├── .github └── workflows │ └── ci.yaml ├── .gitignore ├── LICENSE ├── Quickstart.md ├── README.md ├── src ├── Config.cpp ├── Config.hpp ├── ConsumerThread.cpp ├── ConsumerThread.hpp ├── ConsumerThreadp.cpp ├── ConsumerThreadp.hpp ├── ConsumerThreadx.cpp ├── ConsumerThreadx.hpp ├── ReadItem.cpp ├── ReadItem.hpp ├── bwt │ ├── Makefile │ ├── bwt.c │ ├── bwt.h │ ├── common.h │ ├── compactfmi.c │ ├── compactfmi.h │ ├── fmi.h │ ├── fmicommon.h │ ├── mkbwt.c │ ├── mkbwt_vars.h │ ├── mkfmi.c │ ├── mkfmi_vars.h │ ├── multikeyqsort.c │ ├── multikeyqsort.h │ ├── readFasta.c │ ├── readFasta.h │ ├── sequence.c │ ├── sequence.h │ ├── suffixArray.c │ └── suffixArray.h ├── include │ ├── ProducerConsumerQueue │ │ └── src │ │ │ ├── ProducerConsumerQueue.hpp │ │ │ └── ProducerConsumerQueue.tpp │ ├── ncbi-blast+ │ │ ├── algo │ │ │ └── blast │ │ │ │ ├── composition_adjustment │ │ │ │ ├── composition_constants.h │ │ │ │ ├── matrix_frequency_data.c │ │ │ │ └── matrix_frequency_data.h │ │ │ │ └── core │ │ │ │ ├── blast_def.h │ │ │ │ ├── blast_dynarray.c │ │ │ │ ├── blast_dynarray.h │ │ │ │ ├── blast_encoding.c │ │ │ │ ├── blast_encoding.h │ │ │ │ ├── blast_export.h │ │ │ │ ├── blast_filter.c │ │ │ │ ├── blast_filter.h │ │ │ │ ├── blast_hits.h │ │ │ │ ├── blast_hits_priv.h │ │ │ │ ├── blast_hspfilter.h │ │ │ │ ├── blast_message.c │ │ │ │ ├── blast_message.h │ │ │ │ ├── blast_options.c │ │ │ │ ├── blast_options.h │ │ │ │ ├── blast_parameters.h │ │ │ │ ├── blast_posit.c │ │ │ │ ├── blast_posit.h │ │ │ │ ├── blast_program.c │ │ │ │ ├── blast_program.h │ │ │ │ ├── blast_psi.c │ │ │ │ ├── blast_psi.h │ │ │ │ ├── blast_psi_priv.c │ │ │ │ ├── blast_psi_priv.h │ │ │ │ ├── blast_query_info.c │ │ │ │ ├── blast_query_info.h │ │ │ │ ├── blast_rps.h │ │ │ │ ├── blast_seg.c │ │ │ │ ├── blast_seg.h │ │ │ │ ├── blast_seqsrc.h │ │ │ │ ├── blast_stat.c │ │ │ │ ├── blast_stat.h │ │ │ │ ├── blast_toolkit.h │ │ │ │ ├── blast_util.c │ │ │ │ ├── blast_util.h │ │ │ │ ├── gapinfo.h │ │ │ │ ├── hspfilter_besthit.h │ │ │ │ ├── hspfilter_collector.c │ │ │ │ ├── hspfilter_collector.h │ │ │ │ ├── lookup_wrap.h │ │ │ │ ├── matrix_freq_ratios.c │ │ │ │ ├── matrix_freq_ratios.h │ │ │ │ ├── ncbi_erf.c │ │ │ │ ├── ncbi_math.c │ │ │ │ ├── ncbi_math.h │ │ │ │ ├── ncbi_std.c │ │ │ │ ├── ncbi_std.h │ │ │ │ ├── pattern.c │ │ │ │ ├── pattern.h │ │ │ │ └── pattern_priv.h │ │ ├── common │ │ │ ├── ncbi_skew_guard.h │ │ │ └── ncbiconf_impl.h │ │ ├── connect │ │ │ ├── connect_export.h │ │ │ ├── ncbi_core.h │ │ │ └── ncbi_types.h │ │ ├── corelib │ │ │ ├── ncbitype.h │ │ │ └── ncbitype.h.dmnd │ │ ├── ncbiconf.h │ │ ├── ncbiconf_unix.h │ │ └── util │ │ │ └── tables │ │ │ ├── raw_scoremat.c │ │ │ ├── raw_scoremat.h │ │ │ ├── sm_blosum45.c │ │ │ ├── sm_blosum50.c │ │ │ ├── sm_blosum62.c │ │ │ ├── sm_blosum80.c │ │ │ ├── sm_blosum90.c │ │ │ ├── sm_identity.c │ │ │ ├── sm_pam250.c │ │ │ ├── sm_pam30.c │ │ │ ├── sm_pam70.c │ │ │ └── tables_export.h │ └── zstr │ │ ├── LICENSE │ │ ├── strict_fstream.hpp │ │ └── zstr.hpp ├── 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