SYMBOL INDEX (280 symbols across 21 files) FILE: src/avx2_seeding.rs function mm_hash256 (line 7) | pub unsafe fn mm_hash256(kmer: __m256i) -> __m256i { function avx2_fmh_seeds (line 33) | pub unsafe fn avx2_fmh_seeds( FILE: src/chain.rs function switch_qr (line 15) | fn switch_qr(med_ctg_len_r: f64, med_ctg_len_q: f64, q_sk_len: f64,r_sk_... function mean (line 28) | fn mean(data: &[f64]) -> Option { function std_deviation (line 39) | fn std_deviation(data: &[f64]) -> f64 { function bootstrap_interval (line 57) | fn bootstrap_interval(ani_ests: &Vec<(f64,usize)>) -> (f64,f64,f64){ function map_params_from_sketch (line 88) | pub fn map_params_from_sketch <'a>( function chain_seeds (line 144) | pub fn chain_seeds( function calculate_ani (line 173) | fn calculate_ani( function score_anchors (line 558) | pub fn score_anchors(anchor_curr: &Anchor, anchor_past: &Anchor, map_par... function get_anchors (line 608) | fn get_anchors( function chain_anchors_ani (line 838) | fn chain_anchors_ani(anchor_chunks: &AnchorChunks, map_params: &MapParam... function get_chain_intervals (line 939) | fn get_chain_intervals( function get_nonoverlapping_chains (line 1008) | fn get_nonoverlapping_chains( FILE: src/cli.rs type Cli (line 10) | pub struct Cli { type Commands (line 16) | pub enum Commands { type SketchArgs (line 39) | pub struct SketchArgs { type DistArgs (line 106) | pub struct DistArgs { type TriangleArgs (line 241) | pub struct TriangleArgs { type SearchArgs (line 364) | pub struct SearchArgs { FILE: src/cmd_line.rs constant MIN_ALIGN_FRAC (line 1) | pub const MIN_ALIGN_FRAC: &str = "min aligned frac"; constant CMD_MIN_ALIGN_FRAC (line 2) | pub const CMD_MIN_ALIGN_FRAC: &str = "min-af"; constant H_MIN_ALIGN_FRAC (line 3) | pub const H_MIN_ALIGN_FRAC: &str = "Only output ANI values where one gen... constant IND_CTG_QRY (line 5) | pub const IND_CTG_QRY: &str = "individual contig query"; constant CMD_IND_CTG_QRY (line 6) | pub const CMD_IND_CTG_QRY: &str = "qi"; constant H_IND_CTG_QRY (line 7) | pub const H_IND_CTG_QRY: &str = "Use individual sequences for the QUERY ... constant IND_CTG_REF (line 9) | pub const IND_CTG_REF: &str = "individual contig ref"; constant CMD_IND_CTG_REF (line 10) | pub const CMD_IND_CTG_REF: &str = "ri"; constant H_IND_CTG_REF (line 11) | pub const H_IND_CTG_REF: &str = "Use individual sequences for the REFERE... constant NO_FULL_INDEX (line 13) | pub const NO_FULL_INDEX: &str = "no marker index"; constant CMD_NO_FULL_INDEX (line 14) | pub const CMD_NO_FULL_INDEX: &str = "no-marker-index"; constant H_NO_FULL_INDEX (line 15) | pub const H_NO_FULL_INDEX: &str = "Do not use hash-table inverted index ... constant ROBUST (line 17) | pub const ROBUST: &str = "robust"; constant CMD_ROBUST (line 18) | pub const CMD_ROBUST: &str = "robust"; constant H_ROBUST (line 19) | pub const H_ROBUST: &str = "Estimate mean after trimming off 10%/90% qua... constant FULL_MAT (line 21) | pub const FULL_MAT: &str = "full-matrix"; constant CMD_FULL_MAT (line 22) | pub const CMD_FULL_MAT: &str = "full-matrix"; constant H_FULL_MAT (line 23) | pub const H_FULL_MAT: &str = "Output full matrix instead of lower-triang... constant KEEP_REFS (line 25) | pub const KEEP_REFS: &str = "keep-refs"; constant CMD_KEEP_REFS (line 26) | pub const CMD_KEEP_REFS: &str = "keep-refs"; constant H_KEEP_REFS (line 27) | pub const H_KEEP_REFS: &str = "Keep reference sketches in memory if the ... constant C_FACTOR (line 29) | pub const C_FACTOR: &str = "c"; constant CMD_C_FACTOR (line 30) | pub const CMD_C_FACTOR: &str = "c"; constant H_C_FACTOR (line 31) | pub const H_C_FACTOR: &str = "Compression factor (k-mer subsampling rate... constant H_SCREEN (line 33) | pub const H_SCREEN: &str = "Screen out pairs with *approximately* < % id... constant CONF_INTERVAL (line 35) | pub const CONF_INTERVAL: &str = "ci"; constant CMD_CONF_INTERVAL (line 36) | pub const CMD_CONF_INTERVAL: &str = "ci"; constant H_CONF_INTERVAL (line 37) | pub const H_CONF_INTERVAL: &str = "Output [5%,95%] ANI confidence interv... constant H_CONF_INTERVAL_TRI (line 38) | pub const H_CONF_INTERVAL_TRI: &str = "Output [5%,95%] ANI confidence in... constant NO_LEARNED_ANI (line 40) | pub const NO_LEARNED_ANI: &str = "no-learned-ani"; constant CMD_NO_LEARNED_ANI (line 41) | pub const CMD_NO_LEARNED_ANI : &str = "no-learned-ani"; constant H_NO_LEARNED_ANI (line 42) | pub const H_NO_LEARNED_ANI: &str = "Disable regression model for ANI pre... constant MODE_SLOW (line 44) | pub const MODE_SLOW: &str = "slow"; constant CMD_MODE_SLOW (line 45) | pub const CMD_MODE_SLOW : &str = "slow"; constant H_MODE_SLOW (line 46) | pub const H_MODE_SLOW : &str = "Slower skani mode; 4x slower and more me... constant MODE_SMALL_GENOMES (line 48) | pub const MODE_SMALL_GENOMES: &str = "small-genomes"; constant CMD_MODE_SMALL_GENOMES (line 49) | pub const CMD_MODE_SMALL_GENOMES: &str = "small-genomes"; constant H_MODE_SMALL_GENOMES (line 50) | pub const H_MODE_SMALL_GENOMES : &str = "Mode for small genomes such as ... constant MODE_FAST (line 52) | pub const MODE_FAST: &str = "fast"; constant CMD_MODE_FAST (line 53) | pub const CMD_MODE_FAST : &str = "fast"; constant H_MODE_FAST (line 54) | pub const H_MODE_FAST : &str = "Faster skani mode; 2x faster and less me... constant MODE_MEDIUM (line 56) | pub const MODE_MEDIUM: &str = "medium"; constant CMD_MODE_MEDIUM (line 57) | pub const CMD_MODE_MEDIUM : &str = "medium"; constant H_MODE_MEDIUM (line 58) | pub const H_MODE_MEDIUM: &str = "Medium skani mode; 2x slower and more m... constant MARKER_C (line 60) | pub const MARKER_C: &str = "marker_c"; constant CMD_MARKER_C (line 61) | pub const CMD_MARKER_C: char = 'm'; constant H_MARKER_C (line 62) | pub const H_MARKER_C: &str = "Marker k-mer compression factor. Markers a... constant DETAIL_OUT (line 64) | pub const DETAIL_OUT: &str = "detailed"; constant CMD_DETAIL_OUT (line 65) | pub const CMD_DETAIL_OUT: &str = "detailed"; constant H_DETAIL_OUT (line 66) | pub const H_DETAIL_OUT: &str = "Print additional info including contig N... constant DISTANCE_OUT (line 68) | pub const DISTANCE_OUT: &str = "distance"; constant CMD_DISTANCE_OUT (line 69) | pub const CMD_DISTANCE_OUT: &str = "distance"; constant H_DISTANCE_OUT (line 70) | pub const H_DISTANCE_OUT: &str = "Output 100 - ANI instead of ANI, creat... constant INT_WRITE (line 72) | pub const INT_WRITE: &str = "intermediate write count"; constant CMD_INT_WRITE (line 73) | pub const CMD_INT_WRITE: &str = "inter-write"; constant H_INT_WRITE (line 74) | pub const H_INT_WRITE: &str = "Write results to output after --inter-wri... constant FAST_SMALL (line 76) | pub const FAST_SMALL: &str = "faster-small"; constant CMD_FAST_SMALL (line 77) | pub const CMD_FAST_SMALL: &str = "faster-small"; constant H_FAST_SMALL (line 78) | pub const H_FAST_SMALL: &str = "Filter genomes with < 20 marker k-mers m... constant DIAG (line 80) | pub const DIAG: &str = "diagonal"; constant CMD_DIAG (line 81) | pub const CMD_DIAG: &str = "diagonal"; constant H_DIAG (line 82) | pub const H_DIAG: &str = "Output the diagonal of the ANI matrix (i.e. se... FILE: src/dist.rs function dist (line 12) | pub fn dist(command_params: CommandParams, mut sketch_params: SketchPara... FILE: src/file_io.rs function write_header (line 15) | fn write_header(writer: &mut impl Write, id_str: &str, ci: bool, verbose... function write_ani_res_perfect (line 25) | fn write_ani_res_perfect(writer: &mut impl Write, sketch: &Sketch, ci: b... function write_ani_res (line 83) | fn write_ani_res(writer: &mut impl Write, ani_res: &AniEstResult, ci: bo... function fastx_to_sketches (line 141) | pub fn fastx_to_sketches( function fastx_to_multiple_sketch_rewrite (line 253) | pub fn fastx_to_multiple_sketch_rewrite( function write_phyllip_matrix (line 364) | pub fn write_phyllip_matrix( function write_sparse_matrix (line 541) | pub fn write_sparse_matrix( function write_query_ref_list (line 608) | pub fn write_query_ref_list( function sketches_from_sketch (line 680) | pub fn sketches_from_sketch(ref_files: &Vec) -> (SketchParams, V... function marker_sketches_from_marker_file (line 720) | pub fn marker_sketches_from_marker_file(marker_file: &str) -> (SketchPar... FILE: src/main.rs function main (line 20) | fn main() { FILE: src/model.rs constant MODEL (line 1) | pub const MODEL:&str = r#" constant MODEL_C200 (line 4) | pub const MODEL_C200:&str = r#" FILE: src/params.rs constant GB_IN_BYTES (line 4) | pub const GB_IN_BYTES: usize = 1_073_741_824; constant SMALL_VEC_SIZE (line 5) | pub const SMALL_VEC_SIZE: usize = 1; constant KMER_SK_SMALL_VEC_SIZE (line 6) | pub const KMER_SK_SMALL_VEC_SIZE: usize = 3; constant INTERMEDIATE_WRITE_COUNT (line 7) | pub const INTERMEDIATE_WRITE_COUNT: usize = 5000; constant D_FRAGMENT_LENGTH (line 11) | pub const D_FRAGMENT_LENGTH: usize = 200000; constant STOP_CODON (line 12) | pub const STOP_CODON: MarkerBits = 21; constant DEFAULT_C (line 13) | pub const DEFAULT_C: &str = "125"; constant DEFAULT_C_AAI (line 14) | pub const DEFAULT_C_AAI: &str = "15"; constant DEFAULT_K (line 15) | pub const DEFAULT_K: &str = "15"; constant DEFAULT_K_AAI (line 16) | pub const DEFAULT_K_AAI: &str = "6"; constant D_MAX_GAP_LENGTH (line 17) | pub const D_MAX_GAP_LENGTH: f64 = 300.; constant D_MAX_GAP_LENGTH_AAI (line 18) | pub const D_MAX_GAP_LENGTH_AAI: f64 = 50.; constant D_MAX_LIN_LENGTH (line 19) | pub const D_MAX_LIN_LENGTH: f64 = 5000.; constant D_ANCHOR_SCORE_ANI (line 20) | pub const D_ANCHOR_SCORE_ANI: f64 = 20.; constant D_ANCHOR_SCORE_AAI (line 21) | pub const D_ANCHOR_SCORE_AAI: f64 = 20.; constant D_MIN_ANCHORS_ANI (line 22) | pub const D_MIN_ANCHORS_ANI: usize = 3; constant D_MIN_ANCHORS_AAI (line 23) | pub const D_MIN_ANCHORS_AAI: usize = 5; constant D_LENGTH_CUTOFF (line 24) | pub const D_LENGTH_CUTOFF: usize = D_FRAGMENT_LENGTH; constant D_FRAC_COVER_CUTOFF (line 25) | pub const D_FRAC_COVER_CUTOFF: &str = "15"; constant D_ANI_AND_COVER_CUTOFF (line 26) | pub const D_ANI_AND_COVER_CUTOFF: f64 = 0.95; constant D_FRAC_COVER_CUTOFF_AA (line 27) | pub const D_FRAC_COVER_CUTOFF_AA: &str = "5"; constant ORF_SIZE (line 30) | pub const ORF_SIZE: usize = 30; constant MARKER_C_DEFAULT (line 31) | pub const MARKER_C_DEFAULT: &str = "1000"; constant K_MARKER_AA (line 32) | pub const K_MARKER_AA: usize = 10; constant K_MARKER_DNA (line 33) | pub const K_MARKER_DNA: usize = 21; constant SEARCH_STRING (line 34) | pub const SEARCH_STRING: &str = "search"; constant DIST_STRING (line 35) | pub const DIST_STRING: &str = "dist"; constant SKETCH_STRING (line 36) | pub const SKETCH_STRING: &str = "sketch"; constant TRIANGLE_STRING (line 37) | pub const TRIANGLE_STRING: &str = "triangle"; constant CHUNK_SIZE_DNA (line 38) | pub const CHUNK_SIZE_DNA: usize = 20000; constant CHUNK_SIZE_AA (line 39) | pub const CHUNK_SIZE_AA: usize = 20000; constant MIN_LENGTH_CONTIG (line 40) | pub const MIN_LENGTH_CONTIG: usize = 500; constant MIN_LENGTH_COVER_AAI (line 41) | pub const MIN_LENGTH_COVER_AAI: usize = 500; constant MIN_LENGTH_COVER (line 42) | pub const MIN_LENGTH_COVER: usize = 500; constant BP_CHAIN_BAND (line 43) | pub const BP_CHAIN_BAND: usize = 2500; constant BP_CHAIN_BAND_AAI (line 44) | pub const BP_CHAIN_BAND_AAI: usize = 500; constant SEARCH_AAI_CUTOFF_DEFAULT (line 45) | pub const SEARCH_AAI_CUTOFF_DEFAULT: f64 = 0.60; constant SEARCH_ANI_CUTOFF_DEFAULT (line 46) | pub const SEARCH_ANI_CUTOFF_DEFAULT: f64 = 0.80; constant SCREEN_MINIMUM_KMERS (line 47) | pub const SCREEN_MINIMUM_KMERS: usize = 20; constant FULL_INDEX_THRESH (line 48) | pub const FULL_INDEX_THRESH: usize = 50; constant REPET_KMER_THRESHOLD (line 49) | pub const REPET_KMER_THRESHOLD: usize = 8_000_000; constant OVERLAP_ORTHOLOGOUS_FRACTION (line 50) | pub const OVERLAP_ORTHOLOGOUS_FRACTION: f32 = 0.50; constant TOTAL_BASES_REGRESS_CUTOFF (line 51) | pub const TOTAL_BASES_REGRESS_CUTOFF: usize = 150000; constant LEARNED_INFO_HELP (line 52) | pub const LEARNED_INFO_HELP: &str = "Learned ANI mode detected. ANI may ... constant FAST_C (line 54) | pub const FAST_C: usize = 200; constant SLOW_C (line 55) | pub const SLOW_C: usize = 30; constant MEDIUM_C (line 56) | pub const MEDIUM_C: usize = 70; constant SMALL_M (line 57) | pub const SMALL_M: usize = 200; constant ASCII_N (line 59) | pub const ASCII_N: usize = 78; constant ASCII_N_SMALL (line 60) | pub const ASCII_N_SMALL: usize = 110; type Mode (line 65) | pub enum Mode { type MapParams (line 73) | pub struct MapParams<'a> { type CommandParams (line 94) | pub struct CommandParams{ function fragment_length_formula (line 123) | pub fn fragment_length_formula(_n: usize, aa: bool) -> usize { type SketchParams (line 135) | pub struct SketchParams { method new (line 147) | pub fn new(marker_c: usize, c: usize, k: usize, use_syncs: bool, use_a... FILE: src/parse.rs function parse_params (line 12) | pub fn parse_params(matches: &ArgMatches) -> (SketchParams, CommandParam... function parse_params_search (line 380) | pub fn parse_params_search(matches_subc: &ArgMatches) -> (SketchParams, ... function parse_params_from_cli (line 502) | pub fn parse_params_from_cli(cli: &Cli) -> (SketchParams, CommandParams) { function setup_logging_and_threads (line 511) | fn setup_logging_and_threads(threads: &str, debug: bool, trace: bool) { function parse_sketch_args (line 527) | fn parse_sketch_args(args: &SketchArgs) -> (SketchParams, CommandParams) { function parse_dist_args (line 628) | fn parse_dist_args(args: &DistArgs) -> (SketchParams, CommandParams) { function parse_triangle_args (line 790) | fn parse_triangle_args(args: &TriangleArgs) -> (SketchParams, CommandPar... function parse_search_args (line 923) | fn parse_search_args(args: &SearchArgs) -> (SketchParams, CommandParams) { function read_file_list (line 1009) | fn read_file_list(file_path: &str) -> Vec { FILE: src/regression.rs function use_learned_ani (line 8) | pub fn use_learned_ani(c: usize, individual_contig_q: bool, individual_c... function get_model (line 12) | pub fn get_model(c: usize, learned_ani: bool) -> Option{ function predict_from_ani_res (line 30) | pub fn predict_from_ani_res(ani_res: &mut AniEstResult, model: &GBDT) { FILE: src/screen.rs function check_small_contigs (line 10) | pub fn check_small_contigs(ref_sketches: &Vec, query_sketches: &... function screen_refs_indices (line 39) | pub fn screen_refs_indices( function check_markers_quickly (line 84) | pub fn check_markers_quickly( function screen_refs (line 148) | pub fn screen_refs( function kmer_to_sketch_from_refs (line 190) | pub fn kmer_to_sketch_from_refs(ref_sketches: &Vec) -> KmerToSke... FILE: src/search.rs function search (line 16) | pub fn search(command_params: CommandParams) { FILE: src/seeding.rs function _position_min (line 6) | fn _position_min(slice: &[T]) -> Option { function get_nonoverlap_orf (line 14) | pub fn get_nonoverlap_orf(sorted_orfs: Vec) -> Vec { function get_orfs (line 55) | pub fn get_orfs(string: &[u8], sketch_params: &SketchParams) -> Vec { function fmh_seeds_aa_with_orf (line 114) | pub fn fmh_seeds_aa_with_orf( function fmh_seeds (line 225) | pub fn fmh_seeds( function get_repetitive_kmers (line 328) | pub fn get_repetitive_kmers(kmer_seeds: &Option, sketch: &Ske... FILE: src/sketch.rs function sketch (line 15) | pub fn sketch(command_params: CommandParams, sketch_params: SketchParams) { function sketch_separate_files (line 38) | fn sketch_separate_files(command_params: CommandParams, sketch_params: S... function sketch_consolidated_db (line 105) | fn sketch_consolidated_db(command_params: CommandParams, sketch_params: ... FILE: src/sketch_db.rs type IndexEntry (line 11) | pub struct IndexEntry { type SketchDbWriter (line 18) | pub struct SketchDbWriter { method new (line 32) | pub fn new(output_dir: &str) -> Result Result<(), Box Result Result<(SketchParams, Sketch... method sketch_count (line 126) | pub fn sketch_count(&self) -> usize { method len (line 131) | pub fn len(&self) -> usize { method is_empty (line 136) | pub fn is_empty(&self) -> bool { function is_consolidated_db (line 142) | pub fn is_consolidated_db(database_dir: &str) -> bool { function has_separate_sketches (line 149) | pub fn has_separate_sketches(database_dir: &str) -> bool { FILE: src/triangle.rs function triangle (line 13) | pub fn triangle(command_params: CommandParams, mut sketch_params: Sketch... FILE: src/types.rs constant DNA_TO_AA (line 27) | pub const DNA_TO_AA: [u8; 64] = constant BYTE_TO_SEQ (line 40) | pub const BYTE_TO_SEQ: [MarkerBits; 256] = [ type GnPosition (line 52) | pub type GnPosition = u32; type ContigIndex (line 53) | pub type ContigIndex = u32; type MarkerBits (line 55) | pub type MarkerBits = u64; type SeedBits (line 56) | pub type SeedBits = u32; type KmerToSketch (line 57) | pub type KmerToSketch = MMHashMap; type MultiPositionStorage (line 60) | pub type MultiPositionStorage = Vec>; type MMBuildHasher (line 65) | pub type MMBuildHasher = BuildHasherDefault; type MMBuildHasher32 (line 66) | pub type MMBuildHasher32 = BuildHasherDefault; type MMHashMap (line 67) | pub type MMHashMap = HashMap; type MMHashMap32 (line 68) | pub type MMHashMap32 = HashMap; type MMHashSet (line 69) | pub type MMHashSet = HashSet; function mm_hashi64 (line 73) | pub fn mm_hashi64(kmer: i64) -> i64 { function mm_hash64 (line 86) | pub fn mm_hash64(kmer: u64) -> u64 { function mm_hash_bytes_32 (line 99) | pub fn mm_hash_bytes_32(bytes: &[u8]) -> usize { function mm_hash (line 112) | pub fn mm_hash(bytes: &[u8]) -> usize { type SeedPosition (line 125) | pub struct SeedPosition{ method new (line 135) | pub fn new(pos: GnPosition, contig_index: ContigIndex, canonical: bool... method canonical (line 147) | pub fn canonical(&self) -> bool { method contig_index (line 153) | pub fn contig_index(&self) -> ContigIndex { method set_canonical (line 159) | pub fn set_canonical(&mut self, canonical: bool) { method set_contig_index (line 169) | pub fn set_contig_index(&mut self, contig_index: ContigIndex) { method pack_to_u64 (line 177) | pub fn pack_to_u64(&self) -> u64 { method unpack_from_u64 (line 184) | pub fn unpack_from_u64(packed: u64) -> Self { type ContigIndexCanonical (line 131) | pub type ContigIndexCanonical = u32; function truncate_contig_name (line 197) | pub fn truncate_contig_name(name: &str, short_header: bool) -> String { type TaggedIndex (line 207) | pub struct TaggedIndex; constant SINGLE_BIT (line 210) | const SINGLE_BIT: u64 = 1; method single (line 214) | pub fn single(seed_position: &SeedPosition) -> u64 { method multiple (line 220) | pub fn multiple(storage_index: usize) -> u64 { method is_single (line 226) | pub fn is_single(tagged_index: u64) -> bool { method get_single (line 232) | pub fn get_single(tagged_index: u64) -> SeedPosition { method get_storage_index (line 240) | pub fn get_storage_index(tagged_index: u64) -> usize { type Sketch (line 253) | pub struct Sketch { method add_seed_position (line 281) | pub fn add_seed_position(&mut self, seed: SeedBits, position: SeedPosi... method get_seed_positions (line 307) | pub fn get_seed_positions(&self, seed: SeedBits) -> Cow<[SeedPosition]> { method get_markers_only (line 322) | pub fn get_markers_only(sketch: &Sketch) -> Sketch{ method new (line 342) | pub fn new(marker_c: usize, c: usize, k: usize, file_name: String, ami... method partial_cmp (line 355) | fn partial_cmp(&self, other: &Self) -> Option { method cmp (line 361) | fn cmp(&self, other: &Self) -> Ordering { method hash (line 368) | fn hash(&self, state: &mut H) { method default (line 373) | fn default() -> Self { type MMHasher32 (line 394) | pub struct MMHasher32 { method write (line 400) | fn write(&mut self, bytes: &[u8]) { method finish (line 404) | fn finish(&self) -> u64 { type MMHasher (line 414) | pub struct MMHasher { method write (line 420) | fn write(&mut self, bytes: &[u8]) { method finish (line 424) | fn finish(&self) -> u64 { type KmerEnc (line 432) | pub struct KmerEnc { method decode (line 450) | pub fn decode(byte: u64) -> u8 { method print_string (line 464) | pub fn print_string(kmer: u64, k: usize) { method print_string_aa (line 475) | pub fn print_string_aa(kmer: u64, k: usize, sketch_params: &SketchPara... method eq (line 443) | fn eq(&self, other: &Self) -> bool { type ChainingResult (line 488) | pub struct ChainingResult { type ChainingResultANI (line 495) | pub struct ChainingResultANI { type Anchor (line 500) | pub struct Anchor { method new (line 530) | pub fn new( type ChainInterval (line 509) | pub struct ChainInterval { method query_range_len (line 521) | pub fn query_range_len(&self) -> GnPosition { method ref_range_len (line 524) | pub fn ref_range_len(&self) -> GnPosition { type AnchorChunks (line 546) | pub struct AnchorChunks { type Orf (line 553) | pub struct Orf{ type AniEstResult (line 560) | pub struct AniEstResult{ FILE: tests/int_test_new.rs type AniResult (line 10) | pub struct AniResult{ function run_skani (line 20) | fn run_skani<'a>(args: &'a [&str], stderr: bool) -> String{ function get_result_from_out (line 35) | fn get_result_from_out(tsv_res : &str) -> Vec{ function fast_test_small_genomes (line 57) | fn fast_test_small_genomes() { function test_diag_triangle (line 90) | fn test_diag_triangle(){ function fast_test_screen (line 102) | fn fast_test_screen(){ function fast_show_degenerate_inputs (line 136) | fn fast_show_degenerate_inputs(){ FILE: tests/integration_test.rs function full_test_sketch_and_search (line 7) | fn full_test_sketch_and_search() { function full_test_dist (line 176) | fn full_test_dist() { function full_test_triangle (line 457) | fn full_test_triangle() { function test_consolidated_database_functionality (line 599) | fn test_consolidated_database_functionality() { function test_consolidated_database_multiple_files (line 704) | fn test_consolidated_database_multiple_files() { function test_short_header_functionality (line 765) | fn test_short_header_functionality() { function test_individual_contigs_with_search (line 893) | fn test_individual_contigs_with_search() { function test_sketch_search_individual_contigs_matches_dist (line 981) | fn test_sketch_search_individual_contigs_matches_dist() { function test_both_min_af_functionality (line 1107) | fn test_both_min_af_functionality() { FILE: tests/tests.rs function default_params (line 8) | fn default_params(mode: Mode) -> (CommandParams, SketchParams) { function fast_ecoli_test_simple (line 43) | fn fast_ecoli_test_simple() { function fast_ecoli_plasmid_test (line 63) | fn fast_ecoli_plasmid_test() { function fast_eukaryote_test (line 83) | fn fast_eukaryote_test() { function fast_avx2_vs_normal_code (line 131) | fn fast_avx2_vs_normal_code(){ function fast_NNN_test_code (line 150) | fn fast_NNN_test_code(){