[med-svn] [ncbi-blast+] 02/03: Updated version 2.6.0 from 'upstream/2.6.0'
Olivier Sallou
osallou at debian.org
Sun Jan 15 17:29:29 UTC 2017
This is an automated email from the git hooks/post-receive script.
osallou pushed a commit to branch master
in repository ncbi-blast+.
commit 667fb2225817990665e137caf98f1b924db3d67c
Merge: 43a0f40 edfc131
Author: Olivier Sallou <osallou at debian.org>
Date: Sun Jan 15 17:12:12 2017 +0000
Updated version 2.6.0 from 'upstream/2.6.0'
with Debian dir e42d5a2a50d036aecd1289ba1e5ef2e49790dfa4
.../algo/blast/api/blast_seqinfosrc_aux.hpp | 19 +-
c++/include/algo/blast/blastinput/blast_args.hpp | 51 +-
.../algo/blast/blastinput/blast_scope_src.hpp | 6 +-
.../algo/blast/blastinput/cmdline_flags.hpp | 21 +-
.../algo/blast/blastinput/kblastp_args.hpp} | 67 +-
c++/include/algo/blast/core/blast_query_info.h | 19 +-
c++/include/algo/blast/format/blast_format.hpp | 5 +-
c++/include/algo/blast/igblast/igblast.hpp | 7 +-
c++/include/cgi/user_agent.hpp | 6 +-
c++/include/common/ncbi_package_ver.h | 2 +-
c++/include/connect/ncbi_connutil.h | 26 +-
c++/include/connect/ncbi_http_session.hpp | 24 +-
c++/include/connect/services/netcache_search.hpp | 169 ++
c++/include/connect/services/neticache_client.hpp | 22 +-
c++/include/corelib/ncbi_cookies.hpp | 13 +-
c++/include/corelib/ncbiapp.hpp | 10 +-
c++/include/corelib/ncbidiag.hpp | 4 +-
c++/include/corelib/ncbifile.hpp | 61 +-
.../dbapi/driver/impl/dbapi_impl_context.hpp | 8 +-
c++/include/dbapi/error_codes.hpp | 4 +-
c++/include/ncbi_pch.hpp | 2 +-
c++/include/ncbi_source_ver.h | 2 +-
c++/include/ncbiconf.h | 2 +-
.../objects/genomecoll/genomic_collections_cli.hpp | 7 +-
c++/include/objects/macro/Suspect_rule.hpp | 30 +-
c++/include/objects/seq/Seq_inst.hpp | 4 +-
c++/include/objects/seqfeat/Gb_qual.hpp | 6 +-
c++/include/objects/seqfeat/OrgMod.hpp | 4 +-
c++/include/objects/seqfeat/SeqFeatData.hpp | 3 +-
c++/include/objects/seqfeat/Seq_feat.hpp | 6 +-
c++/include/objects/seqset/Bioseq_set.hpp | 5 +-
c++/include/objects/trackmgr/gridrpcclient.hpp | 4 +-
c++/include/objects/valerr/ValidErrItem.hpp | 16 +-
c++/include/objects/valerr/ValidError.hpp | 6 +-
c++/include/objmgr/annot_selector.hpp | 18 +-
c++/include/objmgr/annot_types_ci.hpp | 5 +-
c++/include/objmgr/impl/annot_collector.hpp | 7 +-
c++/include/objmgr/impl/annot_object_index.hpp | 8 +-
c++/include/objmgr/impl/seq_entry_info.hpp | 43 +-
c++/include/objmgr/impl/seq_table_setters.hpp | 10 +-
c++/include/objmgr/impl/seq_vector_cvt_gen.hpp | 26 +-
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/seq_vector_ci.hpp | 11 +-
c++/include/objmgr/split/size.hpp | 4 +-
c++/include/objmgr/util/obj_sniff.hpp | 23 +-
c++/include/objmgr/util/sequence.hpp | 46 +-
.../objtools/align_format/align_format_util.hpp | 3 +-
c++/include/objtools/align_format/format_flags.hpp | 5 +-
c++/include/objtools/align_format/showalign.hpp | 5 +-
c++/include/objtools/align_format/showdefline.hpp | 5 +-
c++/include/objtools/alnmgr/sparse_aln.hpp | 29 +-
.../blast/blastdb_format/blastdb_dataextract.hpp | 87 +-
.../blast/blastdb_format/seq_formatter.hpp | 197 ++
.../objtools/blast/blastdb_format/seq_writer.hpp | 6 +-
.../blast/seqdb_reader/impl/seqdbatlas.hpp | 16 +-
.../blast/seqdb_reader/impl/seqdbgeneral.hpp | 13 +-
c++/include/objtools/blast/seqdb_reader/seqdb.hpp | 5 +-
.../objtools/blast/seqdb_writer/build_db.hpp | 15 +-
.../objtools/blast/seqdb_writer/writedb.hpp | 10 +-
c++/include/objtools/cleanup/cleanup.hpp | 53 +-
c++/include/objtools/cleanup/cleanup_change.hpp | 3 +-
.../objtools/edit/autodef_feature_clause.hpp | 5 +-
.../objtools/edit/autodef_feature_clause_base.hpp | 38 +-
c++/include/objtools/edit/mail_report.hpp | 4 +-
c++/include/objtools/edit/string_constraint.hpp | 4 +-
.../objtools/format/items/flat_qual_slots.hpp | 3 +-
c++/include/objtools/readers/bed_reader.hpp | 22 +-
c++/include/objtools/readers/fasta.hpp | 71 +-
c++/include/objtools/readers/gff2_reader.hpp | 96 +-
c++/include/objtools/readers/gff3_sofa.hpp | 15 +-
c++/include/objtools/readers/gvf_reader.hpp | 19 +-
c++/include/objtools/readers/microarray_reader.hpp | 8 +-
c++/include/objtools/readers/reader_base.hpp | 11 +-
c++/include/objtools/readers/struct_cmt_reader.hpp | 96 +
c++/include/objtools/readers/track_data.hpp | 4 +-
c++/include/serial/impl/enumerated.hpp | 14 +-
c++/include/serial/rpcbase.hpp | 12 +-
c++/include/util/bitset/bm.h | 94 +-
c++/include/util/bitset/bmblocks.h | 20 +-
c++/include/util/bitset/bmfunc.h | 2 +-
c++/include/util/bitset/bmserial.h | 2 +-
c++/include/util/bitset/encoding.h | 4 +-
c++/include/util/format_guess.hpp | 5 +-
c++/scripts/common/add_vdb.sh | 10 +-
c++/scripts/common/impl/compress_tests.sh | 2 +-
c++/scripts/common/impl/install.sh | 2 +-
.../projects/blast/post_build/macosx/ncbi-blast.sh | 5 +-
.../projects/blast/post_build/rpm/ncbi-blast.spec | 2 +-
c++/scripts/projects/igblast/ChangeLog | 10 +
c++/scripts/projects/igblast/LICENSE | 505 ++++
c++/scripts/projects/igblast/Manifest | 7 +-
c++/scripts/projects/igblast/components.link | 16 +-
.../projects/igblast/post_build/blast_utils.py | 6 +-
.../projects/igblast/post_build/make_installers.py | 35 +-
.../projects/igblast/post_build/win/make_win.py | 11 +-
.../projects/igblast/post_build/win/ncbi-blast.nsi | 6 +
c++/scripts/projects/igblast/project.lst | 3 +
c++/scripts/projects/magicblast/ChangeLog | 9 +
c++/scripts/projects/magicblast/Manifest | 2 +-
c++/scripts/projects/magicblast/README | 3 -
c++/scripts/projects/ncbi_applog/ChangeLog | 6 +-
c++/scripts/projects/ncbi_applog/Manifest | 5 +-
c++/scripts/projects/ncbi_applog/project.lst | 2 +
c++/scripts/projects/netcache/ChangeLog | 29 +
c++/scripts/projects/netschedule/ChangeLog | 39 +
c++/scripts/projects/netschedule/Manifest | 9 +-
c++/scripts/projects/netstorage/Manifest | 4 +-
c++/scripts/projects/public/Manifest | 31 +-
c++/scripts/projects/public/components.link | 23 +-
c++/scripts/projects/python_ncbi_dbapi/ChangeLog | 8 +
.../projects/python_ncbi_dbapi/components.link | 6 +-
c++/scripts/projects/testres-kernel/ChangeLog | 7 +-
c++/scripts/projects/testres-kernel/Manifest | 7 +-
.../projects/testres-kernel/components.link | 6 +-
c++/scripts/projects/testres-scheduler/ChangeLog | 3 +
c++/scripts/projects/testres-scheduler/Manifest | 6 +-
.../projects/testres-scheduler/components.link | 6 +-
c++/scripts/projects/xmlwrapp/Manifest | 4 +-
c++/src/Makefile.in | 2 +-
.../algo/blast/api/bioseq_extract_data_priv.cpp | 30 +-
.../algo/blast/api/bioseq_extract_data_priv.hpp | 8 +-
c++/src/algo/blast/api/blast_objmgr_priv.hpp | 10 +-
c++/src/algo/blast/api/blast_seqalign.cpp | 101 +-
c++/src/algo/blast/api/blast_seqalign.hpp | 6 +-
c++/src/algo/blast/api/blast_seqinfosrc_aux.cpp | 41 +-
c++/src/algo/blast/api/blast_setup.hpp | 7 +-
c++/src/algo/blast/api/blast_setup_cxx.cpp | 20 +-
c++/src/algo/blast/api/prelim_search_runner.hpp | 19 +-
.../algo/blast/blastinput/Makefile.blastinput.lib | 3 +-
c++/src/algo/blast/blastinput/blast_args.cpp | 51 +-
c++/src/algo/blast/blastinput/blast_asn1_input.cpp | 82 +-
.../algo/blast/blastinput/blast_fasta_input.cpp | 175 +-
c++/src/algo/blast/blastinput/blast_scope_src.cpp | 25 +-
c++/src/algo/blast/blastinput/cmdline_flags.cpp | 12 +-
c++/src/algo/blast/blastinput/igblastn_args.cpp | 4 +-
c++/src/algo/blast/blastinput/kblastp_args.cpp | 105 +
c++/src/algo/blast/blastinput/magicblast_args.cpp | 4 +-
c++/src/algo/blast/blastinput/psiblast_args.cpp | 4 +-
.../unit_test/blast_input_unit_test_aux.hpp | 37 +-
.../unit_test/blast_scope_src_unit_test.cpp | 14 +-
.../blastinput/unit_test/blastinput_unit_test.cpp | 306 ++-
.../blastinput/unit_test/data/paired_reads.asn | 84 +
.../blastinput/unit_test/data/paired_reads.fa | 12 +
.../blastinput/unit_test/data/paired_reads.fastq | 24 +
.../blastinput/unit_test/data/paired_reads_1.asn | 42 +
.../blastinput/unit_test/data/paired_reads_1.fa | 6 +
.../blastinput/unit_test/data/paired_reads_1.fastq | 12 +
.../blastinput/unit_test/data/paired_reads_2.asn | 42 +
.../blastinput/unit_test/data/paired_reads_2.fa | 6 +
.../blastinput/unit_test/data/paired_reads_2.fastq | 12 +
.../blast/composition_adjustment/redo_alignment.c | 13 +-
c++/src/algo/blast/core/blast_engine.c | 6 +-
c++/src/algo/blast/core/blast_gapalign.c | 13 +-
c++/src/algo/blast/core/blast_hits.c | 15 +-
c++/src/algo/blast/core/blast_kappa.c | 610 ++---
c++/src/algo/blast/core/blast_query_info.c | 6 +-
c++/src/algo/blast/core/blast_util.c | 7 +-
c++/src/algo/blast/core/hspfilter_mapper.c | 19 +-
c++/src/algo/blast/format/blast_format.cpp | 32 +
c++/src/algo/blast/format/sam.cpp | 3 +
c++/src/algo/blast/igblast/igblast.cpp | 70 +-
.../blast/unit_tests/api/blasthits_unit_test.cpp | 21 +-
.../unit_tests/api/data/magicblast_paired.asn | 13 +-
.../blast/unit_tests/api/magicblast_unit_test.cpp | 12 +-
.../blast/unit_tests/api/magicblast_unit_test.ini | 5 +-
.../blast/unit_tests/api/traceback_unit_test.cpp | 6 +-
.../unit_tests/api/tracebacksearch_unit_test.cpp | 103 +-
.../unit_tests/api/version_reference_unit_test.cpp | 4 +-
.../unit_tests/seqdb_reader/seqdb_unit_test.ini | 10 +-
c++/src/app/blastdb/blastdb_aliastool.cpp | 57 +-
c++/src/app/blastdb/blastdbcmd.cpp | 580 ++---
c++/src/app/blastdb/makeblastdb.cpp | 12 +-
c++/src/build-system/configure | 60 +-
c++/src/build-system/configure.ac | 43 +-
c++/src/build-system/helpers/run_with_lock.c | 22 +-
c++/src/build-system/install.sh.in | 2 +-
c++/src/build-system/ncbi_package_version | 2 +-
c++/src/build-system/project_tree_builder.ini | 27 +-
c++/src/build-system/relocate.sh.in | 2 +-
c++/src/cgi/user_agent.cpp | 11 +-
c++/src/connect/ncbi_comm.h | 5 +-
c++/src/connect/ncbi_conn_test.cpp | 50 +-
c++/src/connect/ncbi_connutil.c | 49 +-
c++/src/connect/ncbi_dispd.c | 4 +-
c++/src/connect/ncbi_gnutls.c | 4 +-
c++/src/connect/ncbi_http_session.cpp | 184 +-
c++/src/connect/ncbi_service.c | 22 +-
c++/src/connect/ncbi_service_connector.c | 13 +-
c++/src/connect/ncbi_socket.c | 52 +-
c++/src/connect/services/Makefile.xconnserv.lib | 4 +-
c++/src/connect/services/grid_worker_impl.hpp | 3 +-
c++/src/connect/services/netcache_api.cpp | 6 +-
c++/src/connect/services/netcache_api_impl.hpp | 16 +-
c++/src/connect/services/netcache_search.cpp | 556 +++++
c++/src/connect/services/neticache_client.cpp | 35 +-
c++/src/connect/services/netschedule_api.cpp | 134 +-
.../connect/services/netschedule_api_executor.cpp | 97 +-
.../connect/services/netschedule_api_getjob.cpp | 55 +-
.../connect/services/netschedule_api_getjob.hpp | 6 +-
c++/src/connect/services/netschedule_api_impl.hpp | 35 +-
.../connect/services/netschedule_api_reader.cpp | 14 +-
c++/src/connect/services/netstorageobjectinfo.cpp | 19 +-
c++/src/connect/services/wn_main_loop.cpp | 5 +-
c++/src/corelib/ncbi_cookies.cpp | 16 +-
c++/src/corelib/ncbi_url.cpp | 4 +-
c++/src/corelib/ncbiapp.cpp | 121 +-
c++/src/corelib/ncbidiag.cpp | 11 +-
c++/src/corelib/ncbifile.cpp | 36 +-
c++/src/corelib/test_boost.cpp | 47 +-
c++/src/dbapi/driver/dbapi_driver_conn_params.cpp | 3 +-
c++/src/dbapi/driver/dbapi_impl_context.cpp | 23 +-
c++/src/misc/CMakeLists.txt | 22 +
c++/src/misc/third_party/CMakeLists.txt | 6 +
c++/src/misc/third_party_static/CMakeLists.txt | 6 +
c++/src/objects/entrez2/entrez2.def | 2 +-
c++/src/objects/macro/Suspect_rule.cpp | 377 ++-
c++/src/objects/seq/Delta_ext.cpp | 6 +-
c++/src/objects/seq/Seq_gap.cpp | 4 +-
c++/src/objects/seq/Seq_inst.cpp | 86 +-
c++/src/objects/seq/seq_id_tree.cpp | 16 +-
c++/src/objects/seq/seq_loc_from_string.cpp | 5 +-
c++/src/objects/seq/seq_loc_mapper_base.cpp | 80 +-
c++/src/objects/seq/sofa_map.cpp | 8 +-
c++/src/objects/seqalign/Sparse_align.cpp | 7 +-
c++/src/objects/seqalign/Sparse_seg.cpp | 5 +-
c++/src/objects/seqalign/Spliced_seg.cpp | 12 +-
c++/src/objects/seqalign/Std_seg.cpp | 5 +-
c++/src/objects/seqfeat/BioSource.cpp | 8 +-
c++/src/objects/seqfeat/Delta_item.cpp | 4 +-
c++/src/objects/seqfeat/Gb_qual.cpp | 20 +-
c++/src/objects/seqfeat/Genetic_code_table.cpp | 67 +-
c++/src/objects/seqfeat/OrgMod.cpp | 11 +-
c++/src/objects/seqfeat/SeqFeatData.cpp | 441 +++-
c++/src/objects/seqfeat/Seq_feat.cpp | 28 +-
c++/src/objects/seqfeat/SubSource.cpp | 122 +-
c++/src/objects/seqfeat/Trna_ext.cpp | 6 +-
c++/src/objects/seqfeat/Variation_ref.cpp | 4 +-
c++/src/objects/seqfeat/ecnum_specific.inc | 19 +-
c++/src/objects/seqfeat/ecnum_specific.txt | 17 +-
c++/src/objects/seqfeat/institution_codes.inc | 419 +++-
c++/src/objects/seqfeat/institution_codes.txt | 417 +++-
c++/src/objects/seqfeat/lat_lon_country.inc | 12 +-
c++/src/objects/seqfeat/lat_lon_country.txt | 282 +--
c++/src/objects/seqloc/Seq_id.cpp | 2 +-
c++/src/objects/seqloc/Seq_loc.cpp | 15 +-
c++/src/objects/seqloc/accguide.inc | 48 +-
c++/src/objects/seqloc/accguide.txt | 46 +-
c++/src/objects/seqset/Bioseq_set.cpp | 26 +-
c++/src/objects/valerr/ValidErrItem.cpp | 1420 +++++------
c++/src/objects/valerr/ValidError.cpp | 19 +-
c++/src/objects/valid/validrules.inc | 9 +-
c++/src/objects/valid/validrules.prt | 7 +-
c++/src/objmgr/annot_collector.cpp | 41 +-
c++/src/objmgr/annot_object_index.cpp | 4 +-
c++/src/objmgr/annot_selector.cpp | 6 +-
c++/src/objmgr/annot_types_ci.cpp | 8 +-
c++/src/objmgr/bioseq_info.cpp | 10 +-
c++/src/objmgr/edits_db_saver.cpp | 282 ++-
c++/src/objmgr/gc_assembly_parser.cpp | 6 +-
c++/src/objmgr/prefetch_actions.cpp | 4 +-
c++/src/objmgr/scope_impl.cpp | 12 +-
c++/src/objmgr/scope_info.cpp | 15 +-
c++/src/objmgr/seq_annot_info.cpp | 24 +-
c++/src/objmgr/seq_entry_info.cpp | 58 +-
c++/src/objmgr/seq_loc_mapper.cpp | 6 +-
c++/src/objmgr/seq_map.cpp | 12 +-
c++/src/objmgr/seq_map_ci.cpp | 4 +-
c++/src/objmgr/seq_map_switch.cpp | 14 +-
c++/src/objmgr/seq_table_info.cpp | 16 +-
c++/src/objmgr/seq_table_setters.cpp | 28 +-
c++/src/objmgr/seq_vector.cpp | 22 +-
c++/src/objmgr/snp_annot_info.cpp | 12 +-
c++/src/objmgr/split/annot_piece.cpp | 4 +-
c++/src/objmgr/split/blob_splitter_impl.cpp | 5 +-
c++/src/objmgr/split/blob_splitter_maker.cpp | 20 +-
c++/src/objmgr/split/id_range.cpp | 12 +-
c++/src/objmgr/split/object_splitinfo.cpp | 4 +-
c++/src/objmgr/split/size.cpp | 8 +-
c++/src/objmgr/split_parser.cpp | 8 +-
c++/src/objmgr/tse_handle.cpp | 4 +-
c++/src/objmgr/tse_info.cpp | 14 +-
c++/src/objmgr/tse_split_info.cpp | 11 +-
c++/src/objmgr/unsupp_editsaver.cpp | 6 +-
c++/src/objmgr/util/create_defline.cpp | 33 +-
c++/src/objmgr/util/feature.cpp | 31 +-
c++/src/objmgr/util/obj_sniff.cpp | 75 +-
c++/src/objmgr/util/objutil.cpp | 11 +-
c++/src/objmgr/util/seq_loc_util.cpp | 20 +-
c++/src/objmgr/util/seqtitle.cpp | 6 +-
c++/src/objmgr/util/sequence.cpp | 272 ++-
c++/src/objmgr/util/weight.cpp | 6 +-
.../objtools/align_format/align_format_util.cpp | 55 +-
c++/src/objtools/align_format/format_flags.cpp | 11 +-
c++/src/objtools/align_format/showalign.cpp | 37 +-
c++/src/objtools/align_format/showdefline.cpp | 16 +-
c++/src/objtools/align_format/tabular.cpp | 14 +-
.../data/in_showalign_use_this_gi_ext.asn | 1073 ++++++++
.../align_format/unit_test/showalign_unit_test.cpp | 82 +-
.../unit_test/tabularinof_unit_test.cpp | 6 +-
c++/src/objtools/alnmgr/alnvec.cpp | 5 +-
c++/src/objtools/alnmgr/sparse_aln.cpp | 23 +-
.../blastdb_format/Makefile.blastdb_format.lib | 4 +-
.../blast/blastdb_format/blastdb_dataextract.cpp | 376 ++-
.../blast/blastdb_format/seq_formatter.cpp | 543 +++++
.../objtools/blast/blastdb_format/seq_writer.cpp | 73 +-
.../Makefile.blastdb_format_unit_test.app | 6 +-
.../unit_test/seq_formatter_unit_test.cpp | 386 +++
c++/src/objtools/blast/seqdb_reader/seqdb.cpp | 11 +-
.../objtools/blast/seqdb_reader/seqdbcommon.cpp | 24 +-
c++/src/objtools/blast/seqdb_reader/seqdbimpl.cpp | 46 +-
c++/src/objtools/blast/seqdb_reader/seqdbvol.cpp | 11 +-
.../objtools/blast/seqdb_writer/build-alias-index | 2 +-
c++/src/objtools/blast/seqdb_writer/build_db.cpp | 39 +-
.../seqdb_writer/unit_test/writedb_unit_test.cpp | 88 +-
c++/src/objtools/blast/seqdb_writer/writedb.cpp | 9 +-
.../objtools/blast/seqdb_writer/writedb_impl.cpp | 47 +-
.../objtools/blast/seqdb_writer/writedb_impl.hpp | 20 +-
c++/src/objtools/cleanup/Makefile.cleanup.lib | 4 +-
c++/src/objtools/cleanup/autogenerated_cleanup.cpp | 309 +--
c++/src/objtools/cleanup/autogenerated_cleanup.hpp | 43 +-
c++/src/objtools/cleanup/autogenerated_cleanup.txt | 2 +-
.../cleanup/autogenerated_extended_cleanup.cpp | 3 +-
.../cleanup/autogenerated_extended_cleanup.txt | 2 -
c++/src/objtools/cleanup/cleanup.cpp | 545 +++--
c++/src/objtools/cleanup/cleanup_utils.cpp | 3 +-
c++/src/objtools/cleanup/newcleanupp.cpp | 95 +-
.../data_loaders/genbank/gicache/Makefile.in | 4 +-
.../gicache/Makefile.ncbi_xreader_gicache.lib | 7 +-
.../data_loaders/genbank/gicache/gicache.c | 2572 +++++++-------------
.../data_loaders/genbank/gicache/gicache.h | 61 +-
.../data_loaders/genbank/gicache/gicache_cxx.cpp | 38 -
.../genbank/gicache/reader_gicache.cpp | 15 +-
.../objtools/edit/autodef_available_modifier.cpp | 75 +-
c++/src/objtools/edit/autodef_feature_clause.cpp | 54 +-
.../objtools/edit/autodef_feature_clause_base.cpp | 82 +-
c++/src/objtools/edit/autodef_mod_combo.cpp | 4 +-
c++/src/objtools/edit/feattable_edit.cpp | 58 +-
c++/src/objtools/edit/gaps_edit.cpp | 4 +-
c++/src/objtools/edit/mail_report.cpp | 24 +-
c++/src/objtools/edit/rna_edit.cpp | 8 +-
c++/src/objtools/edit/seq_entry_edit.cpp | 13 +-
c++/src/objtools/edit/string_constraint.cpp | 66 +-
c++/src/objtools/format/context.cpp | 4 +-
c++/src/objtools/format/feature_item.cpp | 17 +-
c++/src/objtools/format/flat_qual_slots.cpp | 3 +-
c++/src/objtools/format/gather_items.cpp | 116 +-
c++/src/objtools/format/locus_item.cpp | 4 +-
c++/src/objtools/readers/Makefile.xobjread.lib | 6 +-
c++/src/objtools/readers/bed_reader.cpp | 160 +-
c++/src/objtools/readers/fasta.cpp | 304 ++-
c++/src/objtools/readers/gff2_data.cpp | 22 +-
c++/src/objtools/readers/gff2_reader.cpp | 784 +++++-
c++/src/objtools/readers/gff3_reader.cpp | 8 +-
c++/src/objtools/readers/gff3_sofa.cpp | 34 +-
c++/src/objtools/readers/gtf_reader.cpp | 4 +-
c++/src/objtools/readers/gvf_reader.cpp | 130 +-
c++/src/objtools/readers/microarray_reader.cpp | 50 +-
c++/src/objtools/readers/reader_base.cpp | 48 +-
c++/src/objtools/readers/readfeat.cpp | 137 +-
c++/src/objtools/readers/source_mod_parser.cpp | 10 +-
c++/src/objtools/readers/struct_cmt_reader.cpp | 130 +
c++/src/objtools/readers/track_data.cpp | 44 +-
c++/src/serial/datatool/dtdaux.cpp | 4 +-
c++/src/serial/datatool/dtdparser.cpp | 14 +-
c++/src/serial/datatool/enumtype.cpp | 7 +-
c++/src/serial/datatool/exceptions.hpp | 8 +-
c++/src/serial/datatool/filecode.cpp | 4 +-
c++/src/serial/datatool/fileutil.cpp | 6 +-
c++/src/serial/datatool/module.cpp | 6 +-
c++/src/serial/datatool/srcutil.cpp | 4 +-
c++/src/serial/datatool/statictype.cpp | 4 +-
.../serial/datatool/traversal_code_generator.cpp | 18 +-
c++/src/serial/datatool/traversal_node.cpp | 14 +-
.../datatool/traversal_pattern_match_callback.cpp | 4 +-
.../serial/datatool/traversal_spec_file_parser.cpp | 7 +-
c++/src/serial/datatool/type.cpp | 12 +-
c++/src/serial/datatool/typestr.cpp | 4 +-
c++/src/serial/datatool/wsdlparser.cpp | 22 +-
c++/src/serial/datatool/wsdlstr.cpp | 8 +-
c++/src/serial/datatool/xsdlexer.cpp | 6 +-
c++/src/serial/datatool/xsdparser.cpp | 8 +-
c++/src/util/format_guess.cpp | 53 +-
384 files changed, 15297 insertions(+), 6689 deletions(-)
--
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