dgit.raspbian.org Git - ncbi-blast+.git/commit

author	Olivier Sallou <osallou@debian.org>
	Sat, 10 Feb 2018 17:32:50 +0000 (17:32 +0000)
committer	Olivier Sallou <osallou@debian.org>
	Sat, 10 Feb 2018 17:32:50 +0000 (17:32 +0000)
commit	b81ad62686e79451c429d7064391be4cec8290c4
tree	61be0b965e2116bd71b129ace53da9bd3451b771	tree \| snapshot
parent	edfc13137ba904f5260790dee3746cf7ab5cc041	commit \| diff

New upstream version 2.7.1

1924 files changed:

c++/compilers/cygwin/build.sh		diff \| blob \| history
c++/compilers/vs2013/datatool.bat		diff \| blob \| history
c++/compilers/vs2013/make.bat		diff \| blob \| history
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c++/compilers/xcode30_prj/static/UtilityProjects/PTB.xcodeproj/project.pbxproj		diff \| blob \| history
c++/include/algo/blast/api/blast_options.hpp		diff \| blob \| history
c++/include/algo/blast/api/blast_options_builder.hpp		diff \| blob \| history
c++/include/algo/blast/api/blast_results.hpp		diff \| blob \| history
c++/include/algo/blast/api/blast_seqinfosrc.hpp		diff \| blob \| history
c++/include/algo/blast/api/blast_seqinfosrc_aux.hpp		diff \| blob \| history
c++/include/algo/blast/api/blast_types.hpp		diff \| blob \| history
c++/include/algo/blast/api/blastp_kmer_options.hpp	[new file with mode: 0644]	blob
c++/include/algo/blast/api/magicblast.hpp		diff \| blob \| history
c++/include/algo/blast/api/magicblast_options.hpp		diff \| blob \| history
c++/include/algo/blast/api/prelim_stage.hpp		diff \| blob \| history
c++/include/algo/blast/api/remote_blast.hpp		diff \| blob \| history
c++/include/algo/blast/api/seqinfosrc_seqdb.hpp		diff \| blob \| history
c++/include/algo/blast/api/setup_factory.hpp		diff \| blob \| history
c++/include/algo/blast/blastinput/blast_args.hpp		diff \| blob \| history
c++/include/algo/blast/blastinput/blast_asn1_input.hpp		diff \| blob \| history
c++/include/algo/blast/blastinput/blast_fasta_input.hpp		diff \| blob \| history
c++/include/algo/blast/blastinput/blast_input.hpp		diff \| blob \| history
c++/include/algo/blast/blastinput/blast_input_aux.hpp		diff \| blob \| history
c++/include/algo/blast/blastinput/blast_scope_src.hpp		diff \| blob \| history
c++/include/algo/blast/blastinput/cmdline_flags.hpp		diff \| blob \| history
c++/include/algo/blast/blastinput/kblastp_args.hpp		diff \| blob \| history
c++/include/algo/blast/blastinput/rpsblast_args.hpp		diff \| blob \| history
c++/include/algo/blast/core/blast_hits.h		diff \| blob \| history
c++/include/algo/blast/core/blast_hspstream.h		diff \| blob \| history
c++/include/algo/blast/core/blast_lookup.h		diff \| blob \| history
c++/include/algo/blast/core/blast_nalookup.h		diff \| blob \| history
c++/include/algo/blast/core/blast_options.h		diff \| blob \| history
c++/include/algo/blast/core/blast_query_info.h		diff \| blob \| history
c++/include/algo/blast/core/hspfilter_mapper.h		diff \| blob \| history
c++/include/algo/blast/core/lookup_wrap.h		diff \| blob \| history
c++/include/algo/blast/core/spliced_hits.h	[new file with mode: 0644]	blob
c++/include/algo/blast/dbindex/dbindex.hpp		diff \| blob \| history
c++/include/algo/blast/dbindex/sequence_istream_fasta.hpp		diff \| blob \| history
c++/include/algo/blast/format/blast_async_format.hpp	[new file with mode: 0644]	blob
c++/include/algo/blast/format/blast_format.hpp		diff \| blob \| history
c++/include/algo/blast/igblast/igblast.hpp		diff \| blob \| history
c++/include/algo/blast/proteinkmer/blastkmer.hpp	[new file with mode: 0644]	blob
c++/include/algo/blast/proteinkmer/blastkmerindex.hpp	[new file with mode: 0644]	blob
c++/include/algo/blast/proteinkmer/blastkmeroptions.hpp	[new file with mode: 0644]	blob
c++/include/algo/blast/proteinkmer/blastkmerresults.hpp	[new file with mode: 0644]	blob
c++/include/algo/blast/proteinkmer/blastkmerutils.hpp	[new file with mode: 0644]	blob
c++/include/algo/blast/proteinkmer/kblastapi.hpp	[new file with mode: 0644]	blob
c++/include/algo/blast/proteinkmer/mhfile.hpp	[new file with mode: 0644]	blob
c++/include/algo/winmask/seq_masker_istat.hpp		diff \| blob \| history
c++/include/algo/winmask/seq_masker_ostat.hpp		diff \| blob \| history
c++/include/cgi/cgi_exception.hpp		diff \| blob \| history
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c++/include/cgi/cgiapp.hpp		diff \| blob \| history
c++/include/cgi/cgictx.hpp		diff \| blob \| history
c++/include/cgi/ncbicgi.hpp		diff \| blob \| history
c++/include/cgi/ncbicgir.hpp		diff \| blob \| history
c++/include/cgi/user_agent.hpp		diff \| blob \| history
c++/include/common/boost_skew_guard.hpp		diff \| blob \| history
c++/include/common/config/ncbiconf_msvc.h		diff \| blob \| history
c++/include/common/config/ncbiconf_universal.h		diff \| blob \| history
c++/include/common/config/ncbiconf_xcode.h		diff \| blob \| history
c++/include/common/ncbi_build_ver.h.in		diff \| blob \| history
c++/include/common/ncbi_export.h		diff \| blob \| history
c++/include/common/ncbi_package_ver.h		diff \| blob \| history
c++/include/common/ncbi_skew_guard.h		diff \| blob \| history
c++/include/common/ncbi_source_ver.h		diff \| blob \| history
c++/include/common/ncbiconf_impl.h		diff \| blob \| history
c++/include/common/test_data_path.h		diff \| blob \| history
c++/include/connect/error_codes.hpp		diff \| blob \| history
c++/include/connect/impl/thread_pool_for_server.hpp		diff \| blob \| history
c++/include/connect/ncbi_conn_stream.hpp		diff \| blob \| history
c++/include/connect/ncbi_conn_test.hpp		diff \| blob \| history
c++/include/connect/ncbi_connector.h		diff \| blob \| history
c++/include/connect/ncbi_connutil.h		diff \| blob \| history
c++/include/connect/ncbi_core.h		diff \| blob \| history
c++/include/connect/ncbi_core_cxx.hpp		diff \| blob \| history
c++/include/connect/ncbi_gnutls.h		diff \| blob \| history
c++/include/connect/ncbi_heapmgr.h		diff \| blob \| history
c++/include/connect/ncbi_host_info.h		diff \| blob \| history
c++/include/connect/ncbi_http_session.hpp		diff \| blob \| history
c++/include/connect/ncbi_iprange.h	[new file with mode: 0644]	blob
c++/include/connect/ncbi_ipv6.h	[new file with mode: 0644]	blob
c++/include/connect/ncbi_lbos.hpp		diff \| blob \| history
c++/include/connect/ncbi_localip.h	[new file with mode: 0644]	blob
c++/include/connect/ncbi_mbedtls.h	[new file with mode: 0644]	blob
c++/include/connect/ncbi_monkey.hpp		diff \| blob \| history
c++/include/connect/ncbi_namedpipe_connector.hpp		diff \| blob \| history
c++/include/connect/ncbi_pipe_connector.hpp		diff \| blob \| history
c++/include/connect/ncbi_sendmail.h		diff \| blob \| history
c++/include/connect/ncbi_server_info.h		diff \| blob \| history
c++/include/connect/ncbi_service.h		diff \| blob \| history
c++/include/connect/ncbi_service_connector.h		diff \| blob \| history
c++/include/connect/ncbi_socket.h		diff \| blob \| history
c++/include/connect/ncbi_tls.h	[new file with mode: 0644]	blob
c++/include/connect/ncbi_types.h		diff \| blob \| history
c++/include/connect/ncbi_util.h		diff \| blob \| history
c++/include/connect/services/grid_app_version_info.hpp		diff \| blob \| history
c++/include/connect/services/grid_client.hpp		diff \| blob \| history
c++/include/connect/services/grid_globals.hpp		diff \| blob \| history
c++/include/connect/services/grid_rw_impl.hpp		diff \| blob \| history
c++/include/connect/services/grid_worker.hpp		diff \| blob \| history
c++/include/connect/services/grid_worker_app.hpp		diff \| blob \| history
c++/include/connect/services/impl/netschedule_api_int.hpp		diff \| blob \| history
c++/include/connect/services/impl/netstorage_impl.hpp		diff \| blob \| history
c++/include/connect/services/impl/netstorage_int.hpp		diff \| blob \| history
c++/include/connect/services/json_over_uttp.hpp		diff \| blob \| history
c++/include/connect/services/netcache_admin.hpp		diff \| blob \| history
c++/include/connect/services/netcache_api.hpp		diff \| blob \| history
c++/include/connect/services/netcache_search.hpp		diff \| blob \| history
c++/include/connect/services/netcomponent.hpp		diff \| blob \| history
c++/include/connect/services/neticache_client.hpp		diff \| blob \| history
c++/include/connect/services/netschedule_api.hpp		diff \| blob \| history
c++/include/connect/services/netservice_api.hpp		diff \| blob \| history
c++/include/connect/services/netstorage.hpp		diff \| blob \| history
c++/include/connect/services/netstorage_impl.hpp	[deleted file]	blob \| history
c++/include/connect/services/ns_output_parser.hpp		diff \| blob \| history
c++/include/connect/services/remote_app.hpp		diff \| blob \| history
c++/include/connect/services/srv_connections.hpp		diff \| blob \| history
c++/include/connect/services/util.hpp		diff \| blob \| history
c++/include/corelib/error_codes.hpp		diff \| blob \| history
c++/include/corelib/impl/ncbi_dbsvcmapper.hpp		diff \| blob \| history
c++/include/corelib/impl/rwstreambuf.hpp		diff \| blob \| history
c++/include/corelib/ncbi_cookies.hpp		diff \| blob \| history
c++/include/corelib/ncbi_process.hpp		diff \| blob \| history
c++/include/corelib/ncbi_safe_static.hpp		diff \| blob \| history
c++/include/corelib/ncbi_stack.hpp		diff \| blob \| history
c++/include/corelib/ncbi_system.hpp		diff \| blob \| history
c++/include/corelib/ncbi_tree.hpp		diff \| blob \| history
c++/include/corelib/ncbi_url.hpp		diff \| blob \| history
c++/include/corelib/ncbiapp.hpp		diff \| blob \| history
c++/include/corelib/ncbiargs.hpp		diff \| blob \| history
c++/include/corelib/ncbidiag.hpp		diff \| blob \| history
c++/include/corelib/ncbidll.hpp		diff \| blob \| history
c++/include/corelib/ncbierror.hpp		diff \| blob \| history
c++/include/corelib/ncbiexpt.hpp		diff \| blob \| history
c++/include/corelib/ncbifile.hpp		diff \| blob \| history
c++/include/corelib/ncbimisc.hpp		diff \| blob \| history
c++/include/corelib/ncbimtx.hpp		diff \| blob \| history
c++/include/corelib/ncbiobj.hpp		diff \| blob \| history
c++/include/corelib/ncbireg.hpp		diff \| blob \| history
c++/include/corelib/ncbistr.hpp		diff \| blob \| history
c++/include/corelib/ncbistr_util.hpp		diff \| blob \| history
c++/include/corelib/ncbistre.hpp		diff \| blob \| history
c++/include/corelib/ncbithr.hpp		diff \| blob \| history
c++/include/corelib/ncbiutil.hpp		diff \| blob \| history
c++/include/corelib/perf_log.hpp		diff \| blob \| history
c++/include/corelib/request_ctx.hpp		diff \| blob \| history
c++/include/corelib/request_status.hpp		diff \| blob \| history
c++/include/corelib/syslog.hpp		diff \| blob \| history
c++/include/corelib/teamcity_messages.h	[new file with mode: 0644]	blob
c++/include/corelib/tempstr.hpp		diff \| blob \| history
c++/include/corelib/test_boost.hpp		diff \| blob \| history
c++/include/corelib/version.hpp		diff \| blob \| history
c++/include/db/error_codes.hpp	[new file with mode: 0644]	blob
c++/include/db/sqlite/sqlitewrapp.hpp	[new file with mode: 0644]	blob
c++/include/dbapi/dbapi.hpp		diff \| blob \| history
c++/include/dbapi/driver/dbapi_conn_factory.hpp		diff \| blob \| history
c++/include/dbapi/driver/dbapi_driver_conn_mgr.hpp		diff \| blob \| history
c++/include/dbapi/driver/dbapi_svc_mapper.hpp		diff \| blob \| history
c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp		diff \| blob \| history
c++/include/dbapi/driver/impl/dbapi_impl_cmd.hpp		diff \| blob \| history
c++/include/dbapi/driver/impl/dbapi_impl_connection.hpp		diff \| blob \| history
c++/include/dbapi/driver/impl/dbapi_impl_context.hpp		diff \| blob \| history
c++/include/dbapi/driver/interfaces.hpp		diff \| blob \| history
c++/include/dbapi/driver/odbc/interfaces.hpp		diff \| blob \| history
c++/include/dbapi/driver/public.hpp		diff \| blob \| history
c++/include/dbapi/error_codes.hpp		diff \| blob \| history
c++/include/dbapi/variant.hpp		diff \| blob \| history
c++/include/html/html.hpp		diff \| blob \| history
c++/include/html/node.hpp		diff \| blob \| history
c++/include/ncbi_pch.hpp		diff \| blob \| history
c++/include/ncbi_source_ver.h		diff \| blob \| history
c++/include/ncbiconf.h		diff \| blob \| history
c++/include/objects/general/Dbtag.hpp		diff \| blob \| history
c++/include/objects/general/Name_std.hpp		diff \| blob \| history
c++/include/objects/genomecoll/GC_Assembly.hpp		diff \| blob \| history
c++/include/objects/genomecoll/GC_AssemblyUnit.hpp		diff \| blob \| history
c++/include/objects/genomecoll/cached_assembly.hpp		diff \| blob \| history
c++/include/objects/genomecoll/genomic_collections_cli.hpp		diff \| blob \| history
c++/include/objects/id2/ID2_Reply_Data.hpp	[new file with mode: 0644]	blob
c++/include/objects/id2/id2processor.hpp		diff \| blob \| history
c++/include/objects/id2/id2processor_interface.hpp		diff \| blob \| history
c++/include/objects/macro/Location_constraint.hpp		diff \| blob \| history
c++/include/objects/macro/Search_func.hpp		diff \| blob \| history
c++/include/objects/macro/String_constraint.hpp		diff \| blob \| history
c++/include/objects/macro/Suspect_rule.hpp		diff \| blob \| history
c++/include/objects/misc/sequence_util_macros.hpp		diff \| blob \| history
c++/include/objects/pub/Pub.hpp		diff \| blob \| history
c++/include/objects/seq/Seq_inst.hpp		diff \| blob \| history
c++/include/objects/seq/seq_id_handle.hpp		diff \| blob \| history
c++/include/objects/seq/seq_loc_mapper_base.hpp		diff \| blob \| history
c++/include/objects/seq/so_map.hpp	[new file with mode: 0644]	blob
c++/include/objects/seq/sofa_map.hpp		diff \| blob \| history
c++/include/objects/seqalign/Dense_seg.hpp		diff \| blob \| history
c++/include/objects/seqalign/Seq_align.hpp		diff \| blob \| history
c++/include/objects/seqfeat/BioSource.hpp		diff \| blob \| history
c++/include/objects/seqfeat/Gb_qual.hpp		diff \| blob \| history
c++/include/objects/seqfeat/Genetic_code_table.hpp		diff \| blob \| history
c++/include/objects/seqfeat/OrgMod.hpp		diff \| blob \| history
c++/include/objects/seqfeat/OrgName.hpp		diff \| blob \| history
c++/include/objects/seqfeat/Org_ref.hpp		diff \| blob \| history
c++/include/objects/seqfeat/RNA_gen.hpp		diff \| blob \| history
c++/include/objects/seqfeat/SeqFeatData.hpp		diff \| blob \| history
c++/include/objects/seqfeat/Seq_feat.hpp		diff \| blob \| history
c++/include/objects/seqfeat/SubSource.hpp		diff \| blob \| history
c++/include/objects/seqloc/Seq_id.hpp		diff \| blob \| history
c++/include/objects/seqloc/Seq_loc.hpp		diff \| blob \| history
c++/include/objects/seqset/Bioseq_set.hpp		diff \| blob \| history
c++/include/objects/taxon1/taxon1.hpp		diff \| blob \| history
c++/include/objects/taxon3/T3Data.hpp		diff \| blob \| history
c++/include/objects/taxon3/itaxon3.hpp		diff \| blob \| history
c++/include/objects/taxon3/taxon3.hpp		diff \| blob \| history
c++/include/objects/trackmgr/gridrpcclient.hpp		diff \| blob \| history
c++/include/objects/trackmgr/primary_snp.hpp	[new file with mode: 0644]	blob
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c++/include/objects/valerr/ValidErrItem.hpp		diff \| blob \| history
c++/include/objects/valerr/ValidError.hpp		diff \| blob \| history
c++/include/objmgr/align_ci.hpp		diff \| blob \| history
c++/include/objmgr/annot_selector.hpp		diff \| blob \| history
c++/include/objmgr/annot_types_ci.hpp		diff \| blob \| history
c++/include/objmgr/data_loader.hpp		diff \| blob \| history
c++/include/objmgr/feat_ci.hpp		diff \| blob \| history
c++/include/objmgr/graph_ci.hpp		diff \| blob \| history
c++/include/objmgr/impl/annot_collector.hpp		diff \| blob \| history
c++/include/objmgr/impl/annot_object_index.hpp		diff \| blob \| history
c++/include/objmgr/impl/bioseq_set_info.hpp		diff \| blob \| history
c++/include/objmgr/impl/data_source.hpp		diff \| blob \| history
c++/include/objmgr/impl/scope_impl.hpp		diff \| blob \| history
c++/include/objmgr/impl/scope_info.hpp		diff \| blob \| history
c++/include/objmgr/impl/seq_entry_info.hpp		diff \| blob \| history
c++/include/objmgr/impl/seq_table_setters.hpp		diff \| blob \| history
c++/include/objmgr/impl/seq_vector_cvt_gen.hpp		diff \| blob \| history
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c++/include/objmgr/impl/tse_chunk_info.hpp		diff \| blob \| history
c++/include/objmgr/impl/tse_info.hpp		diff \| blob \| history
c++/include/objmgr/impl/tse_info_object.hpp		diff \| blob \| history
c++/include/objmgr/impl/tse_split_info.hpp		diff \| blob \| history
c++/include/objmgr/objmgr_exception.hpp		diff \| blob \| history
c++/include/objmgr/seq_entry_ci.hpp		diff \| blob \| history
c++/include/objmgr/seq_loc_mapper.hpp		diff \| blob \| history
c++/include/objmgr/seq_vector_ci.hpp		diff \| blob \| history
c++/include/objmgr/split/size.hpp		diff \| blob \| history
c++/include/objmgr/tse_handle.hpp		diff \| blob \| history
c++/include/objmgr/util/autodef.hpp	[new file with mode: 0644]	blob
c++/include/objmgr/util/autodef_available_modifier.hpp	[new file with mode: 0644]	blob
c++/include/objmgr/util/autodef_feature_clause.hpp	[new file with mode: 0644]	blob
c++/include/objmgr/util/autodef_feature_clause_base.hpp	[new file with mode: 0644]	blob
c++/include/objmgr/util/autodef_mod_combo.hpp	[new file with mode: 0644]	blob
c++/include/objmgr/util/autodef_options.hpp	[new file with mode: 0644]	blob
c++/include/objmgr/util/autodef_source_desc.hpp	[new file with mode: 0644]	blob
c++/include/objmgr/util/autodef_source_group.hpp	[new file with mode: 0644]	blob
c++/include/objmgr/util/create_defline.hpp		diff \| blob \| history
c++/include/objmgr/util/feature_edit.hpp	[new file with mode: 0644]	blob
c++/include/objmgr/util/indexer.hpp	[new file with mode: 0644]	blob
c++/include/objmgr/util/obj_sniff.hpp		diff \| blob \| history
c++/include/objmgr/util/objutil.hpp		diff \| blob \| history
c++/include/objmgr/util/seq_align_util.hpp		diff \| blob \| history
c++/include/objmgr/util/sequence.hpp		diff \| blob \| history
c++/include/objtools/align_format/align_format_util.hpp		diff \| blob \| history
c++/include/objtools/align_format/format_flags.hpp		diff \| blob \| history
c++/include/objtools/align_format/showalign.hpp		diff \| blob \| history
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c++/include/objtools/align_format/taxFormat.hpp		diff \| blob \| history
c++/include/objtools/alnmgr/aln_stats.hpp		diff \| blob \| history
c++/include/objtools/alnmgr/alnmatch.hpp		diff \| blob \| history
c++/include/objtools/alnmgr/pairwise_aln.hpp		diff \| blob \| history
c++/include/objtools/alnmgr/seqids_extractor.hpp		diff \| blob \| history
c++/include/objtools/alnmgr/sparse_aln.hpp		diff \| blob \| history
c++/include/objtools/blast/blastdb_format/blastdb_dataextract.hpp		diff \| blob \| history
c++/include/objtools/blast/blastdb_format/seq_writer.hpp		diff \| blob \| history
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c++/include/objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp		diff \| blob \| history
c++/include/objtools/blast/seqdb_reader/impl/seqdbisam.hpp		diff \| blob \| history
c++/include/objtools/blast/seqdb_reader/impl/seqdbtax.hpp		diff \| blob \| history
c++/include/objtools/blast/seqdb_reader/impl/seqdbvol.hpp		diff \| blob \| history
c++/include/objtools/blast/seqdb_reader/seqdb.hpp		diff \| blob \| history
c++/include/objtools/blast/seqdb_reader/seqdbcommon.hpp		diff \| blob \| history
c++/include/objtools/blast/seqdb_writer/build_db.hpp		diff \| blob \| history
c++/include/objtools/blast/seqdb_writer/impl/criteria.hpp		diff \| blob \| history
c++/include/objtools/blast/seqdb_writer/writedb.hpp		diff \| blob \| history
c++/include/objtools/blast/seqdb_writer/writedb_files.hpp		diff \| blob \| history
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c++/include/objtools/cleanup/cleanup_change.hpp		diff \| blob \| history
c++/include/objtools/cleanup/newcleanup.hpp		diff \| blob \| history
c++/include/objtools/data_loaders/blastdb/blastdb_adapter.hpp		diff \| blob \| history
c++/include/objtools/data_loaders/genbank/gbloader.hpp		diff \| blob \| history
c++/include/objtools/data_loaders/genbank/impl/reader_id2_base.hpp		diff \| blob \| history
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c++/include/objtools/data_loaders/genbank/readers/id2/reader_id2.hpp		diff \| blob \| history
c++/include/objtools/edit/autodef.hpp		diff \| blob \| history
c++/include/objtools/edit/autodef_available_modifier.hpp	[deleted file]	blob \| history
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