-blast+/files/patch-src_build-system_configure b/biology/ncbi-blast+/files/patch-src_build-system_configure
index 7dc6dcba2793..03a625d3dbe6 100644
--- a/biology/ncbi-blast+/files/patch-src_build-system_configure
+++ b/biology/ncbi-blast+/files/patch-src_build-system_configure
@@ -1,11 +1,30 @@
---- src/build-system/configure.orig	2016-09-09 21:04:16.000000000 +0900
-+++ src/build-system/configure	2016-12-02 15:04:04.258800000 +0900
-@@ -1715,7 +1715,7 @@
-       | --silent | --cache-file=* | -C | --config-cache | -n | --no-create \
-       | --no-recursion | --prefix=* | --exec-prefix=* | --bindir=* \
+--- src/build-system/configure.orig	2017-10-18 15:21:39 UTC
++++ src/build-system/configure
+@@ -1755,7 +1755,7 @@ for x_arg in "$@" ; do
        | --libdir=* | --includedir=* | --build=* | --host=* | --target=* \
+       | --mandir=* | --infodir=* | --docdir=* | --htmldir=* \
+       | --datadir=* | --sysconfdir=* | --localstatedir=* \
 -      | --with-runpath=* | --with-relative-runpath=* \
 +      | --with-runpath=* | --with-relative-runpath=* | --localstatedir=* \
        | --with-experimental=* | --with-extra-action=* | --with-build-root=* \
        | --with-fake-root=* | --with-build-root-sfx=* | --with-check=* \
        | --with-check-tools=* | --with-ftds=[0-9]* | --with-fastcgi=[0-9]* \
+@@ -1828,9 +1828,7 @@ Fine tuning of the installation director
+   --oldincludedir=DIR    C header files for non-gcc [/usr/include]
+   --datarootdir=DIR      read-only arch.-independent data root [PREFIX/share]
+   --datadir=DIR          read-only architecture-independent data [DATAROOTDIR]
+-  --infodir=DIR          info documentation [DATAROOTDIR/info]
+   --localedir=DIR        locale-dependent data [DATAROOTDIR/locale]
+-  --mandir=DIR           man documentation [DATAROOTDIR/man]
+   --docdir=DIR           documentation root [DATAROOTDIR/doc/ncbi-tools--]
+   --htmldir=DIR          html documentation [DOCDIR]
+   --dvidir=DIR           dvi documentation [DOCDIR]
+@@ -8086,7 +8084,7 @@ case "$host_os:$compiler" in
+ esac
+ 
+ if test "$with_mt" != "no" ; then
+-   CPPFLAGS="$CPPFLAGS -D_MT -D_REENTRANT -D_THREAD_SAFE"
++   CPPFLAGS="$CPPFLAGS -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL -D__RUNETYPE_INTERNAL"
+    LIBS="$LIBS $THREAD_LIBS"
+    case "$host_os:$compiler" in
+      solaris2.??:* | solaris*:GCC | *:Compaq | irix* | aix* | darwin* | cygwin*)
diff --git a/biology/ncbi-blast+/pkg-descr b/biology/ncbi-blast+/pkg-descr
index 29274eae3373..19fcc057c3f0 100644
--- a/biology/ncbi-blast+/pkg-descr
+++ b/biology/ncbi-blast+/pkg-descr
@@ -1,8 +1,7 @@
-The Basic Local Alignment Search Tool (BLAST) finds regions of local
-similarity between sequences. The program compares nucleotide or protein
-sequences to sequence databases and calculates the statistical
-significance of matches. BLAST can be used to infer functional and
-evolutionary relationships between sequences as well as help identify
-members of gene families.
+The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity
+between sequences. The program compares nucleotide or protein sequences to
+sequence databases and calculates the statistical significance of matches.
+BLAST can be used to infer functional and evolutionary relationships between
+sequences as well as help identify members of gene families.
 
 WWW: http://blast.ncbi.nlm.nih.gov
diff --git a/biology/ncbi-blast+/pkg-plist b/biology/ncbi-blast+/pkg-plist
index d319174a3821..b39ffddff602 100644
--- a/biology/ncbi-blast+/pkg-plist
+++ b/biology/ncbi-blast+/pkg-plist
@@ -10,6 +10,7 @@ bin/convert2blastmask
 bin/datatool
 bin/deltablast
 bin/dustmasker
+bin/gc_cli
 bin/gene_info_reader
 bin/legacy_blast.pl
 bin/makeblastdb
@@ -45,6 +46,7 @@ include/ncbi-tools++/algo/blast/api/blast_rps_options.hpp
 include/ncbi-tools++/algo/blast/api/blast_seqinfosrc.hpp
 include/ncbi-tools++/algo/blast/api/blast_seqinfosrc_aux.hpp
 include/ncbi-tools++/algo/blast/api/blast_types.hpp
+include/ncbi-tools++/algo/blast/api/blastp_kmer_options.hpp
 include/ncbi-tools++/algo/blast/api/blastx_options.hpp
 include/ncbi-tools++/algo/blast/api/cdd_pssm_input.hpp
 include/ncbi-tools++/algo/blast/api/deltablast.hpp
@@ -105,6 +107,7 @@ include/ncbi-tools++/algo/blast/blastinput/cmdline_flags.hpp
 include/ncbi-tools++/algo/blast/blastinput/deltablast_args.hpp
 include/ncbi-tools++/algo/blast/blastinput/igblastn_args.hpp
 include/ncbi-tools++/algo/blast/blastinput/igblastp_args.hpp
+include/ncbi-tools++/algo/blast/blastinput/kblastp_args.hpp
 include/ncbi-tools++/algo/blast/blastinput/magicblast_args.hpp
 include/ncbi-tools++/algo/blast/blastinput/psiblast_args.hpp
 include/ncbi-tools++/algo/blast/blastinput/rmblastn_args.hpp
@@ -175,12 +178,14 @@ include/ncbi-tools++/algo/blast/core/pattern.h
 include/ncbi-tools++/algo/blast/core/phi_extend.h
 include/ncbi-tools++/algo/blast/core/phi_gapalign.h
 include/ncbi-tools++/algo/blast/core/phi_lookup.h
+include/ncbi-tools++/algo/blast/core/spliced_hits.h
 include/ncbi-tools++/algo/blast/core/split_query.h
 include/ncbi-tools++/algo/blast/dbindex/dbindex.hpp
 include/ncbi-tools++/algo/blast/dbindex/dbindex_sp.hpp
 include/ncbi-tools++/algo/blast/dbindex/sequence_istream.hpp
 include/ncbi-tools++/algo/blast/dbindex/sequence_istream_bdb.hpp
 include/ncbi-tools++/algo/blast/dbindex/sequence_istream_fasta.hpp
+include/ncbi-tools++/algo/blast/format/blast_async_format.hpp
 include/ncbi-tools++/algo/blast/format/blast_format.hpp
 include/ncbi-tools++/algo/blast/format/blastfmtutil.hpp
 include/ncbi-tools++/algo/blast/format/blastxml2_format.hpp
@@ -191,6 +196,13 @@ include/ncbi-tools++/algo/blast/format/data4xmlformat.hpp
 include/ncbi-tools++/algo/blast/format/sam.hpp
 include/ncbi-tools++/algo/blast/format/vecscreen_run.hpp
 include/ncbi-tools++/algo/blast/igblast/igblast.hpp
+include/ncbi-tools++/algo/blast/proteinkmer/blastkmer.hpp
+include/ncbi-tools++/algo/blast/proteinkmer/blastkmerindex.hpp
+include/ncbi-tools++/algo/blast/proteinkmer/blastkmeroptions.hpp
+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/dustmask/sdust.tex
 include/ncbi-tools++/algo/dustmask/symdust.hpp
 include/ncbi-tools++/algo/segmask/segmask.hpp
@@ -284,7 +296,11 @@ include/ncbi-tools++/connect/ncbi_heapmgr.h
 include/ncbi-tools++/connect/ncbi_host_info.h
 include/ncbi-tools++/connect/ncbi_http_connector.h
 include/ncbi-tools++/connect/ncbi_http_session.hpp
+include/ncbi-tools++/connect/ncbi_iprange.h
+include/ncbi-tools++/connect/ncbi_ipv6.h
 include/ncbi-tools++/connect/ncbi_lbos.hpp
+include/ncbi-tools++/connect/ncbi_localip.h
+include/ncbi-tools++/connect/ncbi_mbedtls.h
 include/ncbi-tools++/connect/ncbi_memory_connector.h
 include/ncbi-tools++/connect/ncbi_misc.hpp
 include/ncbi-tools++/connect/ncbi_monkey.hpp
@@ -301,6 +317,7 @@ include/ncbi-tools++/connect/ncbi_socket.hpp
 include/ncbi-tools++/connect/ncbi_socket_connector.h
 include/ncbi-tools++/connect/ncbi_socket_unix.h
 include/ncbi-tools++/connect/ncbi_socket_unix.hpp
+include/ncbi-tools++/connect/ncbi_tls.h
 include/ncbi-tools++/connect/ncbi_types.h
 include/ncbi-tools++/connect/ncbi_userhost.hpp
 include/ncbi-tools++/connect/ncbi_util.h
@@ -327,6 +344,7 @@ include/ncbi-tools++/connect/services/netcache_admin.hpp
 include/ncbi-tools++/connect/services/netcache_api.hpp
 include/ncbi-tools++/connect/services/netcache_api_expt.hpp
 include/ncbi-tools++/connect/services/netcache_key.hpp
+include/ncbi-tools++/connect/services/netcache_search.hpp
 include/ncbi-tools++/connect/services/netcomponent.hpp
 include/ncbi-tools++/connect/services/neticache_client.hpp
 include/ncbi-tools++/connect/services/netschedule_api.hpp
@@ -337,7 +355,6 @@ include/ncbi-tools++/connect/services/netservice_api_expt.hpp
 include/ncbi-tools++/connect/services/netservice_protocol_parser.hpp
 include/ncbi-tools++/connect/services/netstorage.hpp
 include/ncbi-tools++/connect/services/netstorage_ft.hpp
-include/ncbi-tools++/connect/services/netstorage_impl.hpp
 include/ncbi-tools++/connect/services/ns_client_factory.hpp
 include/ncbi-tools++/connect/services/ns_job_serializer.hpp
 include/ncbi-tools++/connect/services/ns_output_parser.hpp
@@ -446,10 +463,13 @@ include/ncbi-tools++/corelib/resource_info.hpp
 include/ncbi-tools++/corelib/rwstream.hpp
 include/ncbi-tools++/corelib/stream_utils.hpp
 include/ncbi-tools++/corelib/syslog.hpp
+include/ncbi-tools++/corelib/teamcity_messages.h
 include/ncbi-tools++/corelib/tempstr.hpp
 include/ncbi-tools++/corelib/test_boost.hpp
 include/ncbi-tools++/corelib/test_mt.hpp
 include/ncbi-tools++/corelib/version.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
@@ -506,15 +526,14 @@ include/ncbi-tools++/html/selection.hpp
 include/ncbi-tools++/html/writer_htmlenc.hpp
 include/ncbi-tools++/misc/error_codes.hpp
 include/ncbi-tools++/ncbi_pch.hpp
+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/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/Affil.hpp
 include/ncbi-tools++/objects/biblio/Affil_.hpp
 include/ncbi-tools++/objects/biblio/ArticleId.hpp
@@ -577,7 +596,6 @@ 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/BioTreeContainer.hpp
 include/ncbi-tools++/objects/biotree/BioTreeContainer_.hpp
 include/ncbi-tools++/objects/biotree/DistanceMatrix.hpp
@@ -596,8 +614,6 @@ 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/.cvsignore.extra
 include/ncbi-tools++/objects/blast/Blas_get_searc_resul_reply.hpp
 include/ncbi-tools++/objects/blast/Blas_get_searc_resul_reply_.hpp
 include/ncbi-tools++/objects/blast/Blas_get_searc_resul_reque.hpp
@@ -727,7 +743,6 @@ 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/Blast_db_mask_info.hpp
 include/ncbi-tools++/objects/blastdb/Blast_db_mask_info_.hpp
 include/ncbi-tools++/objects/blastdb/Blast_def_line.hpp
@@ -741,7 +756,6 @@ 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/BlastOutput.hpp
 include/ncbi-tools++/objects/blastxml/BlastOutput_.hpp
 include/ncbi-tools++/objects/blastxml/Hit.hpp
@@ -756,7 +770,6 @@ 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/BlastOutput2.hpp
 include/ncbi-tools++/objects/blastxml2/BlastOutput2_.hpp
 include/ncbi-tools++/objects/blastxml2/BlastXML2.hpp
@@ -787,7 +800,6 @@ 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/Algorithm_type.hpp
 include/ncbi-tools++/objects/cdd/Algorithm_type_.hpp
 include/ncbi-tools++/objects/cdd/Align_annot.hpp
@@ -856,7 +868,6 @@ 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/Cn3d_GL_matrix.hpp
 include/ncbi-tools++/objects/cn3d/Cn3d_GL_matrix_.hpp
 include/ncbi-tools++/objects/cn3d/Cn3d_backbone_label_style.hpp
@@ -899,14 +910,12 @@ 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/HGVS_Coordinate.hpp
 include/ncbi-tools++/objects/coords/HGVS_Coordinate_.hpp
 include/ncbi-tools++/objects/coords/HGVS_Coordinate_Set.hpp
 include/ncbi-tools++/objects/coords/HGVS_Coordinate_Set_.hpp
 include/ncbi-tools++/objects/coords/NCBI_HGVSCoordinate_module.hpp
 include/ncbi-tools++/objects/coords/objcoords__.hpp
-include/ncbi-tools++/objects/docsum/.cvsignore
 include/ncbi-tools++/objects/docsum/Assay.hpp
 include/ncbi-tools++/objects/docsum/Assay_.hpp
 include/ncbi-tools++/objects/docsum/Assembly.hpp
@@ -933,8 +942,6 @@ 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/.cvsignore.extra
 include/ncbi-tools++/objects/entrez2/E2Reply.hpp
 include/ncbi-tools++/objects/entrez2/E2Reply_.hpp
 include/ncbi-tools++/objects/entrez2/E2Request.hpp
@@ -1013,7 +1020,6 @@ 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/Entrezgene.hpp
 include/ncbi-tools++/objects/entrezgene/Entrezgene_.hpp
 include/ncbi-tools++/objects/entrezgene/Entrezgene_Set.hpp
@@ -1032,7 +1038,6 @@ 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/FeatDef.hpp
 include/ncbi-tools++/objects/featdef/FeatDefGroupSet.hpp
 include/ncbi-tools++/objects/featdef/FeatDefGroupSet_.hpp
@@ -1047,7 +1052,6 @@ 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/AbstractProjectItem.hpp
 include/ncbi-tools++/objects/gbproj/AbstractProjectItem_.hpp
 include/ncbi-tools++/objects/gbproj/DummyObsoleteType.hpp
@@ -1078,7 +1082,6 @@ 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/GBAltSeqData.hpp
 include/ncbi-tools++/objects/gbseq/GBAltSeqData_.hpp
 include/ncbi-tools++/objects/gbseq/GBAltSeqItem.hpp
@@ -1117,7 +1120,6 @@ 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/Date.hpp
 include/ncbi-tools++/objects/general/Date_.hpp
 include/ncbi-tools++/objects/general/Date_std.hpp
@@ -1141,7 +1143,6 @@ 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/GBL_Data.hpp
 include/ncbi-tools++/objects/genesbyloc/GBL_Data_.hpp
 include/ncbi-tools++/objects/genesbyloc/GBL_Gene.hpp
@@ -1150,8 +1151,6 @@ 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/.cvsignore.extra
 include/ncbi-tools++/objects/genomecoll/GCClientRequest.hpp
 include/ncbi-tools++/objects/genomecoll/GCClientRequest_.hpp
 include/ncbi-tools++/objects/genomecoll/GCClientResponse.hpp
@@ -1229,7 +1228,6 @@ 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/HG_Alignment.hpp
 include/ncbi-tools++/objects/homologene/HG_AlignmentSet.hpp
 include/ncbi-tools++/objects/homologene/HG_AlignmentSet_.hpp
@@ -1258,8 +1256,6 @@ 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/.cvsignore.extra
 include/ncbi-tools++/objects/id1/Entry_complexities.hpp
 include/ncbi-tools++/objects/id1/Entry_complexities_.hpp
 include/ncbi-tools++/objects/id1/ID1SeqEntry_info.hpp
@@ -1280,7 +1276,6 @@ 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/ID2S_Reply_Get_Chunk.hpp
 include/ncbi-tools++/objects/id2/ID2S_Reply_Get_Chunk_.hpp
 include/ncbi-tools++/objects/id2/ID2S_Reply_Get_Split_Info.hpp
@@ -1341,7 +1336,6 @@ 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/INSDAltSeqData.hpp
 include/ncbi-tools++/objects/insdseq/INSDAltSeqData_.hpp
 include/ncbi-tools++/objects/insdseq/INSDAltSeqItem.hpp
@@ -1380,7 +1374,6 @@ 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/AECRParse_action.hpp
 include/ncbi-tools++/objects/macro/AECRParse_action_.hpp
 include/ncbi-tools++/objects/macro/AECR_action.hpp
@@ -1741,14 +1734,12 @@ 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/Medlars_entry.hpp
 include/ncbi-tools++/objects/medlars/Medlars_entry_.hpp
 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/DocRef.hpp
 include/ncbi-tools++/objects/medline/DocRef_.hpp
 include/ncbi-tools++/objects/medline/Medline_entry.hpp
@@ -1765,7 +1756,6 @@ 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/Mim_allelic_variant.hpp
 include/ncbi-tools++/objects/mim/Mim_allelic_variant_.hpp
 include/ncbi-tools++/objects/mim/Mim_author.hpp
@@ -1797,8 +1787,6 @@ 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/.cvsignore.extra
 include/ncbi-tools++/objects/mla/Error_val.hpp
 include/ncbi-tools++/objects/mla/Error_val_.hpp
 include/ncbi-tools++/objects/mla/Mla_back.hpp
@@ -1815,7 +1803,6 @@ 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/Atom.hpp
 include/ncbi-tools++/objects/mmdb1/Atom_.hpp
 include/ncbi-tools++/objects/mmdb1/Atom_id.hpp
@@ -1877,7 +1864,6 @@ 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/Alternate_conformation_id.hpp
 include/ncbi-tools++/objects/mmdb2/Alternate_conformation_id_.hpp
 include/ncbi-tools++/objects/mmdb2/Alternate_conformation_ids.hpp
@@ -1924,7 +1910,6 @@ 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/Align_stats.hpp
 include/ncbi-tools++/objects/mmdb3/Align_stats_.hpp
 include/ncbi-tools++/objects/mmdb3/Atom_pntrs.hpp
@@ -2001,7 +1986,6 @@ 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/Biostruc_align.hpp
 include/ncbi-tools++/objects/ncbimime/Biostruc_align_.hpp
 include/ncbi-tools++/objects/ncbimime/Biostruc_align_seq.hpp
@@ -2022,7 +2006,6 @@ 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/NCBI_ObjPrt_module.hpp
 include/ncbi-tools++/objects/objprt/PrintForm.hpp
 include/ncbi-tools++/objects/objprt/PrintFormBlock.hpp
@@ -2045,7 +2028,6 @@ 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/MSBioseq.hpp
 include/ncbi-tools++/objects/omssa/MSBioseqSet.hpp
 include/ncbi-tools++/objects/omssa/MSBioseqSet_.hpp
@@ -2132,7 +2114,6 @@ 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/NCBI_PCAssay_module.hpp
 include/ncbi-tools++/objects/pcassay/PC_AnnotatedXRef.hpp
 include/ncbi-tools++/objects/pcassay/PC_AnnotatedXRef_.hpp
@@ -2167,7 +2148,6 @@ 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/pcsubstance/NCBI_PCSubstance_module.hpp
 include/ncbi-tools++/objects/pcsubstance/PC_AtomInt.hpp
 include/ncbi-tools++/objects/pcsubstance/PC_AtomInt_.hpp
@@ -2244,7 +2224,6 @@ 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/NCBI_Project_module.hpp
 include/ncbi-tools++/objects/proj/Projdesc.hpp
 include/ncbi-tools++/objects/proj/Projdesc_.hpp
@@ -2257,7 +2236,6 @@ 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/NCBI_Pub_module.hpp
 include/ncbi-tools++/objects/pub/Pub.hpp
 include/ncbi-tools++/objects/pub/Pub_.hpp
@@ -2267,15 +2245,12 @@ 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/NCBI_PubMed_module.hpp
 include/ncbi-tools++/objects/pubmed/Pubmed_entry.hpp
 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/.cvsignore.extra
 include/ncbi-tools++/objects/remap/NCBI_Remap_module.hpp
 include/ncbi-tools++/objects/remap/RMReply.hpp
 include/ncbi-tools++/objects/remap/RMReply_.hpp
@@ -2296,7 +2271,6 @@ 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/BlockProperty.hpp
 include/ncbi-tools++/objects/scoremat/BlockProperty_.hpp
 include/ncbi-tools++/objects/scoremat/CoreBlock.hpp
@@ -2323,7 +2297,6 @@ 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/Align_def.hpp
 include/ncbi-tools++/objects/seq/Align_def_.hpp
 include/ncbi-tools++/objects/seq/Annot_descr.hpp
@@ -2422,9 +2395,9 @@ include/ncbi-tools++/objects/seq/seq_loc_reverse_complementer.hpp
 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/Dense_diag.hpp
 include/ncbi-tools++/objects/seqalign/Dense_diag_.hpp
 include/ncbi-tools++/objects/seqalign/Dense_seg.hpp
@@ -2465,7 +2438,6 @@ 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/EMBL_General_module.hpp
 include/ncbi-tools++/objects/seqblock/EMBL_block.hpp
 include/ncbi-tools++/objects/seqblock/EMBL_block_.hpp
@@ -2494,7 +2466,6 @@ 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/NCBI_SeqCode_module.hpp
 include/ncbi-tools++/objects/seqcode/Seq_code_set.hpp
 include/ncbi-tools++/objects/seqcode/Seq_code_set_.hpp
@@ -2505,7 +2476,6 @@ 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/NCBI_SeqEdit_module.hpp
 include/ncbi-tools++/objects/seqedit/SeqEdit_Cmd.hpp
 include/ncbi-tools++/objects/seqedit/SeqEdit_Cmd_.hpp
@@ -2554,7 +2524,6 @@ 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/BinomialOrgName.hpp
 include/ncbi-tools++/objects/seqfeat/BinomialOrgName_.hpp
 include/ncbi-tools++/objects/seqfeat/BioSource.hpp
@@ -2675,7 +2644,6 @@ 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/Giimport_id.hpp
 include/ncbi-tools++/objects/seqloc/Giimport_id_.hpp
 include/ncbi-tools++/objects/seqloc/NCBI_Seqloc_module.hpp
@@ -2711,7 +2679,6 @@ 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/Byte_graph.hpp
 include/ncbi-tools++/objects/seqres/Byte_graph_.hpp
 include/ncbi-tools++/objects/seqres/Int_graph.hpp
@@ -2722,7 +2689,6 @@ 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/Bioseq_set.hpp
 include/ncbi-tools++/objects/seqset/Bioseq_set_.hpp
 include/ncbi-tools++/objects/seqset/NCBI_Seqset_module.hpp
@@ -2732,7 +2698,6 @@ 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/ID2S_Bioseq_Ids.hpp
 include/ncbi-tools++/objects/seqsplit/ID2S_Bioseq_Ids_.hpp
 include/ncbi-tools++/objects/seqsplit/ID2S_Bioseq_Info.hpp
@@ -2789,7 +2754,6 @@ 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/BVector_data.hpp
 include/ncbi-tools++/objects/seqtable/BVector_data_.hpp
 include/ncbi-tools++/objects/seqtable/CommonBytes_table.hpp
@@ -2816,7 +2780,6 @@ 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/NCBI_SeqTest_module.hpp
 include/ncbi-tools++/objects/seqtest/SeqTestResults.hpp
 include/ncbi-tools++/objects/seqtest/SeqTestResults_.hpp
@@ -2825,7 +2788,6 @@ 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/Contact_info.hpp
 include/ncbi-tools++/objects/submit/Contact_info_.hpp
 include/ncbi-tools++/objects/submit/NCBI_Submit_module.hpp
@@ -2835,7 +2797,6 @@ 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/NCBI_Taxon1_module.hpp
 include/ncbi-tools++/objects/taxon1/Taxon1_data.hpp
 include/ncbi-tools++/objects/taxon1/Taxon1_data_.hpp
@@ -2853,7 +2814,6 @@ include/ncbi-tools++/objects/taxon1/Taxon2_data.hpp
 include/ncbi-tools++/objects/taxon1/Taxon2_data_.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/NCBI_Taxon3_module.hpp
 include/ncbi-tools++/objects/taxon3/SequenceOfInt.hpp
 include/ncbi-tools++/objects/taxon3/SequenceOfInt_.hpp
@@ -2877,14 +2837,12 @@ 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/NCBI_TSeq_module.hpp
 include/ncbi-tools++/objects/tinyseq/TSeq.hpp
 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/NCBI_TrackManager_module.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_ACL_AccessLevel.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_ACL_AccessLevel_.hpp
@@ -2974,6 +2932,10 @@ include/ncbi-tools++/objects/trackmgr/TMgr_RetrieveTracksetReply.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_RetrieveTracksetReply_.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_RetrieveTracksetReque.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_RetrieveTracksetReque_.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_SeqTrackIdReply.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_SeqTrackIdReply_.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_SeqTrackIdRequest.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_SeqTrackIdRequest_.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_Status.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_Status_.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_SupportedAssembliesRe.hpp
@@ -3012,6 +2974,7 @@ include/ncbi-tools++/objects/trackmgr/createusertrack_client.hpp
 include/ncbi-tools++/objects/trackmgr/displaytrack_client.hpp
 include/ncbi-tools++/objects/trackmgr/gridrpcclient.hpp
 include/ncbi-tools++/objects/trackmgr/item_resolver_client.hpp
+include/ncbi-tools++/objects/trackmgr/primary_snp.hpp
 include/ncbi-tools++/objects/trackmgr/removeusertrack_client.hpp
 include/ncbi-tools++/objects/trackmgr/supported_assemblies_client.hpp
 include/ncbi-tools++/objects/trackmgr/switch_context_client.hpp
@@ -3021,14 +2984,12 @@ 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/NCBI_ValErrors_module.hpp
 include/ncbi-tools++/objects/valerr/ValidErrItem.hpp
 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/Comment_rule.hpp
 include/ncbi-tools++/objects/valid/Comment_rule_.hpp
 include/ncbi-tools++/objects/valid/Comment_set.hpp
@@ -3047,7 +3008,6 @@ 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/NCBI_VariationPackage_module.hpp
 include/ncbi-tools++/objects/variation/VariantPlacement.hpp
 include/ncbi-tools++/objects/variation/VariantPlacement_.hpp
@@ -3058,7 +3018,6 @@ 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/varrep/.cvsignore
 include/ncbi-tools++/objects/varrep/AaInterval.hpp
 include/ncbi-tools++/objects/varrep/AaInterval_.hpp
 include/ncbi-tools++/objects/varrep/AaLocation.hpp
@@ -3237,8 +3196,18 @@ include/ncbi-tools++/objmgr/split/split_exceptions.hpp
 include/ncbi-tools++/objmgr/table_field.hpp
 include/ncbi-tools++/objmgr/tse_handle.hpp
 include/ncbi-tools++/objmgr/unsupp_editsaver.hpp
+include/ncbi-tools++/objmgr/util/autodef.hpp
+include/ncbi-tools++/objmgr/util/autodef_available_modifier.hpp
+include/ncbi-tools++/objmgr/util/autodef_feature_clause.hpp
+include/ncbi-tools++/objmgr/util/autodef_feature_clause_base.hpp
+include/ncbi-tools++/objmgr/util/autodef_mod_combo.hpp
+include/ncbi-tools++/objmgr/util/autodef_options.hpp
+include/ncbi-tools++/objmgr/util/autodef_source_desc.hpp
+include/ncbi-tools++/objmgr/util/autodef_source_group.hpp
 include/ncbi-tools++/objmgr/util/create_defline.hpp
 include/ncbi-tools++/objmgr/util/feature.hpp
+include/ncbi-tools++/objmgr/util/feature_edit.hpp
+include/ncbi-tools++/objmgr/util/indexer.hpp
 include/ncbi-tools++/objmgr/util/obj_sniff.hpp
 include/ncbi-tools++/objmgr/util/objutil.hpp
 include/ncbi-tools++/objmgr/util/seq_align_util.hpp
@@ -3290,6 +3259,7 @@ include/ncbi-tools++/objtools/blast/blastdb_format/blastdb_dataextract.hpp
 include/ncbi-tools++/objtools/blast/blastdb_format/blastdb_formatter.hpp
 include/ncbi-tools++/objtools/blast/blastdb_format/blastdb_seqid.hpp
 include/ncbi-tools++/objtools/blast/blastdb_format/invalid_data_exception.hpp
+include/ncbi-tools++/objtools/blast/blastdb_format/seq_formatter.hpp
 include/ncbi-tools++/objtools/blast/blastdb_format/seq_writer.hpp
 include/ncbi-tools++/objtools/blast/gene_info_reader/file_utils.hpp
 include/ncbi-tools++/objtools/blast/gene_info_reader/gene_info.hpp
@@ -3372,19 +3342,16 @@ include/ncbi-tools++/objtools/data_loaders/genbank/writer_interface.hpp
 include/ncbi-tools++/objtools/data_loaders/loaders.hpp
 include/ncbi-tools++/objtools/edit/apply_object.hpp
 include/ncbi-tools++/objtools/edit/autodef.hpp
-include/ncbi-tools++/objtools/edit/autodef_available_modifier.hpp
-include/ncbi-tools++/objtools/edit/autodef_feature_clause.hpp
-include/ncbi-tools++/objtools/edit/autodef_feature_clause_base.hpp
-include/ncbi-tools++/objtools/edit/autodef_mod_combo.hpp
 include/ncbi-tools++/objtools/edit/autodef_options.hpp
 include/ncbi-tools++/objtools/edit/autodef_source_desc.hpp
-include/ncbi-tools++/objtools/edit/autodef_source_group.hpp
+include/ncbi-tools++/objtools/edit/autodef_with_tax.hpp
 include/ncbi-tools++/objtools/edit/capitalization_string.hpp
 include/ncbi-tools++/objtools/edit/cds_fix.hpp
 include/ncbi-tools++/objtools/edit/dblink_field.hpp
 include/ncbi-tools++/objtools/edit/edit_exception.hpp
 include/ncbi-tools++/objtools/edit/feattable_edit.hpp
 include/ncbi-tools++/objtools/edit/field_handler.hpp
+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
@@ -3420,9 +3387,6 @@ include/ncbi-tools++/objtools/format/gather_iter.hpp
 include/ncbi-tools++/objtools/format/gbseq_formatter.hpp
 include/ncbi-tools++/objtools/format/genbank_formatter.hpp
 include/ncbi-tools++/objtools/format/genbank_gather.hpp
-include/ncbi-tools++/objtools/format/gff3_formatter.hpp
-include/ncbi-tools++/objtools/format/gff_formatter.hpp
-include/ncbi-tools++/objtools/format/gff_gather.hpp
 include/ncbi-tools++/objtools/format/item_formatter.hpp
 include/ncbi-tools++/objtools/format/item_ostream.hpp
 include/ncbi-tools++/objtools/format/items/accession_item.hpp
@@ -3470,6 +3434,7 @@ include/ncbi-tools++/objtools/readers/cigar.hpp
 include/ncbi-tools++/objtools/readers/error_container.hpp
 include/ncbi-tools++/objtools/readers/fasta.hpp
 include/ncbi-tools++/objtools/readers/fasta_exception.hpp
+include/ncbi-tools++/objtools/readers/fasta_reader_utils.hpp
 include/ncbi-tools++/objtools/readers/featuredump.hpp
 include/ncbi-tools++/objtools/readers/format_guess_ex.hpp
 include/ncbi-tools++/objtools/readers/getfeature.hpp
@@ -3495,6 +3460,7 @@ include/ncbi-tools++/objtools/readers/readfeat.hpp
 include/ncbi-tools++/objtools/readers/rm_reader.hpp
 include/ncbi-tools++/objtools/readers/source_mod_parser.hpp
 include/ncbi-tools++/objtools/readers/source_mod_parser_wrapper.hpp
+include/ncbi-tools++/objtools/readers/struct_cmt_reader.hpp
 include/ncbi-tools++/objtools/readers/table_filter.hpp
 include/ncbi-tools++/objtools/readers/track_data.hpp
 include/ncbi-tools++/objtools/readers/ucscregion_reader.hpp
@@ -3624,6 +3590,9 @@ include/ncbi-tools++/util/bitset/bmfwd.h
 include/ncbi-tools++/util/bitset/bmgamma.h
 include/ncbi-tools++/util/bitset/bmrandom.h
 include/ncbi-tools++/util/bitset/bmserial.h
+include/ncbi-tools++/util/bitset/bmsparsevec.h
+include/ncbi-tools++/util/bitset/bmsparsevec_algo.h
+include/ncbi-tools++/util/bitset/bmsparsevec_serial.h
 include/ncbi-tools++/util/bitset/bmsse2.h
 include/ncbi-tools++/util/bitset/bmsse4.h
 include/ncbi-tools++/util/bitset/bmsse_util.h
@@ -3709,6 +3678,14 @@ include/ncbi-tools++/util/request_control.hpp
 include/ncbi-tools++/util/resize_iter.hpp
 include/ncbi-tools++/util/resource_pool.hpp
 include/ncbi-tools++/util/retry_ctx.hpp
+include/ncbi-tools++/util/row_reader.hpp
+include/ncbi-tools++/util/row_reader.inl
+include/ncbi-tools++/util/row_reader_base.hpp
+include/ncbi-tools++/util/row_reader_char_delimited.hpp
+include/ncbi-tools++/util/row_reader_excel_csv.hpp
+include/ncbi-tools++/util/row_reader_iana_csv.hpp
+include/ncbi-tools++/util/row_reader_iana_tsv.hpp
+include/ncbi-tools++/util/row_reader_ncbi_tsv.hpp
 include/ncbi-tools++/util/scheduler.hpp
 include/ncbi-tools++/util/sequtil/sequtil.hpp
 include/ncbi-tools++/util/sequtil/sequtil_convert.hpp
@@ -3748,258 +3725,264 @@ include/ncbi-tools++/util/xregexp/arg_regexp.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
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