[med-svn] [ncbi-blast+] branch upstream updated (74e6c3d -> edfc131)
Olivier Sallou
osallou at debian.org
Sun Jan 15 17:29:31 UTC 2017
This is an automated email from the git hooks/post-receive script.
osallou pushed a change to branch upstream
in repository ncbi-blast+.
from 74e6c3d Imported Upstream version 2.4.0
new edfc131 New upstream version 2.6.0
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
c++/compilers/unix/GCC.sh | 2 +-
c++/compilers/unix/ICC.sh | 2 +-
c++/compilers/vs2013/build_exec.bat | 3 +-
c++/compilers/vs2013/configure.bat | 2 +-
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c++/compilers/vs2013/dll/build/ncbi_cpp_dll.sln | 32 +-
c++/compilers/vs2013/make.bat | 12 +-
c++/compilers/vs2013/ptb.bat | 12 +-
c++/compilers/vs2013/static/build/gui/ncbi_gui.sln | 32 +-
c++/compilers/vs2013/static/build/ncbi_cpp.sln | 20 +-
c++/compilers/vs2013/user/build/ncbi_user.sln | 32 +-
.../{vs2013 => vs2015}/Makefile.WinMain.app.msvc | 0
.../{vs2013 => vs2015}/Makefile.wxWidgets.app.msvc | 0
c++/compilers/vs2015/build.sh | 264 +
c++/compilers/vs2015/build_exec.bat | 51 +
c++/compilers/vs2015/build_util.sh | 67 +
c++/compilers/vs2015/check.sh | 276 +
c++/compilers/vs2015/configure.bat | 384 +
c++/compilers/vs2015/datatool.bat | 188 +
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c++/compilers/vs2015/dll/build/all.bat | 42 +
c++/compilers/vs2015/dll/build/all_gbench.bat | 75 +
c++/compilers/vs2015/dll/build/all_gui.bat | 75 +
c++/compilers/vs2015/dll/build/all_ncbi.bat | 75 +
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c++/compilers/vs2015/static/build/all.bat | 39 +
c++/compilers/vs2015/static/build/all_gui.bat | 79 +
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c++/compilers/vs2015/static/build/gui/ncbi_gui.sln | 35 +
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c++/compilers/vs2015/third_party_install.meta.mk | 330 +
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c++/compilers/vs2015/user/build/ncbi_user.sln | 35 +
c++/compilers/xcode30_prj/configure | 34 +-
c++/compilers/xcode30_prj/ptb.sh | 12 +-
c++/configure | 2 +-
c++/include/algo/blast/api/blast_aux.hpp | 26 +-
c++/include/algo/blast/api/blast_options.hpp | 22 +-
.../algo/blast/api/blast_options_handle.hpp | 3 +-
c++/include/algo/blast/api/blast_seqinfosrc.hpp | 2 +-
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c++/include/algo/blast/api/blast_types.hpp | 3 +-
c++/include/algo/blast/api/magicblast.hpp | 115 +
c++/include/algo/blast/api/magicblast_options.hpp | 211 +
.../algo/blast/api/objmgrfree_query_data.hpp | 5 +-
c++/include/algo/blast/api/remote_blast.hpp | 2 +-
c++/include/algo/blast/api/seqinfosrc_seqdb.hpp | 2 +-
c++/include/algo/blast/api/seqinfosrc_seqvec.hpp | 2 +-
c++/include/algo/blast/api/setup_factory.hpp | 4 +-
c++/include/algo/blast/blastinput/blast_args.hpp | 162 +-
.../algo/blast/blastinput/blast_asn1_input.hpp | 119 +
.../algo/blast/blastinput/blast_fasta_input.hpp | 82 +-
c++/include/algo/blast/blastinput/blast_input.hpp | 51 +-
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.../algo/blast/blastinput/blast_scope_src.hpp | 6 +-
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c++/include/algo/blast/blastinput/kblastp_args.hpp | 75 +
.../algo/blast/blastinput/magicblast_args.hpp | 63 +
.../composition_adjustment.h | 2 +-
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c++/include/algo/blast/core/blast_engine.h | 23 +-
c++/include/algo/blast/core/blast_gapalign.h | 9 +-
c++/include/algo/blast/core/blast_hits.h | 102 +-
c++/include/algo/blast/core/blast_hspfilter.h | 12 +-
c++/include/algo/blast/core/blast_hspstream.h | 19 +-
c++/include/algo/blast/core/blast_kappa.h | 2 +-
c++/include/algo/blast/core/blast_lookup.h | 53 +-
c++/include/algo/blast/core/blast_nalookup.h | 112 +-
c++/include/algo/blast/core/blast_options.h | 30 +-
c++/include/algo/blast/core/blast_program.h | 15 +-
c++/include/algo/blast/core/blast_query_info.h | 19 +-
c++/include/algo/blast/core/blast_stat.h | 2 +-
c++/include/algo/blast/core/hspfilter_mapper.h | 101 +
c++/include/algo/blast/core/lookup_util.h | 4 +-
c++/include/algo/blast/core/lookup_wrap.h | 8 +-
c++/include/algo/blast/core/na_ungapped.h | 65 +-
c++/include/algo/blast/format/blast_format.hpp | 38 +-
c++/include/algo/blast/igblast/igblast.hpp | 7 +-
c++/include/cgi/cgi_session.hpp | 2 +-
c++/include/cgi/cgiapp.hpp | 2 +-
c++/include/cgi/cgictx.hpp | 4 +-
c++/include/cgi/error_codes.hpp | 2 +-
c++/include/cgi/ncbicgi.hpp | 2 +-
c++/include/cgi/ncbicgir.hpp | 6 +-
c++/include/cgi/user_agent.hpp | 6 +-
c++/include/common/config/ncbiconf_msvc_site.h | 35 -
c++/include/common/config/ncbiconf_universal.h | 5 +-
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c++/include/common/ncbi_build_ver.h.in | 37 +
c++/include/common/ncbi_export.h | 19 +-
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c++/include/connect/ncbi_base64.h | 8 +-
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c++/include/connect/ncbi_connector.h | 16 +-
c++/include/connect/ncbi_connutil.h | 35 +-
c++/include/connect/ncbi_core.h | 3 +-
c++/include/connect/ncbi_core_cxx.hpp | 7 +-
c++/include/connect/ncbi_gnutls.h | 8 +-
c++/include/connect/ncbi_http_connector.h | 9 +-
c++/include/connect/ncbi_http_session.hpp | 24 +-
c++/include/connect/ncbi_lbos.hpp | 283 +-
c++/include/connect/ncbi_monkey.hpp | 405 +
c++/include/connect/ncbi_server_info.h | 5 +-
c++/include/connect/ncbi_service.h | 47 +-
c++/include/connect/ncbi_socket.h | 26 +-
c++/include/connect/ncbi_types.h | 6 +-
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c++/include/connect/services/json_over_uttp.hpp | 6 +-
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c++/include/connect/services/netschedule_api.hpp | 68 +-
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c++/include/connect/services/ns_output_parser.hpp | 38 +-
c++/include/corelib/ddumpable.hpp | 2 +-
c++/include/corelib/hash_impl/_hash_map.h | 102 +-
c++/include/corelib/hash_impl/_hash_set.h | 105 +-
c++/include/corelib/impl/ncbi_atomic_defs.h | 6 +-
c++/include/corelib/impl/ncbi_dbsvcmapper.hpp | 54 +-
c++/include/corelib/ncbi_base64.h | 8 +-
c++/include/corelib/ncbi_config.hpp | 2 +-
c++/include/corelib/ncbi_cookies.hpp | 13 +-
c++/include/corelib/ncbi_param.hpp | 14 +-
c++/include/corelib/ncbi_stack.hpp | 11 +-
c++/include/corelib/ncbi_xstr.hpp | 22 +-
c++/include/corelib/ncbiapp.hpp | 11 +-
c++/include/corelib/ncbiargs.hpp | 99 +-
c++/include/corelib/ncbiatomic.h | 4 +-
c++/include/corelib/ncbictype.hpp | 15 +-
c++/include/corelib/ncbidbg.hpp | 2 +-
c++/include/corelib/ncbidiag.hpp | 51 +-
c++/include/corelib/ncbidiag.inl | 5 +-
c++/include/corelib/ncbierror.hpp | 79 +-
c++/include/corelib/ncbifile.hpp | 122 +-
c++/include/corelib/ncbimisc.hpp | 119 +-
c++/include/corelib/ncbiobj.hpp | 68 +-
c++/include/corelib/ncbireg.hpp | 10 +-
c++/include/corelib/ncbistl.hpp | 3 +-
c++/include/corelib/ncbistr.hpp | 653 +-
c++/include/corelib/request_ctx.hpp | 81 +-
c++/include/corelib/rwstream.hpp | 40 +-
c++/include/corelib/version.hpp | 3 +-
c++/include/dbapi/dbapi.hpp | 4 +-
c++/include/dbapi/driver/dbapi_driver_conn_mgr.hpp | 2 +-
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c++/include/dbapi/driver/exception.hpp | 12 +-
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c++/include/dbapi/driver/impl/dbapi_impl_cmd.hpp | 2 +-
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c++/include/dbapi/driver/interfaces.hpp | 33 +-
c++/include/dbapi/driver/odbc/interfaces.hpp | 2 +-
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c++/include/dbapi/driver/util/blobstore.hpp | 2 +-
c++/include/dbapi/error_codes.hpp | 2 +-
c++/include/dbapi/variant.hpp | 2 +-
c++/include/html/htmlhelper.hpp | 12 +-
c++/include/html/nodemap.hpp | 4 +-
c++/include/misc/error_codes.hpp | 52 +
c++/include/ncbi_pch.hpp | 2 +-
c++/include/ncbi_source_ver.h | 2 +-
c++/include/ncbiconf.h | 2 +-
c++/include/objects/biblio/MedlineUID.hpp | 76 +
c++/include/objects/biblio/PmcID.hpp | 76 +
c++/include/objects/biblio/PubMedId.hpp | 76 +
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c++/include/objects/general/User_object.hpp | 9 +-
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c++/include/objects/genomecoll/GC_Assembly.hpp | 8 +-
c++/include/objects/genomecoll/cached_assembly.hpp | 4 +
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c++/include/objects/id2/id2processor.hpp | 6 +-
c++/include/objects/macro/String_constraint.hpp | 2 +-
c++/include/objects/macro/Suspect_rule.hpp | 30 +-
c++/include/objects/seq/Seq_gap.hpp | 2 +-
c++/include/objects/seq/Seq_inst.hpp | 4 +-
c++/include/objects/seq/Seq_literal.hpp | 7 +-
c++/include/objects/seq/seq_loc_mapper_base.hpp | 249 +-
c++/include/objects/seq/sofa_map.hpp | 2 +-
c++/include/objects/seqfeat/BioSource.hpp | 38 +-
c++/include/objects/seqfeat/Delta_item.hpp | 94 +
c++/include/objects/seqfeat/Gb_qual.hpp | 6 +-
c++/include/objects/seqfeat/OrgMod.hpp | 13 +-
c++/include/objects/seqfeat/SeqFeatData.hpp | 12 +-
c++/include/objects/seqfeat/Seq_feat.hpp | 6 +-
c++/include/objects/seqfeat/SubSource.hpp | 3 +-
c++/include/objects/seqfeat/Trna_ext.hpp | 2 +-
c++/include/objects/seqfeat/Variation_ref.hpp | 22 +-
c++/include/objects/seqloc/Seq_loc.hpp | 18 +-
c++/include/objects/seqset/Bioseq_set.hpp | 5 +-
c++/include/objects/taxon1/Taxon2_data.hpp | 2 +-
c++/include/objects/taxon1/taxon1.hpp | 7 +-
c++/include/objects/trackmgr/TMgr_ClientInfo.hpp | 2 +-
c++/include/objects/trackmgr/TMgr_DTrackId.hpp | 13 +-
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c++/include/objects/trackmgr/gridrpcclient.hpp | 149 +-
c++/include/objects/valerr/ValidErrItem.hpp | 20 +-
c++/include/objects/valerr/ValidError.hpp | 6 +-
c++/include/objects/valid/Comment_rule.hpp | 2 +-
c++/include/objects/varrep/AaInterval.hpp | 90 +
c++/include/objects/varrep/AaLocation.hpp | 90 +
c++/include/objmgr/annot_selector.hpp | 49 +-
c++/include/objmgr/annot_types_ci.hpp | 5 +-
c++/include/objmgr/bioseq_handle.hpp | 2 +-
c++/include/objmgr/data_loader.hpp | 2 +-
c++/include/objmgr/impl/annot_collector.hpp | 97 +-
c++/include/objmgr/impl/annot_object_index.hpp | 8 +-
c++/include/objmgr/impl/bioseq_base_info.hpp | 6 +-
c++/include/objmgr/impl/bioseq_info.hpp | 2 +-
c++/include/objmgr/impl/data_source.hpp | 2 +-
c++/include/objmgr/impl/scope_impl.hpp | 2 +-
c++/include/objmgr/impl/seq_annot_info.hpp | 56 +-
c++/include/objmgr/impl/seq_entry_info.hpp | 43 +-
c++/include/objmgr/impl/seq_id_sort.hpp | 2 +-
c++/include/objmgr/impl/seq_table_info.hpp | 46 +-
c++/include/objmgr/impl/seq_table_setters.hpp | 10 +-
c++/include/objmgr/impl/seq_vector_cvt_gen.hpp | 26 +-
c++/include/objmgr/impl/snp_annot_info.hpp | 19 +-
c++/include/objmgr/impl/snp_info.hpp | 20 +-
c++/include/objmgr/impl/tse_info.hpp | 3 +-
c++/include/objmgr/impl/tse_info_object.hpp | 5 +-
c++/include/objmgr/impl/tse_split_info.hpp | 3 +-
c++/include/objmgr/object_manager.hpp | 2 +-
c++/include/objmgr/objmgr_exception.hpp | 2 +-
c++/include/objmgr/scope.hpp | 2 +-
c++/include/objmgr/seq_feat_handle.hpp | 39 +-
c++/include/objmgr/seq_loc_mapper.hpp | 86 +-
c++/include/objmgr/seq_map.hpp | 2 +-
c++/include/objmgr/seq_map_ci.hpp | 2 +-
c++/include/objmgr/seq_vector_ci.hpp | 17 +-
c++/include/objmgr/split/size.hpp | 4 +-
c++/include/objmgr/util/create_defline.hpp | 3 +
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c++/include/objmgr/util/obj_sniff.hpp | 23 +-
c++/include/objmgr/util/seq_loc_util.hpp | 6 +-
c++/include/objmgr/util/sequence.hpp | 46 +-
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c++/include/objtools/align_format/taxFormat.hpp | 74 +-
c++/include/objtools/alnmgr/sparse_aln.hpp | 29 +-
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c++/include/objtools/blast/seqdb_reader/seqdb.hpp | 5 +-
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c++/src/objmgr/data_loader.cpp | 2 +-
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c++/src/objmgr/edits_db_saver.cpp | 282 +-
c++/src/objmgr/gc_assembly_parser.cpp | 6 +-
c++/src/objmgr/mapped_feat.cpp | 20 +-
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