[med-svn] [ncbi-blast+] 02/03: Updated version 2.5.0 from 'upstream/2.5.0'
Olivier Sallou
osallou at debian.org
Fri Dec 2 08:55:39 UTC 2016
This is an automated email from the git hooks/post-receive script.
osallou pushed a commit to branch master
in repository ncbi-blast+.
commit d2179e98943ff9942a5be97164a1e3b750624eb7
Merge: f8c16e6 0656496
Author: Olivier Sallou <olivier.sallou at debian.org>
Date: Thu Dec 1 14:39:29 2016 +0100
Updated version 2.5.0 from 'upstream/2.5.0'
with Debian dir e6f7d6e5bafd2b66fe885214be2aeb69a94e79f6
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.../blast_format/blastfmtutil_unit_test.cpp | 4 +-
.../blast_format/vecscreen_run_unit_test.cpp | 8 +-
.../blastdb/Makefile.bdbloader_unit_test.app | 5 +-
.../seqdb_reader/Makefile.seqdb_unit_test.app | 2 +-
.../unit_tests/seqdb_reader/seqdb_unit_test.cpp | 15 +-
c++/src/app/Makefile.in | 8 +-
c++/src/app/blast/Makefile.blastn.app | 5 +-
c++/src/app/blast/Makefile.in | 2 +-
c++/src/app/blast/blast_app_util.cpp | 143 +-
c++/src/app/blast/blast_app_util.hpp | 10 +-
c++/src/app/blast/blast_formatter.cpp | 12 +-
c++/src/app/blast/blastn_app.cpp | 10 +-
c++/src/app/blast/blastp_app.cpp | 10 +-
c++/src/app/blast/blastx_app.cpp | 10 +-
c++/src/app/blast/deltablast_app.cpp | 21 +-
c++/src/app/blast/psiblast_app.cpp | 18 +-
c++/src/app/blast/rpsblast_app.cpp | 12 +-
c++/src/app/blast/rpstblastn_app.cpp | 12 +-
c++/src/app/blast/seedtop_app.cpp | 9 +-
c++/src/app/blast/tblastn_app.cpp | 13 +-
c++/src/app/blast/tblastx_app.cpp | 10 +-
c++/src/app/blast/update_blastdb.pl | 4 +-
c++/src/app/blastdb/Makefile.convert2blastmask.app | 2 +-
c++/src/app/blastdb/Makefile.makeblastdb.app | 2 +-
c++/src/app/blastdb/Makefile.makeprofiledb.app | 2 +-
c++/src/app/blastdb/blastdb_aliastool.cpp | 9 +-
c++/src/app/blastdb/blastdbcheck.cpp | 4 +-
c++/src/app/blastdb/blastdbcmd.cpp | 15 +-
c++/src/app/blastdb/blastdbcp.cpp | 4 +-
c++/src/app/blastdb/convert2blastmask.cpp | 4 +-
c++/src/app/blastdb/makeblastdb.cpp | 15 +-
c++/src/app/blastdb/makeprofiledb.cpp | 4 +-
c++/src/app/dustmasker/Makefile.dustmasker.app | 4 +-
c++/src/app/dustmasker/main.cpp | 4 +-
c++/src/app/segmasker/Makefile.segmasker.app | 4 +-
c++/src/app/segmasker/segmasker.cpp | 4 +-
c++/src/app/winmasker/Makefile.winmasker.app | 6 +-
c++/src/app/winmasker/main.cpp | 4 +-
c++/src/build-system/Makefile.app.in | 2 +-
c++/src/build-system/Makefile.meta_l | 4 +-
c++/src/build-system/Makefile.mk.in | 41 +-
c++/src/build-system/Makefile.rules.in | 4 +-
c++/src/build-system/NEWS | 2 +
c++/src/build-system/aclocal.m4 | 14 +-
c++/src/build-system/config.h.in | 33 +-
c++/src/build-system/configure | 1379 +-
c++/src/build-system/configure.ac | 460 +-
c++/src/build-system/datatool_version.txt | 2 +-
.../helpers/Makefile.run_with_lock.app | 2 +-
c++/src/build-system/helpers/run_with_lock.c | 2 +-
c++/src/build-system/install.sh.in | 2 +-
c++/src/build-system/library_relations.txt | 439 +-
c++/src/build-system/ncbi_package_version | 2 +-
c++/src/build-system/project_tree_builder.ini | 128 +-
.../project_tree_builder/msvc_prj_generator.cpp | 2 +-
.../project_tree_builder/msvc_prj_utils.cpp | 14 +-
.../project_tree_builder/msvc_prj_utils.hpp | 3 +-
.../project_tree_builder/proj_builder_app.cpp | 19 +-
.../project_tree_builder/proj_tree_builder.cpp | 292 +-
c++/src/build-system/ptb_version.txt | 2 +-
c++/src/build-system/relocate.sh.in | 2 +-
c++/src/cgi/cgiapp.cpp | 18 +-
c++/src/cgi/cgictx.cpp | 23 +-
c++/src/cgi/fcgi_run.cpp | 8 +-
c++/src/cgi/ncbicgi.cpp | 2 +-
c++/src/cgi/ncbicgir.cpp | 10 +-
c++/src/connect/Makefile.connect.lib | 6 +-
c++/src/connect/Makefile.connect.lib.unix | 3 +-
c++/src/connect/Makefile.connssl.lib | 10 +-
c++/src/connect/Makefile.xconnect.lib | 6 +-
c++/src/connect/Makefile.xthrserv.lib | 6 +-
c++/src/connect/Makefile.xxconnect.lib | 11 +-
c++/src/connect/connection_pool.cpp | 176 +-
c++/src/connect/connection_pool.hpp | 37 +-
c++/src/connect/ncbi_buffer.c | 44 +-
c++/src/connect/ncbi_comm.h | 39 +-
c++/src/connect/ncbi_conn_stream.cpp | 16 +-
c++/src/connect/ncbi_conn_test.cpp | 21 +-
c++/src/connect/ncbi_connection.c | 21 +-
c++/src/connect/ncbi_connector.c | 41 +-
c++/src/connect/ncbi_connutil.c | 130 +-
c++/src/connect/ncbi_core.c | 10 +-
c++/src/connect/ncbi_core_cxx.cpp | 237 +-
c++/src/connect/ncbi_dispd.c | 10 +-
c++/src/connect/ncbi_ftp_connector.c | 196 +-
c++/src/connect/ncbi_gnutls.c | 41 +-
c++/src/connect/ncbi_http_connector.c | 31 +-
c++/src/connect/ncbi_http_session.cpp | 2 +-
c++/src/connect/ncbi_lbos.c | 1067 +-
c++/src/connect/ncbi_lbos.h | 11 +-
c++/src/connect/ncbi_lbos_cxx.cpp | 583 +-
c++/src/connect/ncbi_lbosp.h | 95 +-
c++/src/connect/ncbi_lbosp.hpp | 71 +-
c++/src/connect/ncbi_monkey.cpp | 1681 ++
c++/src/connect/ncbi_monkeyp.hpp | 81 +
c++/src/connect/ncbi_priv.c | 30 +-
c++/src/connect/ncbi_priv.h | 94 +-
c++/src/connect/ncbi_server_info.c | 57 +-
c++/src/connect/ncbi_service_connector.c | 20 +-
c++/src/connect/ncbi_socket.c | 199 +-
c++/src/connect/ncbi_util.c | 6 +-
c++/src/connect/parson.c | 1767 ++
c++/src/connect/parson.h | 223 +
c++/src/connect/server.cpp | 139 +-
c++/src/connect/services/grid_client.cpp | 2 +-
c++/src/connect/services/grid_control_thread.cpp | 2 +-
c++/src/connect/services/grid_worker.cpp | 44 +-
c++/src/connect/services/grid_worker_app.cpp | 2 +-
c++/src/connect/services/grid_worker_impl.hpp | 7 +-
c++/src/connect/services/json_over_uttp.cpp | 300 +-
c++/src/connect/services/netcache_api.cpp | 2 +-
c++/src/connect/services/netcache_api_impl.hpp | 2 +-
c++/src/connect/services/netcache_rw.cpp | 2 +-
c++/src/connect/services/neticache_client.cpp | 2 +-
c++/src/connect/services/netschedule_api.cpp | 2 +-
c++/src/connect/services/netschedule_api_admin.cpp | 2 +-
c++/src/connect/services/netschedule_api_impl.hpp | 4 +-
.../connect/services/netschedule_api_reader.cpp | 2 +-
.../connect/services/netschedule_api_submitter.cpp | 8 +-
c++/src/connect/services/netservice_api.cpp | 5 +-
c++/src/connect/services/netservice_api_impl.hpp | 2 +-
c++/src/connect/services/netstorage.cpp | 11 +-
c++/src/connect/services/netstorage_direct_nc.cpp | 7 +-
c++/src/connect/services/netstorage_direct_nc.hpp | 2 +-
c++/src/connect/services/netstorage_rpc.cpp | 77 +-
c++/src/connect/services/netstorage_rpc.hpp | 15 +-
c++/src/connect/services/netstorageobjectinfo.cpp | 2 +-
c++/src/connect/services/netstorageobjectloc.cpp | 2 +-
c++/src/connect/services/ns_output_parser.cpp | 242 +-
c++/src/connect/services/srv_connections.cpp | 2 +-
c++/src/connect/services/tmp_wn_info.cpp | 22 +-
c++/src/corelib/ddumpable.cpp | 2 +-
c++/src/corelib/env_reg.cpp | 13 +-
c++/src/corelib/expr.cpp | 4 +-
c++/src/corelib/ncbi_param.cpp | 54 +-
c++/src/corelib/ncbi_stack.cpp | 13 +-
c++/src/corelib/ncbi_stack_linux.cpp | 11 +-
c++/src/corelib/ncbi_stack_solaris.cpp | 4 +-
c++/src/corelib/ncbi_stack_win32.cpp | 4 +-
c++/src/corelib/ncbi_stack_win64.cpp | 4 +-
c++/src/corelib/ncbi_system.cpp | 9 +-
c++/src/corelib/ncbi_url.cpp | 2 +-
c++/src/corelib/ncbiapp.cpp | 23 +-
c++/src/corelib/ncbiargs.cpp | 280 +-
c++/src/corelib/ncbidiag.cpp | 263 +-
c++/src/corelib/ncbidiag_p.hpp | 4 +-
c++/src/corelib/ncbienv.cpp | 4 +-
c++/src/corelib/ncbierror.cpp | 185 +-
c++/src/corelib/ncbifile.cpp | 107 +-
c++/src/corelib/ncbimtx.cpp | 16 +-
c++/src/corelib/ncbireg.cpp | 66 +-
c++/src/corelib/ncbistr.cpp | 137 +-
c++/src/corelib/ncbitime.cpp | 16 +-
c++/src/corelib/request_ctx.cpp | 71 +-
c++/src/corelib/stream_utils.cpp | 9 +-
c++/src/corelib/teamcity_boost.cpp | 150 +-
c++/src/corelib/teamcity_messages.cpp | 101 +-
c++/src/corelib/teamcity_messages.h | 32 +-
c++/src/corelib/test_boost.cpp | 6 +-
c++/src/corelib/version.cpp | 10 +-
c++/src/dbapi/blobstream.cpp | 4 +-
c++/src/dbapi/blobstream.hpp | 4 +-
c++/src/dbapi/conn_impl.cpp | 6 +-
c++/src/dbapi/dbapi.cpp | 4 +-
c++/src/dbapi/driver/dbapi_conn_factory.cpp | 40 +-
c++/src/dbapi/driver/dbapi_driver_conn_mgr.cpp | 2 +-
c++/src/dbapi/driver/dbapi_driver_utils.cpp | 33 +-
c++/src/dbapi/driver/dbapi_impl_cmd.cpp | 2 +-
c++/src/dbapi/driver/dbapi_impl_connection.cpp | 13 +-
c++/src/dbapi/driver/dbapi_impl_context.cpp | 54 +-
c++/src/dbapi/driver/dbapi_object_convert.cpp | 2 +-
c++/src/dbapi/driver/dbapi_svc_mapper.cpp | 26 +-
c++/src/dbapi/driver/interfaces.cpp | 6 +-
c++/src/dbapi/driver/memory_store.cpp | 2 +-
c++/src/dbapi/driver/memory_store.hpp | 2 +-
c++/src/dbapi/driver/odbc/bcp.cpp | 2 +-
c++/src/dbapi/driver/odbc/connection.cpp | 23 +-
c++/src/dbapi/driver/odbc/cursor.cpp | 2 +-
c++/src/dbapi/driver/odbc/result.cpp | 2 +-
c++/src/dbapi/driver/public.cpp | 2 +-
c++/src/dbapi/driver/types.cpp | 2 +-
c++/src/dbapi/driver_mgr.cpp | 4 +-
c++/src/dbapi/rs_impl.cpp | 4 +-
c++/src/dbapi/rw_impl.cpp | 2 +-
c++/src/dbapi/rw_impl.hpp | 2 +-
c++/src/dbapi/stmt_impl.cpp | 4 +-
c++/src/dbapi/stmt_impl.hpp | 4 +-
c++/src/dbapi/variant.cpp | 4 +-
c++/src/html/indentstream.cpp | 4 +-
c++/src/html/selection.cpp | 4 +-
c++/src/misc/Makefile.in | 10 +
c++/src/misc/third_party/Makefile.in | 10 +
.../Makefile.third_party_dll_install.msvcproj | 11 +
.../Makefile.third_party_dll_install.msvcproj.msvc | 4 +
.../Makefile.third_party_msvcdll_install.msvcproj | 11 +
c++/src/misc/third_party_static/Makefile.in | 10 +
...akefile.third_party_msvcstatic_install.msvcproj | 11 +
.../Makefile.third_party_static_install.msvcproj | 11 +
...kefile.third_party_static_install.msvcproj.msvc | 4 +
c++/src/objects/Makefile.in | 4 +-
c++/src/objects/biblio/Auth_list.cpp | 6 +-
c++/src/objects/biblio/Cit_gen.cpp | 4 +-
c++/src/objects/biblio/biblio.def | 13 +
c++/src/objects/biotree/DistanceMatrix.cpp | 4 +-
c++/src/objects/blast/doc/blast.htm | 18 +-
c++/src/objects/entrez2/entrez2.def | 16 +
c++/src/objects/general/Dbtag.cpp | 285 +-
c++/src/objects/general/Name_std.cpp | 63 +-
c++/src/objects/general/User_field.cpp | 8 +-
c++/src/objects/general/User_object.cpp | 27 +-
.../genomecoll/GCClient_GetAssemblyBySequ.cpp | 81 +
c++/src/objects/genomecoll/GC_Assembly.cpp | 108 +-
c++/src/objects/genomecoll/cached_assembly.cpp | 56 +-
c++/src/objects/genomecoll/gencoll_client.asn | 38 +-
c++/src/objects/genomecoll/gencoll_client.def | 2 +-
c++/src/objects/genomecoll/genome_collection.asn | 3 +-
.../objects/genomecoll/genomic_collections_cli.cpp | 59 +-
c++/src/objects/macro/String_constraint.cpp | 8 +-
c++/src/objects/macro/product_rules.inc | 17000 ++++++++++++-------
c++/src/objects/macro/product_rules.prt | 16797 +++++++++++-------
c++/src/objects/medline/Medline_entry.cpp | 6 +-
c++/src/objects/medline/medline.def | 8 +
c++/src/objects/pub/Pub.cpp | 6 +-
c++/src/objects/pub/Pub_equiv.cpp | 10 +-
c++/src/objects/pub/pub.def | 4 +
c++/src/objects/seq/Bioseq.cpp | 20 +-
c++/src/objects/seq/Linkage_evidence.cpp | 4 +-
c++/src/objects/seq/Seq_gap.cpp | 2 +-
c++/src/objects/seq/Seq_literal.cpp | 4 +-
c++/src/objects/seq/seq.def | 4 +
c++/src/objects/seq/seq_align_mapper_base.cpp | 63 +-
c++/src/objects/seq/seq_id_handle.cpp | 4 +-
c++/src/objects/seq/seq_id_tree.cpp | 123 +-
c++/src/objects/seq/seq_id_tree.hpp | 14 +-
c++/src/objects/seq/seq_loc_mapper_base.cpp | 309 +-
c++/src/objects/seq/sofa_map.cpp | 91 +-
c++/src/objects/seqcode/seqcode.def | 8 +
c++/src/objects/seqfeat/BioSource.cpp | 321 +-
c++/src/objects/seqfeat/Delta_item.cpp | 81 +
c++/src/objects/seqfeat/Gb_qual.cpp | 13 +-
c++/src/objects/seqfeat/Genetic_code_table.cpp | 2 +-
c++/src/objects/seqfeat/OrgMod.cpp | 89 +-
c++/src/objects/seqfeat/OrgName.cpp | 34 +-
c++/src/objects/seqfeat/RNA_ref.cpp | 2 +-
c++/src/objects/seqfeat/SeqFeatData.cpp | 330 +-
c++/src/objects/seqfeat/Seq_feat.cpp | 7 +-
c++/src/objects/seqfeat/SubSource.cpp | 42 +-
c++/src/objects/seqfeat/Trna_ext.cpp | 2 +-
c++/src/objects/seqfeat/Variation_ref.cpp | 101 +-
c++/src/objects/seqfeat/ecnum_deleted.inc | 2 +-
c++/src/objects/seqfeat/ecnum_replaced.inc | 20 +-
c++/src/objects/seqfeat/ecnum_replaced.txt | 18 +-
c++/src/objects/seqfeat/ecnum_specific.inc | 69 +-
c++/src/objects/seqfeat/ecnum_specific.txt | 67 +-
c++/src/objects/seqfeat/institution_codes.inc | 85 +-
c++/src/objects/seqfeat/institution_codes.txt | 83 +-
c++/src/objects/seqfeat/seqfeat.asn | 5 +-
c++/src/objects/seqloc/Seq_id.cpp | 2 +-
c++/src/objects/seqloc/Seq_loc.cpp | 122 +-
c++/src/objects/seqloc/accguide.inc | 17 +-
c++/src/objects/seqloc/accguide.txt | 15 +-
c++/src/objects/seqset/Bioseq_set.cpp | 9 +-
c++/src/objects/taxon1/Taxon2_data.cpp | 2 +-
c++/src/objects/taxon1/taxon1.cpp | 24 +-
c++/src/objects/taxon1/taxon1.def | 12 +
c++/src/objects/trackmgr/TMgr_ClientInfo.cpp | 4 +-
c++/src/objects/trackmgr/displaytrack_client.cpp | 83 +-
c++/src/objects/trackmgr/trackmgr.asn | 13 +-
c++/src/objects/valerr/ValidErrItem.cpp | 18 +-
c++/src/objects/valid/Comment_rule.cpp | 2 +-
c++/src/objects/valid/Comment_set.cpp | 4 +-
c++/src/objects/valid/validrules.inc | 2 +-
c++/src/objects/varrep/AaInterval.cpp | 82 +
c++/src/objects/varrep/AaLocation.cpp | 77 +
c++/src/objects/varrep/Makefile.in | 3 +
c++/src/objects/varrep/Makefile.varrep.lib | 3 +
c++/src/objects/varrep/varrep.asn | 296 +
c++/src/objects/varrep/varrep.def | 17 +
c++/src/objects/varrep/varrep.module | 1 +
c++/src/objmgr/Makefile.objmgr.lib | 4 +-
c++/src/objmgr/annot_collector.cpp | 271 +-
c++/src/objmgr/annot_selector.cpp | 16 +-
c++/src/objmgr/bioseq_base_info.cpp | 31 +-
c++/src/objmgr/bioseq_handle.cpp | 2 +-
c++/src/objmgr/bioseq_info.cpp | 9 +-
c++/src/objmgr/bioseq_set_info.cpp | 8 +-
c++/src/objmgr/data_loader.cpp | 2 +-
c++/src/objmgr/data_source.cpp | 2 +-
c++/src/objmgr/gc_assembly_parser.cpp | 2 +-
c++/src/objmgr/mapped_feat.cpp | 20 +-
c++/src/objmgr/objmgr_exception.cpp | 2 +-
c++/src/objmgr/scope.cpp | 2 +-
c++/src/objmgr/scope_impl.cpp | 24 +-
c++/src/objmgr/seq_annot_info.cpp | 134 +-
c++/src/objmgr/seq_entry_info.cpp | 5 +-
c++/src/objmgr/seq_feat_handle.cpp | 134 +-
c++/src/objmgr/seq_id_sort.cpp | 2 +-
c++/src/objmgr/seq_loc_cvt.cpp | 16 +-
c++/src/objmgr/seq_loc_mapper.cpp | 89 +-
c++/src/objmgr/seq_map.cpp | 9 +-
c++/src/objmgr/seq_map_ci.cpp | 2 +-
c++/src/objmgr/seq_table_info.cpp | 174 +-
c++/src/objmgr/seq_table_setters.cpp | 4 +-
c++/src/objmgr/snp_annot_info.cpp | 22 +-
c++/src/objmgr/tse_assigner.cpp | 7 +-
c++/src/objmgr/tse_info.cpp | 11 +-
c++/src/objmgr/util/Makefile.util.lib | 4 +-
c++/src/objmgr/util/create_defline.cpp | 34 +-
c++/src/objmgr/util/feature.cpp | 172 +-
c++/src/objmgr/util/objutil.cpp | 4 +-
c++/src/objmgr/util/seq_loc_util.cpp | 14 +-
c++/src/objmgr/util/sequence.cpp | 106 +-
.../objtools/align_format/align_format_util.cpp | 123 +-
c++/src/objtools/align_format/aln_printer.cpp | 5 +-
c++/src/objtools/align_format/format_flags.cpp | 4 +-
c++/src/objtools/align_format/seqalignfilter.cpp | 7 +-
c++/src/objtools/align_format/showalign.cpp | 71 +-
c++/src/objtools/align_format/showdefline.cpp | 37 +-
c++/src/objtools/align_format/tabular.cpp | 34 +-
c++/src/objtools/align_format/taxFormat.cpp | 114 +-
.../unit_test/Makefile.align_format_unit_test.app | 6 +-
.../align_format/unit_test/showalign_unit_test.cpp | 65 +-
.../unit_test/showdefline_unit_test.cpp | 8 +-
.../unit_test/tabularinof_unit_test.cpp | 20 +-
c++/src/objtools/align_format/vectorscreen.cpp | 9 +-
c++/src/objtools/alnmgr/Makefile.alnmgr.lib | 5 +-
c++/src/objtools/alnmgr/Makefile.in | 4 +-
c++/src/objtools/alnmgr/aln_builders.cpp | 2 +-
c++/src/objtools/alnmgr/score_builder_base.cpp | 5 +-
c++/src/objtools/alnmgr/sparse_aln.cpp | 2 +-
.../blast/blastdb_format/blastdb_dataextract.cpp | 119 +-
.../blast/blastdb_format/blastdb_formatter.cpp | 7 +-
.../objtools/blast/blastdb_format/seq_writer.cpp | 79 +-
.../unit_test/seq_writer_unit_test.cpp | 67 +-
.../gene_info_reader/demo/gene_info_reader_app.cpp | 4 +-
.../objtools/blast/gene_info_reader/file_utils.cpp | 7 +-
.../objtools/blast/gene_info_reader/gene_info.cpp | 7 +-
.../blast/gene_info_reader/gene_info_reader.cpp | 7 +-
c++/src/objtools/blast/seqdb_reader/seqdb.cpp | 7 +-
c++/src/objtools/blast/seqdb_reader/seqdbalias.cpp | 7 +-
c++/src/objtools/blast/seqdb_reader/seqdbatlas.cpp | 7 +-
.../objtools/blast/seqdb_reader/seqdbbitset.cpp | 7 +-
c++/src/objtools/blast/seqdb_reader/seqdbblob.cpp | 7 +-
c++/src/objtools/blast/seqdb_reader/seqdbcol.cpp | 7 +-
.../objtools/blast/seqdb_reader/seqdbcommon.cpp | 7 +-
.../objtools/blast/seqdb_reader/seqdbexpert.cpp | 7 +-
c++/src/objtools/blast/seqdb_reader/seqdbfile.cpp | 7 +-
.../objtools/blast/seqdb_reader/seqdbfilter.cpp | 7 +-
.../objtools/blast/seqdb_reader/seqdbgilistset.cpp | 7 +-
.../objtools/blast/seqdb_reader/seqdbgimask.cpp | 7 +-
c++/src/objtools/blast/seqdb_reader/seqdbimpl.cpp | 14 +-
c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp | 20 +-
c++/src/objtools/blast/seqdb_reader/seqdbisam.cpp | 11 +-
c++/src/objtools/blast/seqdb_reader/seqdbobj.cpp | 7 +-
.../objtools/blast/seqdb_reader/seqdboidlist.cpp | 7 +-
c++/src/objtools/blast/seqdb_reader/seqdbtax.cpp | 7 +-
c++/src/objtools/blast/seqdb_reader/seqdbvol.cpp | 12 +-
.../objtools/blast/seqdb_reader/seqdbvolset.cpp | 7 +-
.../blast/seqdb_reader/test/seqdb_perf.cpp | 9 +-
.../objtools/blast/seqdb_writer/build-alias-index | 2 +-
c++/src/objtools/blast/seqdb_writer/build_db.cpp | 43 +-
.../blast/seqdb_writer/mask_info_registry.cpp | 5 -
.../blast/seqdb_writer/multisource_util.cpp | 7 +-
c++/src/objtools/blast/seqdb_writer/taxid_set.cpp | 7 +-
.../unit_test/Makefile.writedb_unit_test.app | 4 +-
.../seqdb_writer/unit_test/data/some_prots.fsa | 142 +
.../seqdb_writer/unit_test/writedb_unit_test.cpp | 528 +-
c++/src/objtools/blast/seqdb_writer/writedb.cpp | 7 +-
.../objtools/blast/seqdb_writer/writedb_column.cpp | 7 +-
.../blast/seqdb_writer/writedb_convert.cpp | 7 +-
.../objtools/blast/seqdb_writer/writedb_files.cpp | 7 +-
.../blast/seqdb_writer/writedb_general.cpp | 7 +-
.../objtools/blast/seqdb_writer/writedb_gimask.cpp | 7 +-
.../objtools/blast/seqdb_writer/writedb_impl.cpp | 51 +-
.../objtools/blast/seqdb_writer/writedb_isam.cpp | 7 +-
.../objtools/blast/seqdb_writer/writedb_volume.cpp | 10 +-
.../blast/services/Makefile.blast_services.lib | 5 +-
c++/src/objtools/blast/services/blast_services.cpp | 10 +-
c++/src/objtools/cleanup/Makefile.cleanup.lib | 4 +-
c++/src/objtools/cleanup/autogenerated_cleanup.cpp | 2 +-
c++/src/objtools/cleanup/autogenerated_cleanup.hpp | 2 +-
.../cleanup/autogenerated_extended_cleanup.cpp | 2 +-
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c++/src/objtools/cleanup/cleanup.cpp | 484 +-
c++/src/objtools/cleanup/cleanup_utils.cpp | 2 +-
c++/src/objtools/cleanup/newcleanupp.cpp | 493 +-
c++/src/objtools/cleanup/newcleanupp.hpp | 3 +-
c++/src/objtools/data_loaders/Makefile.in | 4 +-
.../objtools/data_loaders/blastdb/bdbloader.cpp | 6 +-
.../data_loaders/blastdb/bdbloader_rmt.cpp | 6 +-
.../data_loaders/blastdb/cached_sequence.cpp | 6 +-
.../data_loaders/blastdb/local_blastdb_adapter.cpp | 6 +-
.../blastdb/remote_blastdb_adapter.cpp | 6 +-
.../data_loaders/genbank/Makefile.ncbi_xreader.lib | 4 +-
.../data_loaders/genbank/cache/reader_cache.cpp | 2 +-
.../data_loaders/genbank/cache/writer_cache.cpp | 2 +-
.../objtools/data_loaders/genbank/dispatcher.cpp | 2 +-
c++/src/objtools/data_loaders/genbank/gbloader.cpp | 17 +-
.../data_loaders/genbank/gicache/gicache.c | 10 +-
.../data_loaders/genbank/gicache/gicache.h | 3 +-
.../genbank/gicache/reader_gicache.cpp | 2 +-
.../data_loaders/genbank/id1/reader_id1.cpp | 4 +-
.../data_loaders/genbank/id2/reader_id2.cpp | 4 +-
.../objtools/data_loaders/genbank/info_cache.cpp | 2 +-
.../objtools/data_loaders/genbank/processors.cpp | 57 +-
c++/src/objtools/data_loaders/genbank/reader.cpp | 2 +-
.../data_loaders/genbank/reader_id1_base.cpp | 2 +-
.../data_loaders/genbank/reader_id2_base.cpp | 585 +-
.../data_loaders/genbank/reader_service.cpp | 5 +-
.../objtools/data_loaders/genbank/reader_snp.cpp | 2 +-
.../data_loaders/genbank/request_result.cpp | 2 +-
c++/src/objtools/edit/Makefile.edit.lib | 4 +-
c++/src/objtools/edit/apply_object.cpp | 2 +-
c++/src/objtools/edit/autodef.cpp | 46 +-
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c++/src/objtools/edit/autodef_feature_clause.cpp | 112 +-
.../objtools/edit/autodef_feature_clause_base.cpp | 29 +-
c++/src/objtools/edit/autodef_mod_combo.cpp | 2 +-
c++/src/objtools/edit/autodef_options.cpp | 22 +-
c++/src/objtools/edit/cds_fix.cpp | 3 +-
c++/src/objtools/edit/feattable_edit.cpp | 240 +-
c++/src/objtools/edit/gaps_edit.cpp | 133 +-
c++/src/objtools/edit/loc_edit.cpp | 2 +-
c++/src/objtools/edit/publication_edit.cpp | 2 +-
c++/src/objtools/edit/remote_updater.cpp | 2 +-
c++/src/objtools/edit/rna_edit.cpp | 189 +-
c++/src/objtools/edit/seq_entry_edit.cpp | 2 +-
c++/src/objtools/edit/struc_comm_field.cpp | 2 +-
c++/src/objtools/format/Makefile.xformat.lib | 4 +-
c++/src/objtools/format/comment_item.cpp | 102 +-
c++/src/objtools/format/context.cpp | 8 +-
c++/src/objtools/format/dbsource_item.cpp | 9 +-
c++/src/objtools/format/feature_item.cpp | 87 +-
c++/src/objtools/format/flat_file_config.cpp | 57 +-
c++/src/objtools/format/flat_file_generator.cpp | 16 +-
c++/src/objtools/format/flat_seqloc.cpp | 2 +-
c++/src/objtools/format/gather_items.cpp | 15 +-
c++/src/objtools/format/genbank_formatter.cpp | 70 +-
c++/src/objtools/format/genbank_gather.cpp | 2 +-
c++/src/objtools/format/gene_finder.cpp | 3 +-
c++/src/objtools/format/inst_info_map.cpp | 18 +-
c++/src/objtools/format/inst_info_map.hpp | 2 +-
c++/src/objtools/format/item_formatter.cpp | 12 +-
c++/src/objtools/format/keywords_item.cpp | 2 +-
c++/src/objtools/format/locus_item.cpp | 5 +-
c++/src/objtools/format/qualifiers.cpp | 14 +-
c++/src/objtools/readers/Makefile.in | 4 +-
c++/src/objtools/readers/Makefile.xobjread.lib | 6 +-
c++/src/objtools/readers/Makefile.xobjreadex.lib | 4 +-
c++/src/objtools/readers/agp_util.cpp | 31 +-
c++/src/objtools/readers/aln_reader.cpp | 24 +-
c++/src/objtools/readers/bed_reader.cpp | 583 +-
c++/src/objtools/readers/fasta.cpp | 17 +-
c++/src/objtools/readers/gff2_data.cpp | 203 +-
c++/src/objtools/readers/gff2_reader.cpp | 24 +-
c++/src/objtools/readers/gff3_reader.cpp | 242 +-
c++/src/objtools/readers/gff3_sofa.cpp | 2 +-
c++/src/objtools/readers/gff_reader.cpp | 2 +-
c++/src/objtools/readers/gtf_reader.cpp | 160 +-
c++/src/objtools/readers/gvf_reader.cpp | 545 +-
c++/src/objtools/readers/idmapper_config.cpp | 6 +-
c++/src/objtools/readers/microarray_reader.cpp | 2 +-
c++/src/objtools/readers/read_util.cpp | 2 +-
c++/src/objtools/readers/reader_base.cpp | 13 +-
c++/src/objtools/readers/reader_data.cpp | 52 +-
c++/src/objtools/readers/reader_data.hpp | 29 +-
c++/src/objtools/readers/readfeat.cpp | 348 +-
c++/src/objtools/readers/source_mod_parser.cpp | 2 +-
c++/src/objtools/readers/track_data.cpp | 102 +
c++/src/objtools/readers/vcf_reader.cpp | 33 +-
c++/src/objtools/readers/wiggle_reader.cpp | 3 +-
c++/src/objtools/seqmasks_io/mask_bdb_reader.cpp | 7 +-
c++/src/objtools/seqmasks_io/mask_cmdline_args.cpp | 7 +-
c++/src/objtools/seqmasks_io/mask_fasta_reader.cpp | 7 +-
c++/src/objtools/seqmasks_io/mask_writer.cpp | 7 +-
.../seqmasks_io/mask_writer_blastdb_maskinfo.cpp | 7 +-
c++/src/objtools/seqmasks_io/mask_writer_fasta.cpp | 7 +-
c++/src/objtools/seqmasks_io/mask_writer_int.cpp | 7 +-
.../objtools/seqmasks_io/mask_writer_seqloc.cpp | 7 +-
c++/src/objtools/seqmasks_io/mask_writer_tab.cpp | 7 +-
c++/src/serial/aliasinfo.cpp | 12 +-
c++/src/serial/choice.cpp | 2 +-
c++/src/serial/classinfo.cpp | 2 +-
c++/src/serial/datatool/aliasstr.cpp | 4 +-
c++/src/serial/datatool/choiceptrstr.cpp | 4 +-
c++/src/serial/datatool/choicestr.cpp | 4 +-
c++/src/serial/datatool/classstr.cpp | 4 +-
c++/src/serial/datatool/datatool.cpp | 4 +-
c++/src/serial/datatool/datatool.hpp | 7 +-
c++/src/serial/datatool/fileutil.cpp | 5 +-
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c++/src/serial/datatool/statictype.cpp | 16 +-
c++/src/serial/datatool/statictype.hpp | 7 +-
c++/src/serial/datatool/stdstr.cpp | 9 +-
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c++/src/serial/datatool/typestr.cpp | 9 +-
c++/src/serial/datatool/typestr.hpp | 8 +-
c++/src/serial/enumerated.cpp | 4 +-
c++/src/serial/exception.cpp | 4 +-
c++/src/serial/member.cpp | 6 +-
c++/src/serial/memberid.cpp | 8 +-
c++/src/serial/objectio.cpp | 15 +-
c++/src/serial/objhook.cpp | 41 +-
c++/src/serial/objistr.cpp | 12 +-
c++/src/serial/objistrasn.cpp | 22 +-
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c++/src/serial/objistrjson.cpp | 44 +-
c++/src/serial/objistrxml.cpp | 22 +-
c++/src/serial/objostr.cpp | 24 +-
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c++/src/serial/objostrasnb.cpp | 25 +-
c++/src/serial/objostrjson.cpp | 16 +-
c++/src/serial/objostrxml.cpp | 43 +-
c++/src/serial/objstack.cpp | 4 +-
c++/src/serial/rpcbase.cpp | 5 +-
c++/src/serial/serialobject.cpp | 4 +-
c++/src/serial/stdtypes.cpp | 57 +-
c++/src/serial/typeinfo.cpp | 5 +-
c++/src/util/Makefile.util.lib | 4 +-
c++/src/util/bytesrc.cpp | 10 +-
c++/src/util/compress/api/archive_zip.cpp | 4 +-
c++/src/util/compress/api/stream.cpp | 10 +-
c++/src/util/compress/api/stream_util.cpp | 18 +-
c++/src/util/compress/api/streambuf.cpp | 56 +-
c++/src/util/compress/api/zlib.cpp | 4 +-
c++/src/util/compress/bzip2/CHANGES | 74 +
c++/src/util/compress/bzip2/LICENSE | 13 +-
c++/src/util/compress/bzip2/README | 126 +-
.../compress/bzip2/README.COMPILATION.PROBLEMS | 130 +-
c++/src/util/compress/bzip2/README.XML.STUFF | 45 +
c++/src/util/compress/bzip2/Y2K_INFO | 34 -
c++/src/util/compress/bzip2/blocksort.c | 77 +-
c++/src/util/compress/bzip2/bzdiff | 4 +-
c++/src/util/compress/bzip2/bzgrep | 6 +-
c++/src/util/compress/bzip2/bzip.css | 74 +
c++/src/util/compress/bzip2/bzip2.1 | 17 +-
c++/src/util/compress/bzip2/bzip2.1.preformatted | 398 -
c++/src/util/compress/bzip2/bzip2.c | 219 +-
c++/src/util/compress/bzip2/bzip2.txt | 119 +-
c++/src/util/compress/bzip2/bzip2recover.c | 90 +-
c++/src/util/compress/bzip2/bzlib.c | 151 +-
c++/src/util/compress/bzip2/bzlib_private.h | 98 +-
c++/src/util/compress/bzip2/compress.c | 98 +-
c++/src/util/compress/bzip2/crctable.c | 60 +-
c++/src/util/compress/bzip2/decompress.c | 102 +-
c++/src/util/compress/bzip2/dlltest.c | 5 +-
c++/src/util/compress/bzip2/huffman.c | 85 +-
c++/src/util/compress/bzip2/manual.html | 2657 ++-
c++/src/util/compress/bzip2/manual.pdf | Bin 298267 -> 256905 bytes
c++/src/util/compress/bzip2/manual.texi | 2243 ---
c++/src/util/compress/bzip2/manual.xml | 2964 ++++
c++/src/util/compress/bzip2/manual_1.html | 81 -
c++/src/util/compress/bzip2/manual_2.html | 579 -
c++/src/util/compress/bzip2/manual_3.html | 1855 --
c++/src/util/compress/bzip2/manual_4.html | 530 -
c++/src/util/compress/bzip2/manual_abt.html | 201 -
c++/src/util/compress/bzip2/manual_ovr.html | 54 -
c++/src/util/compress/bzip2/manual_toc.html | 163 -
c++/src/util/compress/bzip2/mk251.c | 15 +
c++/src/util/compress/bzip2/ncbi_bz2_compress.c | 706 +-
c++/src/util/compress/bzip2/randtable.c | 60 +-
c++/src/util/compress/bzip2/spewG.c | 15 +
c++/src/util/compress/bzip2/unzcrash.c | 17 +-
c++/src/util/file_manifest.cpp | 2 +-
c++/src/util/format_guess.cpp | 485 +-
c++/src/util/retry_ctx.cpp | 2 +-
c++/src/util/scheduler.cpp | 10 +-
c++/src/util/sequtil/sequtil_convert_imp.cpp | 10 +-
c++/src/util/sequtil/sequtil_convert_imp.hpp | 2 +-
c++/src/util/strbuffer.cpp | 11 +-
c++/src/util/stream_source.cpp | 2 +-
c++/src/util/table_printer.cpp | 6 +-
c++/src/util/tables/raw_scoremat.c | 9 +-
c++/src/util/thread_pool.cpp | 2 +-
1300 files changed, 88187 insertions(+), 31801 deletions(-)
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