List of all items

Structs

• params::CommandParams
• params::MapParams
• params::SketchParams
• types::Anchor
• types::AnchorChunks
• types::AniEstResult
• types::ChainInterval
• types::ChainingResult
• types::ChainingResultANI
• types::KmerEnc
• types::MMHasher
• types::MMHasher32
• types::Orf
• types::SeedPosition
• types::Sketch

Enums

• params::Mode

Functions

• avx2_seeding::avx2_fmh_seeds
• avx2_seeding::mm_hash256
• chain::chain_seeds
• chain::check_markers_quickly
• chain::map_params_from_sketch
• chain::score_anchors
• dist::dist
• file_io::fastx_to_multiple_sketch_rewrite
• file_io::fastx_to_sketches
• file_io::marker_sketches_from_marker_file
• file_io::sketches_from_sketch
• file_io::write_phyllip_matrix
• file_io::write_query_ref_list
• file_io::write_sparse_matrix
• params::fragment_length_formula
• parse::parse_params
• parse::parse_params_search
• regression::get_model
• regression::predict_from_ani_res
• regression::use_learned_ani
• screen::kmer_to_sketch_from_refs
• screen::screen_refs
• screen::screen_refs_filenames
• search::search
• seeding::fmh_seeds
• seeding::fmh_seeds_aa_with_orf
• seeding::get_nonoverlap_orf
• seeding::get_orfs
• seeding::get_repetitive_kmers
• sketch::sketch
• triangle::triangle
• types::mm_hash
• types::mm_hash64
• types::mm_hash_bytes_32
• types::mm_hashi64

Type Aliases

• types::ContigIndex
• types::GnPosition
• types::KmerSeeds
• types::KmerToSketch
• types::MMBuildHasher
• types::MMBuildHasher32
• types::MMHashMap
• types::MMHashMap32
• types::MMHashSet
• types::MarkerBits
• types::SeedBits

Constants

• cmd_line::CMD_CONF_INTERVAL
• cmd_line::CMD_C_FACTOR
• cmd_line::CMD_DETAIL_OUT
• cmd_line::CMD_FULL_INDEX
• cmd_line::CMD_FULL_MAT
• cmd_line::CMD_IND_CTG_QRY
• cmd_line::CMD_IND_CTG_REF
• cmd_line::CMD_KEEP_REFS
• cmd_line::CMD_LEARNED_ANI
• cmd_line::CMD_MARKER_C
• cmd_line::CMD_MIN_ALIGN_FRAC
• cmd_line::CMD_MODE_FAST
• cmd_line::CMD_MODE_SLOW
• cmd_line::CMD_NO_LEARNED_ANI
• cmd_line::CMD_ROBUST
• cmd_line::CONF_INTERVAL
• cmd_line::C_FACTOR
• cmd_line::DETAIL_OUT
• cmd_line::FULL_INDEX
• cmd_line::FULL_MAT
• cmd_line::H_CONF_INTERVAL
• cmd_line::H_CONF_INTERVAL_TRI
• cmd_line::H_C_FACTOR
• cmd_line::H_DETAIL_OUT
• cmd_line::H_FULL_INDEX
• cmd_line::H_FULL_MAT
• cmd_line::H_IND_CTG_QRY
• cmd_line::H_IND_CTG_REF
• cmd_line::H_KEEP_REFS
• cmd_line::H_LEARNED_ANI
• cmd_line::H_MARKER_C
• cmd_line::H_MIN_ALIGN_FRAC
• cmd_line::H_MODE_FAST
• cmd_line::H_MODE_SLOW
• cmd_line::H_NO_LEARNED_ANI
• cmd_line::H_ROBUST
• cmd_line::H_SCREEN
• cmd_line::IND_CTG_QRY
• cmd_line::IND_CTG_REF
• cmd_line::KEEP_REFS
• cmd_line::LEARNED_ANI
• cmd_line::MARKER_C
• cmd_line::MIN_ALIGN_FRAC
• cmd_line::MODE_FAST
• cmd_line::MODE_SLOW
• cmd_line::NO_LEARNED_ANI
• cmd_line::ROBUST
• model::MODEL
• model::MODEL_C200
• params::BP_CHAIN_BAND
• params::BP_CHAIN_BAND_AAI
• params::CHUNK_SIZE_AA
• params::CHUNK_SIZE_DNA
• params::DEFAULT_C
• params::DEFAULT_C_AAI
• params::DEFAULT_K
• params::DEFAULT_K_AAI
• params::DIST_STRING
• params::D_ANCHOR_SCORE_AAI
• params::D_ANCHOR_SCORE_ANI
• params::D_ANI_AND_COVER_CUTOFF
• params::D_FRAC_COVER_CUTOFF
• params::D_FRAC_COVER_CUTOFF_AA
• params::D_FRAGMENT_LENGTH
• params::D_LENGTH_CUTOFF
• params::D_MAX_GAP_LENGTH
• params::D_MAX_GAP_LENGTH_AAI
• params::D_MAX_LIN_LENGTH
• params::D_MIN_ANCHORS_AAI
• params::D_MIN_ANCHORS_ANI
• params::FAST_C
• params::FULL_INDEX_THRESH
• params::KMER_SK_SMALL_VEC_SIZE
• params::K_MARKER_AA
• params::K_MARKER_DNA
• params::LEARNED_INFO_HELP
• params::MARKER_C_DEFAULT
• params::MIN_LENGTH_CONTIG
• params::MIN_LENGTH_COVER
• params::MIN_LENGTH_COVER_AAI
• params::ORF_SIZE
• params::OVERLAP_ORTHOLOGOUS_FRACTION
• params::REPET_KMER_THRESHOLD
• params::SEARCH_AAI_CUTOFF_DEFAULT
• params::SEARCH_ANI_CUTOFF_DEFAULT
• params::SEARCH_STRING
• params::SKETCH_STRING
• params::SLOW_C
• params::SMALL_VEC_SIZE
• params::STOP_CODON
• params::TOTAL_BASES_REGRESS_CUTOFF
• params::TRIANGLE_STRING
• types::BYTE_TO_SEQ
• types::DNA_TO_AA