385a79042f
Support for new BLAST database format Increased makeblastdb output file size limit to 4GB Other minor bug fixes and enhancements OK wiz@
4188 lines
218 KiB
Text
4188 lines
218 KiB
Text
@comment $NetBSD: PLIST,v 1.2 2019/01/07 15:00:10 bacon Exp $
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bin/blast_formatter
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bin/blastdb_aliastool
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bin/blastdb_convert
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bin/blastdbcheck
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bin/blastdbcmd
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bin/blastdbcp
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bin/blastn
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bin/blastp
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bin/blastx
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bin/convert2blastmask
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bin/datatool
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bin/deltablast
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bin/dustmasker
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bin/gc_cli
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bin/gene_info_reader
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bin/get_species_taxids.sh
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bin/legacy_blast.pl
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bin/lmdbxx_sample
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bin/makeblastdb
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bin/makembindex
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bin/makeprofiledb
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bin/project_tree_builder
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bin/psiblast
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bin/rpsblast
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bin/rpstblastn
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bin/run_with_lock
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bin/seedtop
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bin/segmasker
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bin/seqdb_demo
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bin/seqdb_perf
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bin/tblastn
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bin/tblastx
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bin/update_blastdb.pl
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bin/windowmasker
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bin/windowmasker_2.2.22_adapter.py
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include/ncbi-tools++/algo/blast/api/bl2seq.hpp
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include/ncbi-tools++/algo/blast/api/blast_advprot_options.hpp
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include/ncbi-tools++/algo/blast/api/blast_aux.hpp
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include/ncbi-tools++/algo/blast/api/blast_dbindex.hpp
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include/ncbi-tools++/algo/blast/api/blast_exception.hpp
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include/ncbi-tools++/algo/blast/api/blast_mtlock.hpp
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include/ncbi-tools++/algo/blast/api/blast_nucl_options.hpp
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include/ncbi-tools++/algo/blast/api/blast_options.hpp
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include/ncbi-tools++/algo/blast/api/blast_options_builder.hpp
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include/ncbi-tools++/algo/blast/api/blast_options_handle.hpp
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include/ncbi-tools++/algo/blast/api/blast_prot_options.hpp
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include/ncbi-tools++/algo/blast/api/blast_results.hpp
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include/ncbi-tools++/algo/blast/api/blast_rps_options.hpp
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include/ncbi-tools++/algo/blast/api/blast_seqinfosrc.hpp
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include/ncbi-tools++/algo/blast/api/blast_seqinfosrc_aux.hpp
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include/ncbi-tools++/algo/blast/api/blast_types.hpp
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include/ncbi-tools++/algo/blast/api/blastp_kmer_options.hpp
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include/ncbi-tools++/algo/blast/api/blastx_options.hpp
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include/ncbi-tools++/algo/blast/api/cdd_pssm_input.hpp
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include/ncbi-tools++/algo/blast/api/deltablast.hpp
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include/ncbi-tools++/algo/blast/api/deltablast_options.hpp
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include/ncbi-tools++/algo/blast/api/disc_nucl_options.hpp
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include/ncbi-tools++/algo/blast/api/effsearchspace_calc.hpp
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include/ncbi-tools++/algo/blast/api/hspstream_queue.hpp
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include/ncbi-tools++/algo/blast/api/local_blast.hpp
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include/ncbi-tools++/algo/blast/api/local_db_adapter.hpp
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include/ncbi-tools++/algo/blast/api/local_search.hpp
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include/ncbi-tools++/algo/blast/api/magicblast.hpp
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include/ncbi-tools++/algo/blast/api/magicblast_options.hpp
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include/ncbi-tools++/algo/blast/api/msa_pssm_input.hpp
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include/ncbi-tools++/algo/blast/api/objmgr_query_data.hpp
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include/ncbi-tools++/algo/blast/api/objmgrfree_query_data.hpp
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include/ncbi-tools++/algo/blast/api/phiblast_nucl_options.hpp
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include/ncbi-tools++/algo/blast/api/phiblast_prot_options.hpp
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include/ncbi-tools++/algo/blast/api/prelim_stage.hpp
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include/ncbi-tools++/algo/blast/api/psi_pssm_input.hpp
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include/ncbi-tools++/algo/blast/api/psibl2seq.hpp
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include/ncbi-tools++/algo/blast/api/psiblast.hpp
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include/ncbi-tools++/algo/blast/api/psiblast_iteration.hpp
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include/ncbi-tools++/algo/blast/api/psiblast_options.hpp
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include/ncbi-tools++/algo/blast/api/pssm_engine.hpp
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include/ncbi-tools++/algo/blast/api/pssm_input.hpp
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include/ncbi-tools++/algo/blast/api/query_data.hpp
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include/ncbi-tools++/algo/blast/api/remote_blast.hpp
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include/ncbi-tools++/algo/blast/api/remote_search.hpp
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include/ncbi-tools++/algo/blast/api/repeats_filter.hpp
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include/ncbi-tools++/algo/blast/api/rps_aux.hpp
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include/ncbi-tools++/algo/blast/api/rpsblast_local.hpp
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include/ncbi-tools++/algo/blast/api/rpstblastn_options.hpp
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include/ncbi-tools++/algo/blast/api/search_strategy.hpp
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include/ncbi-tools++/algo/blast/api/seedtop.hpp
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include/ncbi-tools++/algo/blast/api/seqinfosrc_seqdb.hpp
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include/ncbi-tools++/algo/blast/api/seqinfosrc_seqvec.hpp
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include/ncbi-tools++/algo/blast/api/seqsrc_multiseq.hpp
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include/ncbi-tools++/algo/blast/api/seqsrc_seqdb.hpp
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include/ncbi-tools++/algo/blast/api/setup_factory.hpp
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include/ncbi-tools++/algo/blast/api/sseqloc.hpp
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include/ncbi-tools++/algo/blast/api/subj_ranges_set.hpp
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include/ncbi-tools++/algo/blast/api/tblastn_options.hpp
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include/ncbi-tools++/algo/blast/api/tblastx_options.hpp
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include/ncbi-tools++/algo/blast/api/traceback_stage.hpp
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include/ncbi-tools++/algo/blast/api/uniform_search.hpp
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include/ncbi-tools++/algo/blast/api/version.hpp
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include/ncbi-tools++/algo/blast/api/windowmask_filter.hpp
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include/ncbi-tools++/algo/blast/blastinput/blast_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/blast_asn1_input.hpp
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include/ncbi-tools++/algo/blast/blastinput/blast_fasta_input.hpp
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include/ncbi-tools++/algo/blast/blastinput/blast_input.hpp
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include/ncbi-tools++/algo/blast/blastinput/blast_input_aux.hpp
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include/ncbi-tools++/algo/blast/blastinput/blast_scope_src.hpp
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include/ncbi-tools++/algo/blast/blastinput/blastn_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/blastp_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/blastx_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/cmdline_flags.hpp
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include/ncbi-tools++/algo/blast/blastinput/deltablast_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/igblastn_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/igblastp_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/kblastp_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/magicblast_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/psiblast_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/rmblastn_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/rpsblast_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/rpstblastn_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/tblastn_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/tblastx_args.hpp
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include/ncbi-tools++/algo/blast/composition_adjustment/compo_heap.h
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include/ncbi-tools++/algo/blast/composition_adjustment/compo_mode_condition.h
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include/ncbi-tools++/algo/blast/composition_adjustment/redo_alignment.h
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include/ncbi-tools++/algo/blast/composition_adjustment/smith_waterman.h
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include/ncbi-tools++/algo/blast/core/aa_ungapped.h
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include/ncbi-tools++/algo/blast/core/blast_aalookup.h
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include/ncbi-tools++/algo/blast/core/blast_aascan.h
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include/ncbi-tools++/algo/blast/core/blast_def.h
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include/ncbi-tools++/algo/blast/core/blast_diagnostics.h
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include/ncbi-tools++/algo/blast/core/blast_encoding.h
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include/ncbi-tools++/algo/blast/core/blast_gapalign.h
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include/ncbi-tools++/algo/blast/core/blast_hits.h
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include/ncbi-tools++/algo/blast/core/blast_message.h
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include/ncbi-tools++/algo/blast/core/blast_nalookup.h
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include/ncbi-tools++/algo/blast/core/blast_nascan.h
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include/ncbi-tools++/algo/blast/core/blast_options.h
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include/ncbi-tools++/algo/blast/core/blast_parameters.h
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include/ncbi-tools++/algo/blast/core/blast_program.h
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include/ncbi-tools++/algo/blast/core/blast_psi.h
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include/ncbi-tools++/algo/blast/core/blast_query_info.h
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include/ncbi-tools++/algo/blast/core/blast_rps.h
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include/ncbi-tools++/algo/blast/core/blast_seg.h
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include/ncbi-tools++/algo/blast/core/blast_seqsrc.h
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include/ncbi-tools++/algo/blast/core/blast_seqsrc_impl.h
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include/ncbi-tools++/algo/blast/core/blast_setup.h
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include/ncbi-tools++/algo/blast/core/blast_stat.h
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include/ncbi-tools++/algo/blast/core/blast_sw.h
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include/ncbi-tools++/algo/blast/core/blast_toolkit.h
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include/ncbi-tools++/algo/blast/core/blast_traceback.h
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include/ncbi-tools++/algo/blast/core/blast_tune.h
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include/ncbi-tools++/algo/blast/core/blast_util.h
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include/ncbi-tools++/algo/blast/core/gapinfo.h
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include/ncbi-tools++/algo/blast/core/gencode_singleton.h
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include/ncbi-tools++/algo/blast/core/greedy_align.h
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include/ncbi-tools++/algo/blast/core/hspfilter_besthit.h
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include/ncbi-tools++/algo/blast/core/hspfilter_collector.h
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include/ncbi-tools++/algo/blast/core/hspfilter_culling.h
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include/ncbi-tools++/algo/blast/core/hspfilter_mapper.h
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include/ncbi-tools++/algo/blast/core/link_hsps.h
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include/ncbi-tools++/algo/blast/core/lookup_util.h
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include/ncbi-tools++/algo/blast/core/lookup_wrap.h
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include/ncbi-tools++/algo/blast/core/mb_indexed_lookup.h
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include/ncbi-tools++/algo/blast/core/na_ungapped.h
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include/ncbi-tools++/algo/blast/core/ncbi_math.h
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include/ncbi-tools++/algo/blast/core/ncbi_std.h
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include/ncbi-tools++/algo/blast/core/pattern.h
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include/ncbi-tools++/algo/blast/core/phi_extend.h
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include/ncbi-tools++/algo/blast/core/phi_gapalign.h
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include/ncbi-tools++/algo/blast/core/phi_lookup.h
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include/ncbi-tools++/algo/blast/core/spliced_hits.h
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include/ncbi-tools++/algo/blast/core/split_query.h
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include/ncbi-tools++/algo/blast/dbindex/dbindex.hpp
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include/ncbi-tools++/algo/blast/dbindex/dbindex_sp.hpp
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include/ncbi-tools++/algo/blast/dbindex/sequence_istream.hpp
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include/ncbi-tools++/algo/blast/dbindex/sequence_istream_bdb.hpp
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include/ncbi-tools++/algo/blast/dbindex/sequence_istream_fasta.hpp
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include/ncbi-tools++/algo/blast/format/blast_async_format.hpp
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include/ncbi-tools++/algo/blast/format/blast_format.hpp
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include/ncbi-tools++/algo/blast/format/blastxml2_format.hpp
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include/ncbi-tools++/algo/blast/format/blastxml_format.hpp
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include/ncbi-tools++/algo/blast/format/build_archive.hpp
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include/ncbi-tools++/algo/blast/format/data4xml2format.hpp
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include/ncbi-tools++/algo/blast/format/sam.hpp
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include/ncbi-tools++/algo/blast/format/vecscreen_run.hpp
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include/ncbi-tools++/algo/blast/igblast/igblast.hpp
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include/ncbi-tools++/algo/blast/proteinkmer/blastkmer.hpp
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include/ncbi-tools++/algo/blast/proteinkmer/blastkmerindex.hpp
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include/ncbi-tools++/algo/blast/proteinkmer/blastkmerresults.hpp
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include/ncbi-tools++/algo/blast/proteinkmer/mhfile.hpp
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include/ncbi-tools++/algo/segmask/segmask.hpp
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include/ncbi-tools++/algo/winmask/README.API
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include/ncbi-tools++/algo/winmask/seq_masker_cache_boost.hpp
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