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CVS commit: pkgsrc/biology/ncbi-blast+
Module Name: pkgsrc
Committed By: bacon
Date: Sun May 28 22:48:27 UTC 2023
Modified Files:
pkgsrc/biology/ncbi-blast+: Makefile PLIST buildlink3.mk distinfo
pkgsrc/biology/ncbi-blast+/patches:
patch-src_build-system_cmake_cmake-cfg-xcode.sh
patch-src_build-system_configure
Added Files:
pkgsrc/biology/ncbi-blast+/patches:
patch-src_util_checksum_cityhash_city.cc
patch-src_util_checksum_farmhash_farmhash.cc
Log Message:
biology/ncbi-blast+: Update to 2.14.0
Several minor bug fixes, a few other enhancements
Also set only for 64-bit platforms (required for most bioinformatics)
Changes: https://www.ncbi.nlm.nih.gov/sites/books/NBK131777/
To generate a diff of this commit:
cvs rdiff -u -r1.34 -r1.35 pkgsrc/biology/ncbi-blast+/Makefile
cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/ncbi-blast+/PLIST
cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/ncbi-blast+/buildlink3.mk
cvs rdiff -u -r1.7 -r1.8 pkgsrc/biology/ncbi-blast+/distinfo
cvs rdiff -u -r1.2 -r1.3 \
pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh
cvs rdiff -u -r1.3 -r1.4 \
pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure
cvs rdiff -u -r0 -r1.1 \
pkgsrc/biology/ncbi-blast+/patches/patch-src_util_checksum_cityhash_city.cc \
pkgsrc/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.cc
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
Modified files:
Index: pkgsrc/biology/ncbi-blast+/Makefile
diff -u pkgsrc/biology/ncbi-blast+/Makefile:1.34 pkgsrc/biology/ncbi-blast+/Makefile:1.35
--- pkgsrc/biology/ncbi-blast+/Makefile:1.34 Wed Apr 19 08:09:12 2023
+++ pkgsrc/biology/ncbi-blast+/Makefile Sun May 28 22:48:27 2023
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.34 2023/04/19 08:09:12 adam Exp $
+# $NetBSD: Makefile,v 1.35 2023/05/28 22:48:27 bacon Exp $
-DISTNAME= ncbi-blast-2.13.0+-src
+DISTNAME= ncbi-blast-2.14.0+-src
PKGNAME= ${DISTNAME:S/+-src//:S/blast/blast+/}
-PKGREVISION= 6
CATEGORIES= biology
MASTER_SITES= https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \
https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PKGVERSION_NOREV}/
@@ -12,6 +11,9 @@ HOMEPAGE= http://blast.ncbi.nlm.nih.gov/
COMMENT= NCBI implementation of Basic Local Alignment Search Tool
LICENSE= public-domain
+# Nobody does bioinformatics on 32-bit processors anymore
+ONLY_FOR_PLATFORM= ${LP64PLATFORMS}
+
# Fix "undefined _ThreadRuneLocale" error on FreeBSD 10.0
# Fix "unknown options" in configure
SUBST_CLASSES+= configure
@@ -59,7 +61,9 @@ CONFIGURE_ARGS+= --without-openmp
BUILDLINK_TRANSFORM+= rm:-Werror=char-subscripts
post-install:
- ${RM} ${DESTDIR}${PREFIX}/include/ncbi-tools++/*/*/.cvsignore.extra
+ ${FIND} ${DESTDIR}${PREFIX} -name '\.cvs*' -exec rm -rf '{}' \;
+ ${FIND} ${DESTDIR}${PREFIX} -name '\.subversion*' -exec rm -rf '{}' \;
+ ${FIND} ${DESTDIR}${PREFIX} -name '\.git*' -exec rm -rf '{}' \;
.if ${OPSYS} != Darwin
${STRIP} ${DESTDIR}${PREFIX}/lib/ncbi-tools++/*.so
.endif
@@ -67,6 +71,7 @@ post-install:
.include "../../devel/zlib/buildlink3.mk"
.include "../../archivers/lzo/buildlink3.mk"
.include "../../archivers/bzip2/buildlink3.mk"
+.include "../../archivers/zstd/buildlink3.mk"
.include "../../devel/pcre/buildlink3.mk"
.include "../../databases/lmdb/buildlink3.mk"
.include "../../security/gnutls/buildlink3.mk"
Index: pkgsrc/biology/ncbi-blast+/PLIST
diff -u pkgsrc/biology/ncbi-blast+/PLIST:1.4 pkgsrc/biology/ncbi-blast+/PLIST:1.5
--- pkgsrc/biology/ncbi-blast+/PLIST:1.4 Sun Apr 10 20:54:51 2022
+++ pkgsrc/biology/ncbi-blast+/PLIST Sun May 28 22:48:27 2023
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.4 2022/04/10 20:54:51 bacon Exp $
+@comment $NetBSD: PLIST,v 1.5 2023/05/28 22:48:27 bacon Exp $
bin/blast_formatter
bin/blast_report
bin/blastdb_aliastool
@@ -21,6 +21,7 @@ bin/get_species_taxids.sh
bin/legacy_blast.pl
bin/lmdbxx_sample
bin/makeblastdb
+bin/makeclusterdb
bin/makembindex
bin/makeprofiledb
bin/project_tree_builder
@@ -288,6 +289,7 @@ include/ncbi-tools++/common/ncbi_pch_imp
include/ncbi-tools++/common/ncbi_revision.h
include/ncbi-tools++/common/ncbi_revision.h.in
include/ncbi-tools++/common/ncbi_sanitizers.h
+include/ncbi-tools++/common/ncbi_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
@@ -606,14 +608,10 @@ 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
include/ncbi-tools++/objects/biblio/ArticleId.hpp
@@ -676,8 +674,6 @@ include/ncbi-tools++/objects/biblio/Titl
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
include/ncbi-tools++/objects/biotree/DistanceMatrix.hpp
@@ -696,8 +692,6 @@ include/ncbi-tools++/objects/biotree/Nod
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
include/ncbi-tools++/objects/blast/Blas_get_searc_resul_reque.hpp
@@ -827,8 +821,6 @@ include/ncbi-tools++/objects/blast/blast
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
@@ -844,8 +836,6 @@ include/ncbi-tools++/objects/blastdb/Bla
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
include/ncbi-tools++/objects/blastxml/Hit.hpp
@@ -860,8 +850,6 @@ include/ncbi-tools++/objects/blastxml/Pa
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
include/ncbi-tools++/objects/blastxml2/BlastXML2.hpp
@@ -892,8 +880,6 @@ include/ncbi-tools++/objects/blastxml2/S
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
include/ncbi-tools++/objects/cdd/Align_annot.hpp
@@ -962,8 +948,6 @@ include/ncbi-tools++/objects/cdd/Update_
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
include/ncbi-tools++/objects/cn3d/Cn3d_backbone_label_style.hpp
@@ -1006,8 +990,6 @@ include/ncbi-tools++/objects/cn3d/Cn3d_v
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
include/ncbi-tools++/objects/coords/HGVS_Coordinate_Set.hpp
@@ -1018,8 +1000,6 @@ include/ncbi-tools++/objects/dbsnp/prima
include/ncbi-tools++/objects/dbsnp/primary_track/dbsnp.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
include/ncbi-tools++/objects/docsum/Assembly.hpp
@@ -1046,8 +1026,6 @@ include/ncbi-tools++/objects/docsum/Rs_.
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
include/ncbi-tools++/objects/entrez2/E2Request.hpp
@@ -1126,8 +1104,6 @@ include/ncbi-tools++/objects/entrez2/NCB
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
include/ncbi-tools++/objects/entrezgene/Entrezgene_Set.hpp
@@ -1146,8 +1122,6 @@ include/ncbi-tools++/objects/entrezgene/
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
include/ncbi-tools++/objects/featdef/FeatDefGroupSet_.hpp
@@ -1162,8 +1136,6 @@ include/ncbi-tools++/objects/featdef/Fea
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
include/ncbi-tools++/objects/gbproj/DummyObsoleteType.hpp
@@ -1194,8 +1166,6 @@ include/ncbi-tools++/objects/gbproj/View
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
include/ncbi-tools++/objects/gbseq/GBAltSeqItem.hpp
@@ -1234,8 +1204,6 @@ include/ncbi-tools++/objects/gbseq/GBXre
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
include/ncbi-tools++/objects/general/Date_std.hpp
@@ -1259,8 +1227,6 @@ include/ncbi-tools++/objects/general/gen
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
include/ncbi-tools++/objects/genesbyloc/GBL_Gene.hpp
@@ -1269,8 +1235,6 @@ include/ncbi-tools++/objects/genesbyloc/
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
include/ncbi-tools++/objects/genomecoll/GCClientResponse.hpp
@@ -1342,8 +1306,6 @@ include/ncbi-tools++/objects/genomecoll/
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
include/ncbi-tools++/objects/homologene/HG_AlignmentSet_.hpp
@@ -1372,8 +1334,6 @@ include/ncbi-tools++/objects/homologene/
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
include/ncbi-tools++/objects/id1/ID1SeqEntry_info.hpp
@@ -1394,8 +1354,6 @@ include/ncbi-tools++/objects/id1/NCBI_ID
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
include/ncbi-tools++/objects/id2/ID2S_Reply_Get_Split_Info.hpp
@@ -1456,8 +1414,6 @@ include/ncbi-tools++/objects/id2/id2_cli
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
include/ncbi-tools++/objects/insdseq/INSDAltSeqItem.hpp
@@ -1496,8 +1452,6 @@ include/ncbi-tools++/objects/insdseq/INS
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
include/ncbi-tools++/objects/macro/AECR_action.hpp
@@ -1858,16 +1812,12 @@ include/ncbi-tools++/objects/macro/Word_
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
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
include/ncbi-tools++/objects/medline/Medline_entry.hpp
@@ -1884,8 +1834,6 @@ include/ncbi-tools++/objects/medline/Med
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
include/ncbi-tools++/objects/mim/Mim_author.hpp
@@ -1917,8 +1865,6 @@ include/ncbi-tools++/objects/mim/mim__.h
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
include/ncbi-tools++/objects/mla/Mla_back.hpp
@@ -1935,8 +1881,6 @@ include/ncbi-tools++/objects/mla/Title_t
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
include/ncbi-tools++/objects/mmdb1/Atom_id.hpp
@@ -1998,8 +1942,6 @@ include/ncbi-tools++/objects/mmdb1/Resid
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
include/ncbi-tools++/objects/mmdb2/Alternate_conformation_ids.hpp
@@ -2046,8 +1988,6 @@ include/ncbi-tools++/objects/mmdb2/T_mes
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
include/ncbi-tools++/objects/mmdb3/Atom_pntrs.hpp
@@ -2124,8 +2064,6 @@ include/ncbi-tools++/objects/mmdb3/Trans
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
include/ncbi-tools++/objects/ncbimime/Biostruc_align_seq.hpp
@@ -2146,8 +2084,6 @@ include/ncbi-tools++/objects/ncbimime/NC
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
include/ncbi-tools++/objects/objprt/PrintFormBlock.hpp
@@ -2170,8 +2106,6 @@ include/ncbi-tools++/objects/objprt/Temp
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
include/ncbi-tools++/objects/omssa/MSBioseqSet_.hpp
@@ -2258,8 +2192,6 @@ include/ncbi-tools++/objects/omssa/NameV
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
include/ncbi-tools++/objects/pcassay/PC_AnnotatedXRef_.hpp
@@ -2294,8 +2226,6 @@ include/ncbi-tools++/objects/pcassay/PC_
include/ncbi-tools++/objects/pcassay/PC_ResultType.hpp
include/ncbi-tools++/objects/pcassay/PC_ResultType_.hpp
include/ncbi-tools++/objects/pcassay/pcassay__.hpp
-include/ncbi-tools++/objects/pcassay2/.cvsignore
-include/ncbi-tools++/objects/pcassay2/.gitignore
include/ncbi-tools++/objects/pcassay2/NCBI_PCAssay2_module.hpp
include/ncbi-tools++/objects/pcassay2/PC_AnnotatedXRef.hpp
include/ncbi-tools++/objects/pcassay2/PC_AnnotatedXRef_.hpp
@@ -2324,8 +2254,6 @@ include/ncbi-tools++/objects/pcassay2/PC
include/ncbi-tools++/objects/pcassay2/PC_ResultType.hpp
include/ncbi-tools++/objects/pcassay2/PC_ResultType_.hpp
include/ncbi-tools++/objects/pcassay2/pcassay2__.hpp
-include/ncbi-tools++/objects/pcsubstance/.cvsignore
-include/ncbi-tools++/objects/pcsubstance/.gitignore
include/ncbi-tools++/objects/pcsubstance/NCBI_PCSubstance_module.hpp
include/ncbi-tools++/objects/pcsubstance/PC_AtomInt.hpp
include/ncbi-tools++/objects/pcsubstance/PC_AtomInt_.hpp
@@ -2406,8 +2334,6 @@ include/ncbi-tools++/objects/pcsubstance
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
include/ncbi-tools++/objects/proj/Projdesc_.hpp
@@ -2420,8 +2346,6 @@ include/ncbi-tools++/objects/proj/Projec
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
include/ncbi-tools++/objects/pub/Pub_.hpp
@@ -2431,16 +2355,12 @@ include/ncbi-tools++/objects/pub/Pub_set
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
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
include/ncbi-tools++/objects/remap/RMReply_.hpp
@@ -2461,8 +2381,6 @@ include/ncbi-tools++/objects/remap/Remap
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
include/ncbi-tools++/objects/scoremat/CoreBlock.hpp
@@ -2489,8 +2407,6 @@ include/ncbi-tools++/objects/scoremat/Si
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
include/ncbi-tools++/objects/seq/Annot_descr.hpp
@@ -2591,8 +2507,6 @@ include/ncbi-tools++/objects/seq/seqloci
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
include/ncbi-tools++/objects/seqalign/Dense_seg.hpp
@@ -2633,8 +2547,6 @@ include/ncbi-tools++/objects/seqalign/St
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
include/ncbi-tools++/objects/seqblock/EMBL_block_.hpp
@@ -2663,8 +2575,6 @@ include/ncbi-tools++/objects/seqblock/SP
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
include/ncbi-tools++/objects/seqcode/Seq_code_set_.hpp
@@ -2675,8 +2585,6 @@ include/ncbi-tools++/objects/seqcode/Seq
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
include/ncbi-tools++/objects/seqedit/SeqEdit_Cmd_.hpp
@@ -2725,8 +2633,6 @@ include/ncbi-tools++/objects/seqedit/Seq
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
include/ncbi-tools++/objects/seqfeat/BioSource.hpp
@@ -2847,8 +2753,6 @@ include/ncbi-tools++/objects/seqfeat/Var
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
include/ncbi-tools++/objects/seqloc/NCBI_Seqloc_module.hpp
@@ -2884,8 +2788,6 @@ include/ncbi-tools++/objects/seqloc/Text
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
include/ncbi-tools++/objects/seqres/Int_graph.hpp
@@ -2896,8 +2798,6 @@ include/ncbi-tools++/objects/seqres/Real
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
include/ncbi-tools++/objects/seqset/NCBI_Seqset_module.hpp
@@ -2907,8 +2807,6 @@ include/ncbi-tools++/objects/seqset/gb_r
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
include/ncbi-tools++/objects/seqsplit/ID2S_Bioseq_Info.hpp
@@ -2965,8 +2863,6 @@ include/ncbi-tools++/objects/seqsplit/ID
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
include/ncbi-tools++/objects/seqtable/CommonBytes_table.hpp
@@ -2993,8 +2889,6 @@ include/ncbi-tools++/objects/seqtable/Se
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
include/ncbi-tools++/objects/seqtest/SeqTestResults_.hpp
@@ -3003,8 +2897,6 @@ include/ncbi-tools++/objects/seqtest/Seq
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
include/ncbi-tools++/objects/submit/NCBI_Submit_module.hpp
@@ -3014,8 +2906,6 @@ include/ncbi-tools++/objects/submit/Subm
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
include/ncbi-tools++/objects/taxon1/Taxon1_data_.hpp
@@ -3034,8 +2924,6 @@ include/ncbi-tools++/objects/taxon1/Taxo
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
include/ncbi-tools++/objects/taxon3/SequenceOfInt_.hpp
@@ -3059,16 +2947,12 @@ include/ncbi-tools++/objects/taxon3/cach
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
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
include/ncbi-tools++/objects/trackmgr/TMgr_ACL_AccessLevel_.hpp
@@ -3227,16 +3111,12 @@ include/ncbi-tools++/objects/trackmgr/tr
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
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
include/ncbi-tools++/objects/valid/Comment_set.hpp
@@ -3255,8 +3135,6 @@ include/ncbi-tools++/objects/valid/Phras
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
include/ncbi-tools++/objects/variation/VariantPlacement_.hpp
@@ -3267,8 +3145,6 @@ include/ncbi-tools++/objects/variation/V
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
include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/NCBI_search_by_rsid_module.hpp
@@ -3277,8 +3153,6 @@ include/ncbi-tools++/objects/variation_l
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
include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipSection.hpp
@@ -3291,8 +3165,6 @@ include/ncbi-tools++/objects/variation_l
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
include/ncbi-tools++/objects/varrep/AaLocation.hpp
@@ -3574,6 +3446,7 @@ include/ncbi-tools++/objtools/cleanup/cl
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
@@ -3637,6 +3510,7 @@ include/ncbi-tools++/objtools/edit/cds_f
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
@@ -3645,13 +3519,20 @@ include/ncbi-tools++/objtools/edit/gap_t
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
@@ -3673,8 +3554,704 @@ include/ncbi-tools++/objtools/eutils/api
include/ncbi-tools++/objtools/eutils/api/espell.hpp
include/ncbi-tools++/objtools/eutils/api/esummary.hpp
include/ncbi-tools++/objtools/eutils/api/eutils.hpp
-include/ncbi-tools++/objtools/eutils/egquery/.cvsignore
-include/ncbi-tools++/objtools/eutils/egquery/.gitignore
+include/ncbi-tools++/objtools/eutils/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
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+include/ncbi-tools++/objtools/eutils/efetch/PubMedPubDate.hpp
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+include/ncbi-tools++/objtools/eutils/efetch/PublisherName.hpp
+include/ncbi-tools++/objtools/eutils/efetch/PublisherName_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Publisher_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/PubmedArticle.hpp
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+include/ncbi-tools++/objtools/eutils/efetch/PubmedArticle_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/PubmedBookArticle.hpp
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+include/ncbi-tools++/objtools/eutils/efetch/PubmedBookArticle_.hpp
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+include/ncbi-tools++/objtools/eutils/efetch/RefSource.hpp
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+include/ncbi-tools++/objtools/eutils/efetch/ReportNumber.hpp
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+include/ncbi-tools++/objtools/eutils/efetch/SectionTitle.hpp
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+include/ncbi-tools++/objtools/eutils/efetch/Sinh_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/SpaceFlightMission.hpp
+include/ncbi-tools++/objtools/eutils/efetch/SpaceFlightMission_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/StartPage.hpp
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+include/ncbi-tools++/objtools/eutils/efetch/Subset.hpp
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+include/ncbi-tools++/objtools/eutils/efetch/SupplMeshList.hpp
+include/ncbi-tools++/objtools/eutils/efetch/SupplMeshList_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/SupplMeshName.hpp
+include/ncbi-tools++/objtools/eutils/efetch/SupplMeshName_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/TableCellExpression.hpp
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+include/ncbi-tools++/objtools/eutils/efetch/TableRowExpression.hpp
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+include/ncbi-tools++/objtools/eutils/efetch/Tanh.hpp
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+include/ncbi-tools++/objtools/eutils/efetch/Tendsto.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Tendsto_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Text.hpp
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+include/ncbi-tools++/objtools/eutils/efetch/Times.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Times_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Title.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Title_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Token_content.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Token_content_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Transpose.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Transpose_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/True.hpp
+include/ncbi-tools++/objtools/eutils/efetch/True_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/U.hpp
+include/ncbi-tools++/objtools/eutils/efetch/URL.hpp
+include/ncbi-tools++/objtools/eutils/efetch/URL_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/U_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Union.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Union_.hpp
+include/ncbi-tools++/objtools/eutils/efetch/Uplimit.hpp
+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/EGQueryResult.hpp
include/ncbi-tools++/objtools/eutils/egquery/EGQueryResult_.hpp
include/ncbi-tools++/objtools/eutils/egquery/Result.hpp
@@ -3683,16 +4260,12 @@ include/ncbi-tools++/objtools/eutils/egq
include/ncbi-tools++/objtools/eutils/egquery/Result_.hpp
include/ncbi-tools++/objtools/eutils/egquery/egquery__.hpp
include/ncbi-tools++/objtools/eutils/egquery/egquery_module.hpp
-include/ncbi-tools++/objtools/eutils/ehistory/.cvsignore
-include/ncbi-tools++/objtools/eutils/ehistory/.gitignore
include/ncbi-tools++/objtools/eutils/ehistory/EHistoryItem.hpp
include/ncbi-tools++/objtools/eutils/ehistory/EHistoryItem_.hpp
include/ncbi-tools++/objtools/eutils/ehistory/EHistoryResult.hpp
include/ncbi-tools++/objtools/eutils/ehistory/EHistoryResult_.hpp
include/ncbi-tools++/objtools/eutils/ehistory/ehistory__.hpp
include/ncbi-tools++/objtools/eutils/ehistory/ehistory_module.hpp
-include/ncbi-tools++/objtools/eutils/einfo/.cvsignore
-include/ncbi-tools++/objtools/eutils/einfo/.gitignore
include/ncbi-tools++/objtools/eutils/einfo/DbInfo.hpp
include/ncbi-tools++/objtools/eutils/einfo/DbInfo_.hpp
include/ncbi-tools++/objtools/eutils/einfo/DbList.hpp
@@ -3709,8 +4282,6 @@ include/ncbi-tools++/objtools/eutils/ein
include/ncbi-tools++/objtools/eutils/einfo/Link_.hpp
include/ncbi-tools++/objtools/eutils/einfo/einfo__.hpp
include/ncbi-tools++/objtools/eutils/einfo/einfo_module.hpp
-include/ncbi-tools++/objtools/eutils/elink/.cvsignore
-include/ncbi-tools++/objtools/eutils/elink/.gitignore
include/ncbi-tools++/objtools/eutils/elink/ELinkResult.hpp
include/ncbi-tools++/objtools/eutils/elink/ELinkResult_.hpp
include/ncbi-tools++/objtools/eutils/elink/FirstChars.hpp
@@ -3747,16 +4318,12 @@ include/ncbi-tools++/objtools/eutils/eli
include/ncbi-tools++/objtools/eutils/elink/Url_.hpp
include/ncbi-tools++/objtools/eutils/elink/elink__.hpp
include/ncbi-tools++/objtools/eutils/elink/elink_module.hpp
-include/ncbi-tools++/objtools/eutils/epost/.cvsignore
-include/ncbi-tools++/objtools/eutils/epost/.gitignore
include/ncbi-tools++/objtools/eutils/epost/EPostResult.hpp
include/ncbi-tools++/objtools/eutils/epost/EPostResult_.hpp
include/ncbi-tools++/objtools/eutils/epost/InvalidIdList.hpp
include/ncbi-tools++/objtools/eutils/epost/InvalidIdList_.hpp
include/ncbi-tools++/objtools/eutils/epost/epost__.hpp
include/ncbi-tools++/objtools/eutils/epost/epost_module.hpp
-include/ncbi-tools++/objtools/eutils/esearch/.cvsignore
-include/ncbi-tools++/objtools/eutils/esearch/.gitignore
include/ncbi-tools++/objtools/eutils/esearch/ESearchResult.hpp
include/ncbi-tools++/objtools/eutils/esearch/ESearchResult_.hpp
include/ncbi-tools++/objtools/eutils/esearch/ErrorList.hpp
@@ -3775,16 +4342,12 @@ include/ncbi-tools++/objtools/eutils/ese
include/ncbi-tools++/objtools/eutils/esearch/WarningList_.hpp
include/ncbi-tools++/objtools/eutils/esearch/esearch__.hpp
include/ncbi-tools++/objtools/eutils/esearch/esearch_module.hpp
-include/ncbi-tools++/objtools/eutils/espell/.cvsignore
-include/ncbi-tools++/objtools/eutils/espell/.gitignore
include/ncbi-tools++/objtools/eutils/espell/ESpellResult.hpp
include/ncbi-tools++/objtools/eutils/espell/ESpellResult_.hpp
include/ncbi-tools++/objtools/eutils/espell/SpelledQuery.hpp
include/ncbi-tools++/objtools/eutils/espell/SpelledQuery_.hpp
include/ncbi-tools++/objtools/eutils/espell/espell__.hpp
include/ncbi-tools++/objtools/eutils/espell/espell_module.hpp
-include/ncbi-tools++/objtools/eutils/esummary/.cvsignore
-include/ncbi-tools++/objtools/eutils/esummary/.gitignore
include/ncbi-tools++/objtools/eutils/esummary/DocSum.hpp
include/ncbi-tools++/objtools/eutils/esummary/DocSum_.hpp
include/ncbi-tools++/objtools/eutils/esummary/ESummaryResult.hpp
@@ -3793,8 +4356,6 @@ include/ncbi-tools++/objtools/eutils/esu
include/ncbi-tools++/objtools/eutils/esummary/Item_.hpp
include/ncbi-tools++/objtools/eutils/esummary/esummary__.hpp
include/ncbi-tools++/objtools/eutils/esummary/esummary_module.hpp
-include/ncbi-tools++/objtools/eutils/uilist/.cvsignore
-include/ncbi-tools++/objtools/eutils/uilist/.gitignore
include/ncbi-tools++/objtools/eutils/uilist/IdList.hpp
include/ncbi-tools++/objtools/eutils/uilist/IdList_.hpp
include/ncbi-tools++/objtools/eutils/uilist/uilist__.hpp
@@ -4044,9 +4605,11 @@ include/ncbi-tools++/sra/readers/ncbi_tr
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
@@ -4111,6 +4674,7 @@ include/ncbi-tools++/util/bitset/ncbi_bi
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
@@ -4134,6 +4698,7 @@ include/ncbi-tools++/util/compress/zlib.
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
@@ -4151,11 +4716,14 @@ 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
@@ -4172,6 +4740,7 @@ include/ncbi-tools++/util/math/matrix.hp
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
@@ -4290,6 +4859,8 @@ lib/ncbi-tools++/libdbsnp_tooltip_servic
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
Index: pkgsrc/biology/ncbi-blast+/buildlink3.mk
diff -u pkgsrc/biology/ncbi-blast+/buildlink3.mk:1.5 pkgsrc/biology/ncbi-blast+/buildlink3.mk:1.6
--- pkgsrc/biology/ncbi-blast+/buildlink3.mk:1.5 Tue Jun 28 11:31:01 2022
+++ pkgsrc/biology/ncbi-blast+/buildlink3.mk Sun May 28 22:48:27 2023
@@ -1,12 +1,11 @@
-# $NetBSD: buildlink3.mk,v 1.5 2022/06/28 11:31:01 wiz Exp $
+# $NetBSD: buildlink3.mk,v 1.6 2023/05/28 22:48:27 bacon Exp $
BUILDLINK_TREE+= ncbi-blast+
.if !defined(NCBI_BLAST+_BUILDLINK3_MK)
NCBI_BLAST+_BUILDLINK3_MK:=
-BUILDLINK_API_DEPENDS.ncbi-blast++= ncbi-blast+>=2.13.0
-BUILDLINK_ABI_DEPENDS.ncbi-blast+?= ncbi-blast+>=2.13.0nb2
+BUILDLINK_API_DEPENDS.ncbi-blast++= ncbi-blast+>=2.14.0
BUILDLINK_PKGSRCDIR.ncbi-blast+?= ../../biology/ncbi-blast+
.endif # NCBI_BLAST+_BUILDLINK3_MK
Index: pkgsrc/biology/ncbi-blast+/distinfo
diff -u pkgsrc/biology/ncbi-blast+/distinfo:1.7 pkgsrc/biology/ncbi-blast+/distinfo:1.8
--- pkgsrc/biology/ncbi-blast+/distinfo:1.7 Sun Apr 10 20:54:51 2022
+++ pkgsrc/biology/ncbi-blast+/distinfo Sun May 28 22:48:27 2023
@@ -1,12 +1,14 @@
-$NetBSD: distinfo,v 1.7 2022/04/10 20:54:51 bacon Exp $
+$NetBSD: distinfo,v 1.8 2023/05/28 22:48:27 bacon Exp $
-BLAKE2s (ncbi-blast-2.13.0+-src.tar.gz) = a83651c7f2824def1c86a8541cf7060ed77e6d60e8f7bd0383464088591733f3
-SHA512 (ncbi-blast-2.13.0+-src.tar.gz) = 7842ba4dac3d046a23cb182c6289d88cb1173e8570fb6334c1aa88dd2e640aacad43efe1ef7d69b8fedbf9b8093b7d601ef8999812d5735a6789ab2752e97c2b
-Size (ncbi-blast-2.13.0+-src.tar.gz) = 59995353 bytes
+BLAKE2s (ncbi-blast-2.14.0+-src.tar.gz) = fbda12e9d778e0a84df0195964b397a08fba4f067c55525556e3831ecdd7b252
+SHA512 (ncbi-blast-2.14.0+-src.tar.gz) = 30f6292cacb7c2ec0a00803c697ab0255ccee1c82a40923df0f3e4f856204db8da5be212b5ec02e0acb8000396a71f600c35e63f83eaf30e1a9639e4c95c4a83
+Size (ncbi-blast-2.14.0+-src.tar.gz) = 28200227 bytes
SHA1 (patch-compilers_xcode30__prj_configure) = b89b3be8671c6c692ba474476879ee67a76fdbe5
SHA1 (patch-src_algo_blast_core_blast__kappa.c) = 6fcad996b3a8e5b6c2400608bff9de62ebf6927f
SHA1 (patch-src_build-system_Makefile.in.top) = 71d5246867a8c985c1175c338fb0af664094ca01
-SHA1 (patch-src_build-system_cmake_cmake-cfg-xcode.sh) = 9167a5092d30da46a06b0be05199afa3b08680c6
+SHA1 (patch-src_build-system_cmake_cmake-cfg-xcode.sh) = b50a53ac7f2bd191d0d85cf490ac891f2cf20bfa
SHA1 (patch-src_build-system_configure) = 95185d53179a69a1b1cfa6870aca36dd962d2c43
SHA1 (patch-src_build-system_helpers_Makefile.run__with__lock.app) = d69b9e349646c970c3b296707f917defbe39cccd
+SHA1 (patch-src_util_checksum_cityhash_city.cc) = ff8e84d90a4fc0d9d33e17abd05ed8e9f2de12fc
+SHA1 (patch-src_util_checksum_farmhash_farmhash.cc) = 9b56d69ab7c0da328c35bba4dde04134dd80efc6
SHA1 (patch-src_util_checksum_farmhash_farmhash.h) = c3ff60de9a9020d3b706c2bff37f6f4cde4e6b6b
Index: pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh
diff -u pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh:1.2 pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh:1.3
--- pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh:1.2 Sun Apr 10 20:54:51 2022
+++ pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh Sun May 28 22:48:27 2023
@@ -1,15 +1,21 @@
-$NetBSD: patch-src_build-system_cmake_cmake-cfg-xcode.sh,v 1.2 2022/04/10 20:54:51 bacon Exp $
+$NetBSD: patch-src_build-system_cmake_cmake-cfg-xcode.sh,v 1.3 2023/05/28 22:48:27 bacon Exp $
-# Portability
+# sh portability
---- src/build-system/cmake/cmake-cfg-xcode.sh.orig 2021-06-10 11:54:05.800996703 +0000
+--- src/build-system/cmake/cmake-cfg-xcode.sh.orig 2023-05-26 12:05:14.109542442 +0000
+++ src/build-system/cmake/cmake-cfg-xcode.sh
-@@ -218,7 +218,7 @@ CMAKE_ARGS="$CMAKE_ARGS -DBUILD_SHARED_L
-
+@@ -249,12 +249,12 @@ CMAKE_ARGS="$CMAKE_ARGS -DBUILD_SHARED_L
if [ -z "$BUILD_ROOT" ]; then
- BUILD_ROOT=CMake-${CC_NAME}${CC_VERSION}
-- if [ "$BUILD_SHARED_LIBS" == "ON" ]; then
-+ if [ "$BUILD_SHARED_LIBS" = "ON" ]; then
- BUILD_ROOT="$BUILD_ROOT"-DLL
+ if [ -z "$BUILD_TYPE" ]; then
+ BUILD_ROOT=CMake-${CC_NAME}${CC_VERSION}
+- if [ "$BUILD_SHARED_LIBS" == "ON" ]; then
++ if [ "$BUILD_SHARED_LIBS" = "ON" ]; then
+ BUILD_ROOT="$BUILD_ROOT"-DLL
+ fi
+ else
+ BUILD_ROOT=CMake-${CC_NAME}${CC_VERSION}-${BUILD_TYPE}
+- if [ "$BUILD_SHARED_LIBS" == "ON" ]; then
++ if [ "$BUILD_SHARED_LIBS" = "ON" ]; then
+ BUILD_ROOT="$BUILD_ROOT"DLL
+ fi
fi
- fi
Index: pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure
diff -u pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure:1.3 pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure:1.4
--- pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure:1.3 Sun Apr 10 20:54:51 2022
+++ pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure Sun May 28 22:48:27 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-src_build-system_configure,v 1.3 2022/04/10 20:54:51 bacon Exp $
+$NetBSD: patch-src_build-system_configure,v 1.4 2023/05/28 22:48:27 bacon Exp $
# Avert missing --with-libiconv-prefix option
Added files:
Index: pkgsrc/biology/ncbi-blast+/patches/patch-src_util_checksum_cityhash_city.cc
diff -u /dev/null pkgsrc/biology/ncbi-blast+/patches/patch-src_util_checksum_cityhash_city.cc:1.1
--- /dev/null Sun May 28 22:48:27 2023
+++ pkgsrc/biology/ncbi-blast+/patches/patch-src_util_checksum_cityhash_city.cc Sun May 28 22:48:27 2023
@@ -0,0 +1,17 @@
+$NetBSD: patch-src_util_checksum_cityhash_city.cc,v 1.1 2023/05/28 22:48:27 bacon Exp $
+
+Ensure bswap_32() and bswap_64() is defined on NetBSD.
+
+--- src/util/checksum/cityhash/city.cc.orig 2018-09-28 20:34:39.000000000 +0000
++++ src/util/checksum/cityhash/city.cc
+@@ -82,10 +82,8 @@ static uint32 UNALIGNED_LOAD32(const cha
+
+ #include <sys/types.h>
+ #include <machine/bswap.h>
+-#if defined(__BSWAP_RENAME) && !defined(__bswap_32)
+ #define bswap_32(x) bswap32(x)
+ #define bswap_64(x) bswap64(x)
+-#endif
+
+ #else
+
Index: pkgsrc/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.cc
diff -u /dev/null pkgsrc/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.cc:1.1
--- /dev/null Sun May 28 22:48:27 2023
+++ pkgsrc/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.cc Sun May 28 22:48:27 2023
@@ -0,0 +1,21 @@
+$NetBSD: patch-src_util_checksum_farmhash_farmhash.cc,v 1.1 2023/05/28 22:48:27 bacon Exp $
+
+Ensure bswap_32() and bswap_64() gets defined on NetBSD.
+
+--- src/util/checksum/farmhash/farmhash.cc.orig 2018-09-26 12:38:06.000000000 +0000
++++ src/util/checksum/farmhash/farmhash.cc
+@@ -158,12 +158,12 @@
+
+ #include <sys/types.h>
+ #include <machine/bswap.h>
+-#if defined(__BSWAP_RENAME) && !defined(__bswap_32)
++#if defined(bswap_32) && defined(bswap_64)
+ #undef bswap_32
+ #undef bswap_64
++#endif
+ #define bswap_32(x) bswap32(x)
+ #define bswap_64(x) bswap64(x)
+-#endif
+
+ #elif defined(__HAIKU__)
+
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