SYMBOL INDEX (128 symbols across 12 files)

FILE: src/avx2_seeding.rs
  function mm_hash256 (line 6) | pub unsafe fn mm_hash256(kmer: __m256i) -> __m256i {
  function extract_markers_avx2 (line 33) | pub unsafe fn extract_markers_avx2(string: &[u8], kmer_vec: &mut Vec<u64...
  function extract_markers_avx2_positions (line 151) | pub unsafe fn extract_markers_avx2_positions(string: &[u8], kmer_vec: &m...

FILE: src/cmdline.rs
  type Cli (line 6) | pub struct Cli {
  type Mode (line 12) | pub enum Mode {
  type SketchArgs (line 29) | pub struct SketchArgs {
  type ContainArgs (line 86) | pub struct ContainArgs {
  type InspectArgs (line 169) | pub struct InspectArgs {

FILE: src/constants.rs
  constant EM_ABUND_CUTOFF (line 1) | pub const EM_ABUND_CUTOFF: f64 = 0.01;
  constant PAIR_REGEX (line 2) | pub const PAIR_REGEX: &str = r"(.+)(_?1|_?2)(\..+)";
  constant CUTOFF_PVALUE (line 3) | pub const CUTOFF_PVALUE:f64 = 0.9999999999;
  constant SAMPLE_SIZE_CUTOFF (line 4) | pub const SAMPLE_SIZE_CUTOFF: usize = 25;
  constant MEDIAN_ANI_THRESHOLD (line 5) | pub const MEDIAN_ANI_THRESHOLD: f64 = 2.;
  constant QUERY_FILE_SUFFIX (line 6) | pub const QUERY_FILE_SUFFIX: &str = ".syldb";
  constant SAMPLE_FILE_SUFFIX (line 7) | pub const SAMPLE_FILE_SUFFIX: &str = ".sylsp";
  constant QUERY_FILE_SUFFIX_VALID (line 8) | pub const QUERY_FILE_SUFFIX_VALID : [&str;2] = [QUERY_FILE_SUFFIX, ".syl...
  constant SAMPLE_FILE_SUFFIX_VALID (line 9) | pub const SAMPLE_FILE_SUFFIX_VALID : [&str;2] = [SAMPLE_FILE_SUFFIX, ".s...
  constant MIN_ANI_DEF (line 10) | pub const MIN_ANI_DEF: f64 = 0.9;
  constant MIN_ANI_P_DEF (line 11) | pub const MIN_ANI_P_DEF: f64 = 0.95;
  constant MAX_MEDIAN_FOR_MEAN_FINAL_EST (line 12) | pub const MAX_MEDIAN_FOR_MEAN_FINAL_EST: f64 = 15.;
  constant DEREP_PROFILE_ANI (line 13) | pub const DEREP_PROFILE_ANI: f64 = 0.975;
  constant MAX_DEDUP_COUNT (line 14) | pub const MAX_DEDUP_COUNT: u32 = 4;
  constant MAX_DEDUP_LEN (line 15) | pub const MAX_DEDUP_LEN: usize = 10000000;
  constant DEFAULT_FPR (line 16) | pub const DEFAULT_FPR: f64 = 0.0001;
  constant MED_KMER_FOR_ID_EST (line 17) | pub const MED_KMER_FOR_ID_EST: f64 = 3.;

FILE: src/contain.rs
  function print_ani_result (line 18) | fn print_ani_result(ani_result: &AniResult, pseudotax: bool, writer: &mu...
  function get_chunks (line 96) | fn get_chunks(indices: &Vec<usize>, steps: usize) -> Vec<Vec<usize>>{
  function contain (line 115) | pub fn contain(mut args: ContainArgs, pseudotax_in: bool) {
  function derep_if_reassign_threshold (line 365) | fn derep_if_reassign_threshold<'a>(results_old: &Vec<AniResult>, results...
  function estimate_true_cov (line 389) | fn estimate_true_cov(results: &mut Vec<AniResult>, kmer_id_opt: Option<f...
  function estimate_covered_bases (line 403) | fn estimate_covered_bases(results: &Vec<AniResult>, sequence_sketch: &Se...
  function winner_table (line 422) | fn winner_table<'a>(results : &'a Vec<AniResult>, log_reassign: bool) ->...
  function print_header (line 473) | fn print_header(pseudotax: bool, writer: &mut Box<dyn Write + Send>, est...
  function get_genome_sketches (line 494) | fn get_genome_sketches(
  function get_seq_sketch (line 556) | fn get_seq_sketch(
  function get_stats (line 613) | fn get_stats<'a>(
  function ani_from_lambda (line 829) | fn ani_from_lambda(lambda: Option<f64>, _mean: f64, k: f64, full_cov: &[...
  function bootstrap_interval (line 861) | fn bootstrap_interval(
  function get_kmer_identity (line 913) | fn get_kmer_identity(seq_sketch: &SequencesSketch, estimate_unknown: boo...

FILE: src/inference.rs
  function r_from_moments_lambda (line 6) | pub fn r_from_moments_lambda(m: f64, v: f64, lambda: f64) -> f64{
  function ratio_formula (line 12) | pub fn ratio_formula(val: f64, r: f64, lambda: f64) -> f64{
  function ratio_from_moments_lambda (line 21) | fn ratio_from_moments_lambda(val: f64, lambda: f64, m: f64, v: f64) -> O...
  function binary_search_lambda (line 29) | pub fn binary_search_lambda(full_covs: &[u32]) -> Option<f64>{
  function var (line 104) | pub fn var(data: &[u32]) -> Option<f64> {
  function mean (line 116) | pub fn mean(data: &[u32]) -> Option<f64> {
  function mme_lambda (line 126) | pub fn mme_lambda(full_covs: &[u32]) -> Option<f64> {
  function mle_zip (line 157) | pub fn mle_zip(full_covs: &[u32], _k: f64) -> Option<f64> {
  function newton_raphson (line 194) | fn newton_raphson(rat: f64, mean: f64) -> f64 {
  function ratio_lambda (line 207) | pub fn ratio_lambda(full_covs: &Vec<u32>, min_count_correct: f64) -> Opt...

FILE: src/inspect.rs
  function pipe_write (line 11) | fn pipe_write(text: &str, writer: &mut Box<dyn Write + Send>){
  type SequencesSketchInspect (line 20) | struct SequencesSketchInspect{
    method from (line 32) | fn from(
  type GenomeSketchInspect (line 49) | pub struct GenomeSketchInspect{
    method from (line 57) | fn from(
  type DatabaseSketch (line 70) | pub struct DatabaseSketch{
  type DatabaseVisitor (line 79) | struct DatabaseVisitor {
    type Value (line 87) | type Value = Self;
    method expecting (line 88) | fn expecting(&self, formatter: &mut std::fmt::Formatter) -> std::fmt::...
    method visit_seq (line 92) | fn visit_seq<S>(mut self, mut seq: S) -> Result<Self, S::Error>
    method deserialize (line 108) | fn deserialize<D>(deserializer: D) -> Result<Self, D::Error>
  function inspect (line 117) | pub fn inspect(args: InspectArgs){
  function get_db_sketch_inspect (line 184) | fn get_db_sketch_inspect(
  function get_seq_sketch_inspect (line 218) | fn get_seq_sketch_inspect(

FILE: src/main.rs
  function main (line 18) | fn main() {

FILE: src/seeding.rs
  function mm_hash64 (line 4) | pub fn mm_hash64(kmer: u64) -> u64 {
  function rev_hash_64 (line 18) | pub fn rev_hash_64(hashed_key: u64) -> u64 {
  function decode (line 54) | pub fn decode(byte: u64) -> u8 {
  function print_string (line 67) | pub fn print_string(kmer: u64, k: usize) {
  function _position_min (line 78) | fn _position_min<T: Ord>(slice: &[T]) -> Option<usize> {
  function fmh_seeds (line 86) | pub fn fmh_seeds(
  function fmh_seeds_positions (line 148) | pub fn fmh_seeds_positions(

FILE: src/sketch.rs
  type Marker (line 25) | type Marker = u32;
  function check_vram_and_block (line 27) | pub fn check_vram_and_block(max_ram: usize, file: &str) {
  function extract_markers (line 53) | pub fn extract_markers(string: &[u8], kmer_vec: &mut Vec<u64>, c: usize,...
  function extract_markers_positions (line 71) | pub fn extract_markers_positions(
  function is_fastq (line 95) | pub fn is_fastq(file: &str) -> bool {
  function is_fasta (line 109) | pub fn is_fasta(file: &str) -> bool {
  function check_args_valid (line 123) | fn check_args_valid(args: &SketchArgs) {
  function parse_ambiguous_files (line 164) | fn parse_ambiguous_files(
  function parse_reads_and_genomes (line 191) | fn parse_reads_and_genomes(
  function parse_paired_end_reads (line 218) | fn parse_paired_end_reads(
  function parse_line_file (line 252) | fn parse_line_file(file_name: &str, vec: &mut Vec<String>) {
  function parse_sample_names (line 260) | fn parse_sample_names(args: &SketchArgs) -> Option<Vec<String>> {
  function sketch (line 276) | pub fn sketch(args: SketchArgs) {
  function sketch_genome_individual (line 481) | pub fn sketch_genome_individual(
  function sketch_genome (line 551) | pub fn sketch_genome(
  function pair_kmer_single (line 627) | fn pair_kmer_single(s1: &[u8]) -> Option<([Marker; 2], [Marker; 2])> {
  function pair_kmer (line 661) | fn pair_kmer(s1: &[u8], s2: &[u8]) -> Option<([Marker; 2], [Marker; 2])> {
  function dup_removal_lsh_full_exact (line 692) | fn dup_removal_lsh_full_exact(
  function dup_removal_lsh_full (line 735) | fn dup_removal_lsh_full(
  function sketch_pair_sequences (line 773) | pub fn sketch_pair_sequences(
  function sketch_sequences_needle (line 899) | pub fn sketch_sequences_needle(

FILE: src/types.rs
  type AdjustStatus (line 39) | pub enum AdjustStatus {
  method default (line 46) | fn default() -> Self {AdjustStatus::Low }
  type Kmer (line 49) | pub type Kmer = u64;
  constant BYTE_TO_SEQ (line 50) | pub const BYTE_TO_SEQ: [u8; 256] = [
  function mm_hash (line 62) | pub fn mm_hash(bytes: &[u8]) -> usize {
  type MMHasher (line 74) | pub struct MMHasher {
  method write (line 80) | fn write(&mut self, bytes: &[u8]) {
  method finish (line 84) | fn finish(&self) -> u64 {
  method default (line 91) | fn default() -> MMHasher {
  type MMBuildHasher (line 97) | pub type MMBuildHasher = BuildHasherDefault<MMHasher>;
  type MMHashMap (line 98) | pub type MMHashMap<K, V> = HashMap<K, V, MMBuildHasher>;
  type MMHashSet (line 99) | pub type MMHashSet<K> = HashSet<K, MMBuildHasher>;
  type FxHashMapVisitor (line 108) | struct FxHashMapVisitor;
    type Value (line 111) | type Value = FxHashMap<Kmer, u32>;
    method expecting (line 113) | fn expecting(&self, formatter: &mut std::fmt::Formatter) -> std::fmt::...
    method visit_seq (line 117) | fn visit_seq<A>(self, mut seq: A) -> Result<Self::Value, A::Error>
  function serialize (line 132) | pub fn serialize<S>(
  function deserialize (line 140) | pub fn deserialize<'de, D>(deserializer: D) -> Result<FxHashMap<Kmer, u3...
  type SequencesSketch (line 146) | pub struct SequencesSketch{
    method new (line 158) | pub fn new(file_name: String, c: usize, k: usize, paired: bool, sample...
  type GenomeSketch (line 164) | pub struct GenomeSketch{
  type MultGenomeSketch (line 177) | pub struct MultGenomeSketch{
  type AniResult (line 186) | pub struct AniResult<'a>{

FILE: tests/integration_test.rs
  function fresh (line 8) | fn fresh(){
  function test_sketch_commands (line 17) | fn test_sketch_commands() {
  function test_profile_vs_query (line 114) | fn test_profile_vs_query(){
  function test_sketch_list (line 145) | fn test_sketch_list(){
  function test_profile_disabling (line 212) | fn test_profile_disabling(){
  function test_sketch_fasta_fastq_concord (line 248) | fn test_sketch_fasta_fastq_concord(){
  function test_sample_names (line 298) | fn test_sample_names(){
  function test_fpr (line 378) | fn test_fpr(){
  function test_raw_inputs_profile_simple (line 425) | fn test_raw_inputs_profile_simple(){
  function test_estimate_read_counts (line 466) | fn test_estimate_read_counts(){
  function test_raw_inputs_profile_with_sketch (line 512) | fn test_raw_inputs_profile_with_sketch(){
  function test_inspect (line 552) | fn test_inspect(){

FILE: tests/unit_test.rs
  function test_hash (line 4) | fn test_hash(){