SYMBOL INDEX (4731 symbols across 197 files)

FILE: benchmarks/benchmarks.py
  function load_sequences (line 26) | def load_sequences():
  class TimeMinHashSuite (line 36) | class TimeMinHashSuite:
    method setup (line 37) | def setup(self):
    method time_add_sequence (line 48) | def time_add_sequence(self):
    method time_add_protein (line 54) | def time_add_protein(self):
    method time_get_mins (line 60) | def time_get_mins(self):
    method time_add_hash (line 65) | def time_add_hash(self):
    method time_add_many (line 70) | def time_add_many(self):
    method time_similarity (line 74) | def time_similarity(self):
    method time_count_common (line 80) | def time_count_common(self):
    method time_merge (line 86) | def time_merge(self):
    method time_copy (line 92) | def time_copy(self):
    method time_concat (line 97) | def time_concat(self):
  class PeakmemMinHashSuite (line 104) | class PeakmemMinHashSuite:
    method setup (line 105) | def setup(self):
    method peakmem_add_sequence (line 112) | def peakmem_add_sequence(self):
    method peakmem_add_protein (line 118) | def peakmem_add_protein(self):
    method peakmem_add_hash (line 124) | def peakmem_add_hash(self):
    method peakmem_add_many (line 129) | def peakmem_add_many(self):
  class TimeMinAbundanceSuite (line 137) | class TimeMinAbundanceSuite(TimeMinHashSuite):
    method setup (line 138) | def setup(self):
    method time_get_mins_abundance (line 146) | def time_get_mins_abundance(self):
    method time_set_abundances (line 151) | def time_set_abundances(self):
    method time_set_abundances_noclear (line 157) | def time_set_abundances_noclear(self):
  class PeakmemMinAbundanceSuite (line 164) | class PeakmemMinAbundanceSuite(PeakmemMinHashSuite):
    method setup (line 165) | def setup(self):
  class TimeZipStorageSuite (line 173) | class TimeZipStorageSuite:
    method setup (line 174) | def setup(self):
    method time_load_from_zipstorage (line 188) | def time_load_from_zipstorage(self):
    method time_load_small_from_zipstorage (line 193) | def time_load_small_from_zipstorage(self):
    method teardown (line 198) | def teardown(self):
  class PeakmemZipStorageSuite (line 202) | class PeakmemZipStorageSuite:
    method setup (line 203) | def setup(self):
    method peakmem_load_from_zipstorage (line 217) | def peakmem_load_from_zipstorage(self):
    method peakmem_load_small_from_zipstorage (line 222) | def peakmem_load_small_from_zipstorage(self):
    method teardown (line 227) | def teardown(self):

FILE: include/sourmash.h
  type HashFunctions (line 11) | enum HashFunctions {
  type HashFunctions (line 19) | typedef uint32_t HashFunctions;
  type SourmashErrorCode (line 21) | enum SourmashErrorCode {
  type SourmashErrorCode (line 60) | typedef uint32_t SourmashErrorCode;
  type SourmashComputeParameters (line 62) | typedef struct SourmashComputeParameters SourmashComputeParameters;
  type SourmashDatasetPicklist (line 64) | typedef struct SourmashDatasetPicklist SourmashDatasetPicklist;
  type SourmashHyperLogLog (line 66) | typedef struct SourmashHyperLogLog SourmashHyperLogLog;
  type SourmashKmerMinHash (line 68) | typedef struct SourmashKmerMinHash SourmashKmerMinHash;
  type SourmashManifest (line 70) | typedef struct SourmashManifest SourmashManifest;
  type SourmashManifestRowIter (line 72) | typedef struct SourmashManifestRowIter SourmashManifestRowIter;
  type SourmashNodegraph (line 74) | typedef struct SourmashNodegraph SourmashNodegraph;
  type SourmashRevIndex (line 76) | typedef struct SourmashRevIndex SourmashRevIndex;
  type SourmashRevIndex_CounterGather (line 78) | typedef struct SourmashRevIndex_CounterGather SourmashRevIndex_CounterGa...
  type SourmashSearchResult (line 80) | typedef struct SourmashSearchResult SourmashSearchResult;
  type SourmashSignature (line 82) | typedef struct SourmashSignature SourmashSignature;
  type SourmashZipStorage (line 84) | typedef struct SourmashZipStorage SourmashZipStorage;
  type ScaledType (line 86) | typedef uint32_t ScaledType;
  type SourmashStr (line 91) | typedef struct {
  type SourmashManifestRow (line 106) | typedef struct {

FILE: src/core/benches/compute.rs
  function add_sequence (line 10) | fn add_sequence(c: &mut Criterion) {
  function add_sequence_protein (line 76) | fn add_sequence_protein(c: &mut Criterion) {

FILE: src/core/benches/gather.rs
  function gather_stats_benchmarks (line 11) | fn gather_stats_benchmarks(c: &mut Criterion) {

FILE: src/core/benches/minhash.rs
  function intersection (line 11) | fn intersection(c: &mut Criterion) {

FILE: src/core/benches/nodegraph.rs
  function save_load (line 8) | fn save_load(c: &mut Criterion) {

FILE: src/core/build.rs
  function main (line 3) | fn main() {
  function copy_c_bindings (line 9) | fn copy_c_bindings(_crate_dir: &str) {}
  function copy_c_bindings (line 12) | fn copy_c_bindings(crate_dir: &str) {

FILE: src/core/examples/generate_mqfs.rs
  function main (line 12) | fn main() {

FILE: src/core/src/ani_utils.rs
  function exp_n_mutated (line 10) | fn exp_n_mutated(l: f64, k: f64, r1: f64) -> f64 {
  function var_n_mutated (line 15) | fn var_n_mutated(l: f64, k: f64, r1: f64, q: Option<f64>) -> Result<f64,...
  function exp_n_mutated_squared (line 35) | fn exp_n_mutated_squared(l: f64, k: f64, p: f64) -> Result<f64, Error> {
  function probit (line 41) | fn probit(p: f64) -> f64 {
  function r1_to_q (line 45) | fn r1_to_q(k: f64, r1: f64) -> f64 {
  function get_exp_probability_nothing_common (line 59) | fn get_exp_probability_nothing_common(
  function ani_from_containment (line 82) | pub fn ani_from_containment(containment: f64, ksize: f64) -> f64 {
  function ani_ci_from_containment (line 93) | pub fn ani_ci_from_containment(
  function test_containment_to_ani_zero (line 153) | fn test_containment_to_ani_zero() {
  function test_containment_to_ani_one (line 172) | fn test_containment_to_ani_one() {
  function test_containment_to_ani_scaled1 (line 188) | fn test_containment_to_ani_scaled1() {
  function test_containment_to_ani_scaled100 (line 204) | fn test_containment_to_ani_scaled100() {
  function test_containment_to_ani_scaled100_2 (line 220) | fn test_containment_to_ani_scaled100_2() {
  function test_var_n_mutated_zero (line 236) | fn test_var_n_mutated_zero() {
  function test_var_n_mutated_value_error (line 245) | fn test_var_n_mutated_value_error() {
  function test_var_n_mutated_success (line 260) | fn test_var_n_mutated_success() {
  function test_r1_to_q (line 273) | fn test_r1_to_q() {
  function test_exp_n_mutated (line 290) | fn test_exp_n_mutated() {
  function test_get_exp_probability_nothing_common_ani_zero (line 313) | fn test_get_exp_probability_nothing_common_ani_zero() {
  function test_get_exp_probability_nothing_common_ani_one (line 329) | fn test_get_exp_probability_nothing_common_ani_one() {
  function test_get_exp_probability_nothing_common (line 345) | fn test_get_exp_probability_nothing_common() {

FILE: src/core/src/cmd.rs
  method from_params (line 10) | pub fn from_params(params: &ComputeParameters) -> Signature {
  type ComputeParameters (line 24) | pub struct ComputeParameters {
  method default (line 111) | fn default() -> Self {
  function build_template (line 116) | pub fn build_template(params: &ComputeParameters) -> Vec<Sketch> {

FILE: src/core/src/collection.rs
  type Collection (line 18) | pub struct Collection {
    method new (line 100) | pub fn new(manifest: Manifest, storage: InnerStorage) -> Self {
    method iter (line 104) | pub fn iter(&self) -> impl Iterator<Item = (Idx, &Record)> {
    method par_iter (line 109) | pub fn par_iter(&self) -> impl IndexedParallelIterator<Item = (Idx, &R...
    method len (line 116) | pub fn len(&self) -> usize {
    method is_empty (line 120) | pub fn is_empty(&self) -> bool {
    method manifest (line 124) | pub fn manifest(&self) -> &Manifest {
    method storage (line 128) | pub fn storage(&self) -> &InnerStorage {
    method check_superset (line 132) | pub fn check_superset(&self, other: &Collection) -> Result<usize> {
    method from_zipfile (line 141) | pub fn from_zipfile<P: AsRef<Path>>(zipfile: P) -> Result<Self> {
    method from_rocksdb (line 152) | pub fn from_rocksdb<P: AsRef<Path>>(dirname: P) -> Result<Self> {
    method from_sigs (line 162) | pub fn from_sigs(sigs: Vec<Signature>) -> Result<Self> {
    method from_paths (line 190) | pub fn from_paths(paths: &[PathBuf]) -> Result<Self> {
    method record_for_dataset (line 205) | pub fn record_for_dataset(&self, dataset_id: Idx) -> Result<&Record> {
    method sig_for_dataset (line 209) | pub fn sig_for_dataset(&self, dataset_id: Idx) -> Result<SigStore> {
    method sig_from_record (line 224) | pub fn sig_from_record(&self, record: &Record) -> Result<SigStore> {
    method intersect_manifest (line 232) | pub fn intersect_manifest(&mut self, mf: &Manifest) {
    method min_max_scaled (line 237) | pub fn min_max_scaled(&self) -> Option<(&ScaledType, &ScaledType)> {
  type CollectionSet (line 26) | pub struct CollectionSet {
    type Error (line 45) | type Error = crate::Error;
    method try_from (line 47) | fn try_from(collection: Collection) -> Result<Self> {
    method into_inner (line 78) | pub fn into_inner(self) -> Collection {
    method selection (line 82) | pub fn selection(&self) -> Selection {
    method set_storage_unchecked (line 94) | pub unsafe fn set_storage_unchecked(&mut self, storage: InnerStorage) {
  type Target (line 31) | type Target = Collection;
  method deref (line 33) | fn deref(&self) -> &Self::Target {
  method deref_mut (line 39) | fn deref_mut(&mut self) -> &mut Self::Target {
  method select (line 71) | fn select(mut self, selection: &Selection) -> Result<Self> {
  method select (line 249) | fn select(mut self, selection: &Selection) -> Result<Self> {
  function sigstore_selection_with_downsample (line 272) | fn sigstore_selection_with_downsample() {
  function sigstore_selection_with_downsample_too_low (line 298) | fn sigstore_selection_with_downsample_too_low() {
  function sigstore_selection_scaled_handle_num_sig (line 318) | fn sigstore_selection_scaled_handle_num_sig() {
  function sigstore_selection_num (line 340) | fn sigstore_selection_num() {
  function sigstore_selection_num_handle_scaled_sig (line 370) | fn sigstore_selection_num_handle_scaled_sig() {
  function collection_intersect_manifest (line 392) | fn collection_intersect_manifest() {
  function sigstore_sig_from_record (line 418) | fn sigstore_sig_from_record() {
  function sigstore_sig_from_record_2 (line 445) | fn sigstore_sig_from_record_2() {
  function sigstore_selection_moltype_zip (line 461) | fn sigstore_selection_moltype_zip() {
  function sigstore_selection_moltype_sig (line 484) | fn sigstore_selection_moltype_sig() {
  function collection_from_collectionset (line 511) | fn collection_from_collectionset() -> () {
  function collection_selection (line 537) | fn collection_selection() -> () {
  function collection_from_collectionset_fail (line 568) | fn collection_from_collectionset_fail() -> () {
  function collection_from_rocksdb_storage (line 586) | fn collection_from_rocksdb_storage() -> Result<()> {

FILE: src/core/src/encodings.rs
  type Color (line 18) | pub type Color = u64;
  type Idx (line 19) | pub type Idx = u32;
  type IdxTracker (line 20) | type IdxTracker = (vec_collections::VecSet<[Idx; 8]>, u64);
  type ColorToIdx (line 21) | type ColorToIdx = HashMap<Color, IdxTracker, BuildNoHashHasher<Color>>;
  type HashFunctions (line 29) | pub enum HashFunctions {
    method dna (line 40) | pub fn dna(&self) -> bool {
    method protein (line 44) | pub fn protein(&self) -> bool {
    method dayhoff (line 48) | pub fn dayhoff(&self) -> bool {
    method hp (line 52) | pub fn hp(&self) -> bool {
    method skipm1n3 (line 56) | pub fn skipm1n3(&self) -> bool {
    method skipm2n3 (line 60) | pub fn skipm2n3(&self) -> bool {
    method fmt (line 66) | fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
    type Error (line 84) | type Error = Error;
    method try_from (line 86) | fn try_from(moltype: &str) -> Result<Self, Self::Error> {
  constant COMPLEMENT (line 101) | const COMPLEMENT: [u8; 256] = {
  function revcomp (line 112) | pub fn revcomp(seq: &[u8]) -> Vec<u8> {
  function translate_codon (line 323) | pub fn translate_codon(codon: &[u8]) -> Result<u8, Error> {
  function aa_to_dayhoff (line 350) | pub fn aa_to_dayhoff(aa: u8) -> u8 {
  function aa_to_hp (line 357) | pub fn aa_to_hp(aa: u8) -> u8 {
  function to_aa (line 365) | pub fn to_aa(seq: &[u8], dayhoff: bool, hp: bool) -> Result<Vec<u8>, Err...
  constant VALID (line 386) | pub const VALID: [bool; 256] = {
  type Colors (line 396) | pub struct Colors {
    method new (line 401) | pub fn new() -> Colors {
    method update (line 413) | pub fn update<'a, I: IntoIterator<Item = &'a Idx>>(
    method compute_color (line 476) | fn compute_color(idxs: &IdxTracker) -> Color {
    method len (line 481) | pub fn len(&self) -> usize {
    method is_empty (line 485) | pub fn is_empty(&self) -> bool {
    method contains (line 489) | pub fn contains(&self, color: Color, idx: Idx) -> bool {
    method indices (line 497) | pub fn indices(&self, color: &Color) -> Indices<'_> {
    method retain (line 504) | pub fn retain<F>(&mut self, f: F)
  type Indices (line 512) | pub struct Indices<'a> {
  type Item (line 517) | type Item = &'a Idx;
  method next (line 519) | fn next(&mut self) -> Option<Self::Item> {
  type Xxh3Hash128 (line 526) | pub(crate) struct Xxh3Hash128(twox_hash::XxHash3_128);
    method finish (line 530) | fn finish(&self) -> u64 {
    method write (line 537) | fn write(&mut self, bytes: &[u8]) {
  function colors_update (line 548) | fn colors_update() {
  function colors_retain (line 566) | fn colors_retain() {
  function test_dna_method (line 615) | fn test_dna_method() {
  function test_protein_method (line 622) | fn test_protein_method() {
  function test_dayhoff_method (line 629) | fn test_dayhoff_method() {
  function test_hp_method (line 636) | fn test_hp_method() {
  function test_skipm1n3_method (line 643) | fn test_skipm1n3_method() {
  function test_skipm2n3_method (line 650) | fn test_skipm2n3_method() {
  function test_display_hashfunctions (line 657) | fn test_display_hashfunctions() {
  function test_try_from_str_valid (line 671) | fn test_try_from_str_valid() {
  function test_try_from_str_invalid (line 699) | fn test_try_from_str_invalid() {

FILE: src/core/src/errors.rs
  type SourmashError (line 5) | pub enum SourmashError {
  type ReadDataError (line 113) | pub enum ReadDataError {
  type SourmashErrorCode (line 120) | pub enum SourmashErrorCode {
    method from_error (line 170) | pub fn from_error(error: &SourmashError) -> SourmashErrorCode {

FILE: src/core/src/ffi/cmd/compute.rs
  type SourmashComputeParameters (line 8) | pub struct SourmashComputeParameters;
  type RustObject (line 11) | type RustObject = ComputeParameters;
  function computeparams_new (line 15) | pub unsafe extern "C" fn computeparams_new() -> *mut SourmashComputePara...
  function computeparams_free (line 20) | pub unsafe extern "C" fn computeparams_free(ptr: *mut SourmashComputePar...
  function computeparams_seed (line 25) | pub unsafe extern "C" fn computeparams_seed(ptr: *const SourmashComputeP...
  function computeparams_set_seed (line 31) | pub unsafe extern "C" fn computeparams_set_seed(
  function computeparams_ksizes_free (line 51) | pub unsafe extern "C" fn computeparams_ksizes_free(ptr: *mut u32, insize...
  function computeparams_protein (line 79) | pub unsafe extern "C" fn computeparams_protein(ptr: *const SourmashCompu...
  function computeparams_set_protein (line 85) | pub unsafe extern "C" fn computeparams_set_protein(ptr: *mut SourmashCom...
  function computeparams_dayhoff (line 91) | pub unsafe extern "C" fn computeparams_dayhoff(ptr: *const SourmashCompu...
  function computeparams_set_dayhoff (line 97) | pub unsafe extern "C" fn computeparams_set_dayhoff(ptr: *mut SourmashCom...
  function computeparams_hp (line 103) | pub unsafe extern "C" fn computeparams_hp(ptr: *const SourmashComputePar...
  function computeparams_set_hp (line 109) | pub unsafe extern "C" fn computeparams_set_hp(ptr: *mut SourmashComputeP...
  function computeparams_dna (line 115) | pub unsafe extern "C" fn computeparams_dna(ptr: *const SourmashComputePa...
  function computeparams_set_dna (line 121) | pub unsafe extern "C" fn computeparams_set_dna(ptr: *mut SourmashCompute...
  function computeparams_skipm1n3 (line 127) | pub unsafe extern "C" fn computeparams_skipm1n3(ptr: *const SourmashComp...
  function computeparams_set_skipm1n3 (line 133) | pub unsafe extern "C" fn computeparams_set_skipm1n3(ptr: *mut SourmashCo...
  function computeparams_skipm2n3 (line 139) | pub unsafe extern "C" fn computeparams_skipm2n3(ptr: *const SourmashComp...
  function computeparams_set_skipm2n3 (line 145) | pub unsafe extern "C" fn computeparams_set_skipm2n3(ptr: *mut SourmashCo...
  function computeparams_track_abundance (line 151) | pub unsafe extern "C" fn computeparams_track_abundance(
  function computeparams_set_track_abundance (line 159) | pub unsafe extern "C" fn computeparams_set_track_abundance(
  function computeparams_num_hashes (line 168) | pub unsafe extern "C" fn computeparams_num_hashes(ptr: *const SourmashCo...
  function computeparams_set_num_hashes (line 174) | pub unsafe extern "C" fn computeparams_set_num_hashes(
  function computeparams_scaled (line 183) | pub unsafe extern "C" fn computeparams_scaled(ptr: *const SourmashComput...
  function computeparams_set_scaled (line 189) | pub unsafe extern "C" fn computeparams_set_scaled(

FILE: src/core/src/ffi/hyperloglog.rs
  type SourmashHyperLogLog (line 12) | pub struct SourmashHyperLogLog;
  type RustObject (line 15) | type RustObject = HyperLogLog;
  function hll_new (line 19) | pub unsafe extern "C" fn hll_new() -> *mut SourmashHyperLogLog {
  function hll_free (line 24) | pub unsafe extern "C" fn hll_free(ptr: *mut SourmashHyperLogLog) {
  function hll_ksize (line 39) | pub unsafe extern "C" fn hll_ksize(ptr: *const SourmashHyperLogLog) -> u...
  function hll_cardinality (line 44) | pub unsafe extern "C" fn hll_cardinality(ptr: *const SourmashHyperLogLog...
  function hll_similarity (line 49) | pub unsafe extern "C" fn hll_similarity(
  function hll_containment (line 57) | pub unsafe extern "C" fn hll_containment(
  function hll_intersection_size (line 65) | pub unsafe extern "C" fn hll_intersection_size(
  function hll_add_hash (line 92) | pub unsafe extern "C" fn hll_add_hash(ptr: *mut SourmashHyperLogLog, has...
  function hll_matches (line 123) | pub unsafe extern "C" fn hll_matches(

FILE: src/core/src/ffi/index/mod.rs
  type SourmashSearchResult (line 9) | pub struct SourmashSearchResult;
  type RustObject (line 12) | type RustObject = (f64, Signature, String);
  function searchresult_free (line 16) | pub unsafe extern "C" fn searchresult_free(ptr: *mut SourmashSearchResul...
  function searchresult_score (line 21) | pub unsafe extern "C" fn searchresult_score(ptr: *const SourmashSearchRe...
  function searchresult_filename (line 27) | pub unsafe extern "C" fn searchresult_filename(ptr: *const SourmashSearc...
  function searchresult_signature (line 33) | pub unsafe extern "C" fn searchresult_signature(

FILE: src/core/src/ffi/index/revindex.rs
  type SourmashRevIndex (line 26) | pub struct SourmashRevIndex;
  type RustObject (line 28) | type RustObject = module::RevIndex;
  type SourmashDatasetPicklist (line 33) | pub struct SourmashDatasetPicklist;
  type RustObject (line 35) | type RustObject = DatasetPicklist;
  type SourmashRevIndex_CounterGather (line 42) | pub struct SourmashRevIndex_CounterGather;
  type RustObject (line 44) | type RustObject = CounterGather;
  function retrieve_picklist (line 47) | pub unsafe fn retrieve_picklist(
  function revindex_free (line 114) | pub unsafe extern "C" fn revindex_free(ptr: *mut SourmashRevIndex) {
  function revindex_countergather_free (line 119) | pub unsafe extern "C" fn revindex_countergather_free(ptr: *mut SourmashR...
  function dataset_picklist_free (line 145) | pub unsafe extern "C" fn dataset_picklist_free(ptr: *mut SourmashDataset...
  function revindex_len (line 150) | pub unsafe extern "C" fn revindex_len(
  function revindex_ksize (line 179) | pub unsafe extern "C" fn revindex_ksize(ptr: *const SourmashRevIndex) ->...
  function revindex_scaled (line 192) | pub unsafe extern "C" fn revindex_scaled(ptr: *const SourmashRevIndex) -...
  function revindex_moltype (line 204) | pub unsafe extern "C" fn revindex_moltype(ptr: *const SourmashRevIndex) ...
  function from_template (line 552) | pub fn from_template(template: &Sketch) -> Selection {

FILE: src/core/src/ffi/manifest.rs
  type SourmashManifest (line 5) | pub struct SourmashManifest;
  type RustObject (line 8) | type RustObject = Manifest;
  function manifest_free (line 12) | pub unsafe extern "C" fn manifest_free(ptr: *mut SourmashManifest) {
  type ManifestRowIterator (line 18) | pub struct ManifestRowIterator {
  type SourmashManifestRowIter (line 22) | pub struct SourmashManifestRowIter;
  type RustObject (line 25) | type RustObject = ManifestRowIterator;
  function manifest_rows_iter_next (line 29) | pub unsafe extern "C" fn manifest_rows_iter_next(
  function manifest_rows (line 41) | pub unsafe extern "C" fn manifest_rows(
  type SourmashManifestRow (line 51) | pub struct SourmashManifestRow {
    method from (line 76) | fn from(record: &Record) -> SourmashManifestRow {
  type RustObject (line 65) | type RustObject = SourmashManifestRow;
  function manifestrow_free (line 69) | pub unsafe extern "C" fn manifestrow_free(ptr: *mut SourmashManifestRow) {

FILE: src/core/src/ffi/minhash.rs
  type SourmashKmerMinHash (line 12) | pub struct SourmashKmerMinHash;
  type RustObject (line 15) | type RustObject = KmerMinHash;
  function kmerminhash_new (line 19) | pub unsafe extern "C" fn kmerminhash_new(
  function kmerminhash_free (line 33) | pub unsafe extern "C" fn kmerminhash_free(ptr: *mut SourmashKmerMinHash) {
  function kmerminhash_slice_free (line 38) | pub unsafe extern "C" fn kmerminhash_slice_free(ptr: *mut u64, insize: u...
  function kmerminhash_clear (line 130) | pub unsafe extern "C" fn kmerminhash_clear(ptr: *mut SourmashKmerMinHash) {
  function kmerminhash_add_hash (line 137) | pub unsafe extern "C" fn kmerminhash_add_hash(ptr: *mut SourmashKmerMinH...
  function kmerminhash_add_hash_with_abundance (line 144) | pub unsafe extern "C" fn kmerminhash_add_hash_with_abundance(
  function kmerminhash_add_word (line 155) | pub unsafe extern "C" fn kmerminhash_add_word(ptr: *mut SourmashKmerMinH...
  function sourmash_aa_to_dayhoff (line 182) | pub unsafe extern "C" fn sourmash_aa_to_dayhoff(aa: c_char) -> c_char {
  function sourmash_aa_to_hp (line 187) | pub unsafe extern "C" fn sourmash_aa_to_hp(aa: c_char) -> c_char {
  function kmerminhash_remove_hash (line 192) | pub unsafe extern "C" fn kmerminhash_remove_hash(ptr: *mut SourmashKmerM...
  function kmerminhash_remove_many (line 199) | pub unsafe extern "C" fn kmerminhash_remove_many(
  function kmerminhash_get_mins_size (line 274) | pub unsafe extern "C" fn kmerminhash_get_mins_size(ptr: *const SourmashK...
  function kmerminhash_is_protein (line 317) | pub unsafe extern "C" fn kmerminhash_is_protein(ptr: *const SourmashKmer...
  function kmerminhash_dayhoff (line 323) | pub unsafe extern "C" fn kmerminhash_dayhoff(ptr: *const SourmashKmerMin...
  function kmerminhash_hp (line 329) | pub unsafe extern "C" fn kmerminhash_hp(ptr: *const SourmashKmerMinHash)...
  function kmerminhash_skipm1n3 (line 335) | pub unsafe extern "C" fn kmerminhash_skipm1n3(ptr: *const SourmashKmerMi...
  function kmerminhash_skipm2n3 (line 341) | pub unsafe extern "C" fn kmerminhash_skipm2n3(ptr: *const SourmashKmerMi...
  function kmerminhash_seed (line 347) | pub unsafe extern "C" fn kmerminhash_seed(ptr: *const SourmashKmerMinHas...
  function kmerminhash_track_abundance (line 353) | pub unsafe extern "C" fn kmerminhash_track_abundance(ptr: *const Sourmas...
  function kmerminhash_disable_abundance (line 359) | pub unsafe extern "C" fn kmerminhash_disable_abundance(ptr: *mut Sourmas...
  function kmerminhash_num (line 373) | pub unsafe extern "C" fn kmerminhash_num(ptr: *const SourmashKmerMinHash...
  function kmerminhash_ksize (line 379) | pub unsafe extern "C" fn kmerminhash_ksize(ptr: *const SourmashKmerMinHa...
  function kmerminhash_max_hash (line 385) | pub unsafe extern "C" fn kmerminhash_max_hash(ptr: *const SourmashKmerMi...
  function kmerminhash_hash_function (line 391) | pub unsafe extern "C" fn kmerminhash_hash_function(
  function kmerminhash_is_compatible (line 415) | pub unsafe extern "C" fn kmerminhash_is_compatible(

FILE: src/core/src/ffi/mod.rs
  function hash_murmur (line 24) | pub unsafe extern "C" fn hash_murmur(kmer: *const c_char, seed: u64) -> ...
  type HashFunctions (line 35) | pub enum HashFunctions {
    method from (line 62) | fn from(v: crate::encodings::HashFunctions) -> HashFunctions {
  function from (line 45) | fn from(v: HashFunctions) -> crate::encodings::HashFunctions {

FILE: src/core/src/ffi/nodegraph.rs
  type SourmashNodegraph (line 11) | pub struct SourmashNodegraph;
  type RustObject (line 14) | type RustObject = Nodegraph;
  function nodegraph_new (line 18) | pub unsafe extern "C" fn nodegraph_new() -> *mut SourmashNodegraph {
  function nodegraph_free (line 23) | pub unsafe extern "C" fn nodegraph_free(ptr: *mut SourmashNodegraph) {
  function nodegraph_buffer_free (line 28) | pub unsafe extern "C" fn nodegraph_buffer_free(ptr: *mut u8, insize: usi...
  function nodegraph_with_tables (line 36) | pub unsafe extern "C" fn nodegraph_with_tables(
  function nodegraph_count (line 46) | pub unsafe extern "C" fn nodegraph_count(ptr: *mut SourmashNodegraph, h:...
  function nodegraph_count_kmer (line 52) | pub unsafe extern "C" fn nodegraph_count_kmer(
  function nodegraph_get (line 69) | pub unsafe extern "C" fn nodegraph_get(ptr: *const SourmashNodegraph, h:...
  function nodegraph_get_kmer (line 75) | pub unsafe extern "C" fn nodegraph_get_kmer(
  function nodegraph_expected_collisions (line 92) | pub unsafe extern "C" fn nodegraph_expected_collisions(ptr: *const Sourm...
  function nodegraph_ksize (line 98) | pub unsafe extern "C" fn nodegraph_ksize(ptr: *const SourmashNodegraph) ...
  function nodegraph_hashsizes (line 104) | pub unsafe extern "C" fn nodegraph_hashsizes(
  function nodegraph_ntables (line 119) | pub unsafe extern "C" fn nodegraph_ntables(ptr: *const SourmashNodegraph...
  function nodegraph_noccupied (line 125) | pub unsafe extern "C" fn nodegraph_noccupied(ptr: *const SourmashNodegra...
  function nodegraph_matches (line 131) | pub unsafe extern "C" fn nodegraph_matches(
  function nodegraph_update (line 143) | pub unsafe extern "C" fn nodegraph_update(
  function nodegraph_update_mh (line 157) | pub unsafe extern "C" fn nodegraph_update_mh(

FILE: src/core/src/ffi/signature.rs
  type SourmashSignature (line 18) | pub struct SourmashSignature;
  type RustObject (line 21) | type RustObject = Signature;
  function signature_new (line 27) | pub unsafe extern "C" fn signature_new() -> *mut SourmashSignature {
  function signature_from_params (line 32) | pub unsafe extern "C" fn signature_from_params(
  function signature_free (line 42) | pub unsafe extern "C" fn signature_free(ptr: *mut SourmashSignature) {
  function signature_len (line 47) | pub unsafe extern "C" fn signature_len(ptr: *const SourmashSignature) ->...

FILE: src/core/src/ffi/storage.rs
  type SourmashZipStorage (line 9) | pub struct SourmashZipStorage;
  type RustObject (line 12) | type RustObject = Arc<ZipStorage>;
  function zipstorage_free (line 29) | pub unsafe extern "C" fn zipstorage_free(ptr: *mut SourmashZipStorage) {

FILE: src/core/src/ffi/utils.rs
  type ForeignObject (line 22) | pub trait ForeignObject: Sized {
    method from_rust (line 26) | unsafe fn from_rust(object: Self::RustObject) -> *mut Self {
    method from_ref (line 31) | unsafe fn from_ref(object: &Self::RustObject) -> *const Self {
    method as_rust (line 36) | unsafe fn as_rust<'a>(pointer: *const Self) -> &'a Self::RustObject {
    method as_rust_mut (line 41) | unsafe fn as_rust_mut<'a>(pointer: *mut Self) -> &'a mut Self::RustObj...
    method into_rust (line 46) | unsafe fn into_rust(pointer: *mut Self) -> Box<Self::RustObject> {
    method drop (line 51) | unsafe fn drop(pointer: *mut Self) {
    type RustObject (line 321) | type RustObject = SourmashStr;
  type Panic (line 88) | pub struct Panic(String);
  function sourmash_err_get_last_message (line 95) | pub unsafe extern "C" fn sourmash_err_get_last_message() -> SourmashStr {
  function sourmash_err_get_backtrace (line 113) | pub unsafe extern "C" fn sourmash_err_get_backtrace() -> SourmashStr {
  function sourmash_err_clear (line 135) | pub unsafe extern "C" fn sourmash_err_clear() {
  function sourmash_init (line 143) | pub unsafe extern "C" fn sourmash_init() {
  function sourmash_err_get_last_code (line 153) | pub unsafe extern "C" fn sourmash_err_get_last_code() -> SourmashErrorCo...
  function set_last_error (line 163) | fn set_last_error(err: Error) {
  function set_panic_hook (line 169) | pub unsafe fn set_panic_hook() {
  function landingpad (line 197) | pub unsafe fn landingpad<F, T>(f: F) -> T
  type SourmashStr (line 213) | pub struct SourmashStr {
    method new (line 233) | pub fn new(s: &str) -> SourmashStr {
    method from_string (line 241) | pub fn from_string(mut s: String) -> SourmashStr {
    method free (line 252) | pub unsafe fn free(&mut self) {
    method as_str (line 261) | pub fn as_str(&self) -> &str {
    method from (line 273) | fn from(string: String) -> SourmashStr {
    method from (line 279) | fn from(string: &str) -> SourmashStr {
    method from (line 285) | fn from(cow: Cow<'a, str>) -> SourmashStr {
  method default (line 223) | fn default() -> SourmashStr {
  method drop (line 267) | fn drop(&mut self) {
  function sourmash_str_free (line 314) | pub unsafe extern "C" fn sourmash_str_free(s: *mut SourmashStr) {

FILE: src/core/src/index/linear.rs
  type LinearIndex (line 21) | pub struct LinearIndex {
    method from_collection (line 27) | pub fn from_collection(collection: CollectionSet) -> Self {
    method sig_for_dataset (line 36) | pub fn sig_for_dataset(&self, dataset_id: Idx) -> Result<SigStore> {
    method collection (line 40) | pub fn collection(&self) -> &CollectionSet {
    method template (line 44) | pub fn template(&self) -> &Sketch {
    method location (line 48) | pub fn location(&self) -> Option<String> {
    method counter_for_query (line 52) | pub fn counter_for_query(&self, query: &KmerMinHash) -> SigCounter {
    method search (line 115) | pub fn search(
    method gather_round (line 141) | pub fn gather_round(
    method stats_for_match (line 166) | fn stats_for_match(
    method gather (line 247) | pub fn gather(
    method signatures_iter (line 329) | pub fn signatures_iter(&self) -> impl Iterator<Item = SigStore> + '_ {
    type Item (line 354) | type Item = SigStore;
    method insert (line 356) | fn insert(&mut self, _node: Self::Item) -> Result<()> {
    method save (line 360) | fn save<P: AsRef<std::path::Path>>(&self, _path: P) -> Result<()> {
    method load (line 364) | fn load<P: AsRef<std::path::Path>>(_path: P) -> Result<()> {
    method len (line 368) | fn len(&self) -> usize {
    method signatures (line 372) | fn signatures(&self) -> Vec<Self::Item> {
    method signature_refs (line 383) | fn signature_refs(&self) -> Vec<&Self::Item> {
  method select (line 339) | fn select(self, selection: &Selection) -> Result<Self> {

FILE: src/core/src/index/mod.rs
  type GatherResult (line 34) | pub struct GatherResult {
    method get_match (line 122) | pub fn get_match(&self) -> Signature {
  type SigCounter (line 127) | type SigCounter = counter::Counter<Idx>;
  type Index (line 129) | pub trait Index<'a> {
    method find (line 133) | fn find<F>(&self, search_fn: F, sig: &Self::Item, threshold: f64) -> R...
    method search (line 150) | fn search(
    method insert (line 165) | fn insert(&mut self, node: Self::Item) -> Result<()>;
    method batch_insert (line 167) | fn batch_insert(&mut self, nodes: Vec<Self::Item>) -> Result<()> {
    method save (line 175) | fn save<P: AsRef<Path>>(&self, path: P) -> Result<()>;
    method load (line 177) | fn load<P: AsRef<Path>>(path: P) -> Result<()>;
    method signatures (line 179) | fn signatures(&self) -> Vec<Self::Item>;
    method signature_refs (line 181) | fn signature_refs(&self) -> Vec<&Self::Item>;
    method len (line 183) | fn len(&self) -> usize {
    method is_empty (line 187) | fn is_empty(&self) -> bool {
  function similarity (line 200) | fn similarity(&self, other: &L) -> f64 {
  function containment (line 204) | fn containment(&self, other: &L) -> f64 {
  function calculate_gather_stats (line 210) | pub fn calculate_gather_stats(
  constant EPSILON (line 366) | const EPSILON: f64 = 0.01;
  function test_calculate_gather_stats (line 369) | fn test_calculate_gather_stats() {

FILE: src/core/src/index/revindex/disk_revindex.rs
  constant DB_VERSION (line 30) | const DB_VERSION: u8 = 1;
  constant MANIFEST (line 33) | const MANIFEST: &str = "manifest";
  constant STORAGE_SPEC (line 34) | const STORAGE_SPEC: &str = "storage_spec";
  constant VERSION (line 35) | const VERSION: &str = "version";
  constant PROCESSED (line 36) | const PROCESSED: &str = "processed";
  function compute_color (line 38) | fn compute_color(idxs: &Datasets) -> Color {
  type DiskRevIndex (line 44) | pub struct DiskRevIndex {
    method create (line 78) | pub fn create(path: &Path, collection: CollectionSet) -> Result<module...
    method open (line 134) | pub fn open<P: AsRef<Path>>(
    method db (line 183) | pub unsafe fn db(&self) -> Arc<DB> {
    method load_processed (line 187) | fn load_processed(
    method load_collection_from_rocksdb (line 204) | fn load_collection_from_rocksdb(
    method save_collection (line 233) | fn save_collection(&self) -> Result<()> {
    method map_hashes_colors (line 259) | fn map_hashes_colors(&self, dataset_id: Idx) {
  function merge_datasets (line 51) | pub(crate) fn merge_datasets(
  method location (line 297) | fn location(&self) -> &str {
  method counter_for_query (line 301) | fn counter_for_query(
  method prepare_gather_counters (line 338) | fn prepare_gather_counters(
  method gather (line 402) | fn gather(
  method update (line 489) | fn update(mut self, collection: CollectionSet) -> Result<module::RevInde...
  method check (line 541) | fn check(&self, quick: bool) -> DbStats {
  method compact (line 545) | fn compact(&self) {
  method flush (line 552) | fn flush(&self) -> Result<()> {
  method collection (line 563) | fn collection(&self) -> &CollectionSet {
  method internalize_storage (line 567) | fn internalize_storage(&mut self) -> Result<()> {
  method convert (line 603) | fn convert(&self, _output_db: module::RevIndex) -> Result<()> {
  method find_signatures (line 644) | fn find_signatures(

FILE: src/core/src/index/revindex/mem_revindex.rs
  type MemRevIndex (line 26) | pub struct MemRevIndex {
    method new (line 91) | pub fn new(
    method from_zipfile (line 108) | pub fn from_zipfile<P: AsRef<Path>>(
    method merge_queries (line 124) | fn merge_queries(qs: &[KmerMinHash], threshold: usize) -> Option<KmerM...
    method new_with_sigs (line 136) | pub fn new_with_sigs(
    method map_hashes_colors (line 153) | fn map_hashes_colors(
    method search (line 199) | pub fn search(
    method template (line 208) | pub fn template(&self) -> Sketch {
    method scaled (line 212) | pub fn scaled(&self) -> ScaledType {
    type Item (line 413) | type Item = Signature;
    method insert (line 415) | fn insert(&mut self, _node: Self::Item) -> Result<()> {
    method save (line 419) | fn save<P: AsRef<std::path::Path>>(&self, _path: P) -> Result<()> {
    method load (line 423) | fn load<P: AsRef<std::path::Path>>(_path: P) -> Result<()> {
    method len (line 427) | fn len(&self) -> usize {
    method signatures (line 431) | fn signatures(&self) -> Vec<Self::Item> {
    method signature_refs (line 439) | fn signature_refs(&self) -> Vec<&Self::Item> {
  method index (line 33) | fn index(
  method location (line 222) | fn location(&self) -> &str {
  method counter_for_query (line 226) | fn counter_for_query(
  method prepare_gather_counters (line 246) | fn prepare_gather_counters(
  method gather (line 282) | fn gather(
  method update (line 328) | fn update(self, _collection: CollectionSet) -> Result<module::RevIndex> {
  method check (line 332) | fn check(&self, _quick: bool) -> DbStats {
  method compact (line 336) | fn compact(&self) {}
  method flush (line 338) | fn flush(&self) -> Result<()> {
  method collection (line 342) | fn collection(&self) -> &CollectionSet {
  method internalize_storage (line 346) | fn internalize_storage(&mut self) -> Result<()> {
  method convert (line 350) | fn convert(&self, _output_db: module::RevIndex) -> Result<()> {
  method find_signatures (line 354) | fn find_signatures(
  function mem_revindex_new (line 452) | fn mem_revindex_new() -> Result<()> {
  function mem_revindex_many (line 471) | fn mem_revindex_many() -> Result<()> {
  function mem_revindex_from_sigs (line 505) | fn mem_revindex_from_sigs() -> Result<()> {
  function mem_revindex_from_zipstorage (line 540) | fn mem_revindex_from_zipstorage() -> Result<()> {
  function mem_revindex_test_gather_2 (line 593) | fn mem_revindex_test_gather_2() -> Result<()> {
  function mem_revindex_test_gather_3 (line 628) | fn mem_revindex_test_gather_3() -> Result<()> {
  function mem_revindex_load_and_gather_2 (line 670) | fn mem_revindex_load_and_gather_2() -> Result<()> {
  function revindex_load_and_test_counter_gather (line 821) | fn revindex_load_and_test_counter_gather() -> Result<()> {
  function revindex_load_and_gather_picklist (line 877) | fn revindex_load_and_gather_picklist() -> Result<()> {
  function mem_revindex_find_signatures (line 951) | fn mem_revindex_find_signatures() -> Result<()> {

FILE: src/core/src/index/revindex/mod.rs
  type QueryColors (line 29) | type QueryColors = HashMap<Color, Datasets>;
  type HashToColorT (line 31) | type HashToColorT = HashMap<HashIntoType, Color, BuildNoHashHasher<HashI...
  type HashToColor (line 34) | pub struct HashToColor(HashToColorT);
    method new (line 235) | fn new() -> Self {
    method get (line 243) | fn get(&self, hash: &HashIntoType) -> Option<&Color> {
    method len (line 247) | fn len(&self) -> usize {
    method is_empty (line 251) | fn is_empty(&self) -> bool {
    method add_to (line 255) | fn add_to(&mut self, colors: &mut Colors, dataset_id: Idx, matched_has...
    method reduce_hashes_colors (line 264) | fn reduce_hashes_colors(
    method from_iter (line 303) | fn from_iter<T>(iter: T) -> Self
  type CounterGather (line 39) | pub struct CounterGather {
    method is_empty (line 169) | pub fn is_empty(&self) -> bool {
    method len (line 173) | pub fn len(&self) -> usize {
    method found_hashes (line 178) | pub fn found_hashes(&self, template: &KmerMinHash) -> KmerMinHash {
    method peek (line 189) | pub fn peek(&self, threshold: usize) -> Option<(Idx, usize)> {
    method dataset_ids (line 202) | pub fn dataset_ids(&self) -> Vec<Idx> {
    method consume (line 207) | pub fn consume(&mut self, intersect_mh: &KmerMinHash) {
  type RevIndex (line 46) | pub enum RevIndex {
    method create (line 321) | pub fn create<P: AsRef<Path>>(index: P, collection: CollectionSet) -> ...
    method open (line 325) | pub fn open<P: AsRef<Path>>(index: P, read_only: bool, spec: Option<&s...
  type DatasetPicklist (line 52) | pub struct DatasetPicklist {
  type RevIndexOps (line 57) | pub trait RevIndexOps {
    method location (line 62) | fn location(&self) -> &str;
    method len (line 64) | fn len(&self) -> usize {
    method is_empty (line 68) | fn is_empty(&self) -> bool {
    method signatures (line 72) | fn signatures(&self) -> Vec<Signature> {
    method counter_for_query (line 82) | fn counter_for_query(
    method matches_from_counter (line 88) | fn matches_from_counter(&self, counter: SigCounter, threshold: usize) ...
    method records_from_counter (line 112) | fn records_from_counter(&self, counter: SigCounter, threshold: usize) ...
    method prepare_gather_counters (line 130) | fn prepare_gather_counters(
    method update (line 136) | fn update(self, collection: CollectionSet) -> Result<RevIndex>
    method compact (line 140) | fn compact(&self);
    method flush (line 142) | fn flush(&self) -> Result<()>;
    method convert (line 144) | fn convert(&self, output_db: RevIndex) -> Result<()>;
    method check (line 146) | fn check(&self, quick: bool) -> DbStats;
    method gather (line 148) | fn gather(
    method collection (line 156) | fn collection(&self) -> &CollectionSet;
    method internalize_storage (line 158) | fn internalize_storage(&mut self) -> Result<()>;
    method find_signatures (line 160) | fn find_signatures(
  function prepare_query (line 339) | pub fn prepare_query(search_sig: Signature, selection: &Selection) -> Op...
  type Datasets (line 352) | pub enum Datasets {
    method extend (line 390) | fn extend<T>(&mut self, iter: T)
    method new (line 418) | pub fn new(vals: &[Idx]) -> Self {
    method from_slice (line 428) | pub fn from_slice(slice: &[u8]) -> Result<Self> {
    method as_bytes (line 445) | fn as_bytes(&self) -> Option<Vec<u8>> {
    method union (line 463) | fn union(&mut self, other: Datasets) {
    method is_empty (line 485) | pub fn is_empty(&self) -> bool {
    method len (line 489) | pub fn len(&self) -> usize {
    method contains (line 497) | fn contains(&self, value: &Idx) -> bool {
  method hash (line 360) | fn hash<H>(&self, state: &mut H)
  type Item (line 377) | type Item = Idx;
  type IntoIter (line 378) | type IntoIter = Box<dyn Iterator<Item = Self::Item>>;
  method into_iter (line 380) | fn into_iter(self) -> Self::IntoIter {
  type DbStats (line 507) | pub struct DbStats {
  function stats_for_cf (line 524) | fn stats_for_cf(db: Arc<DB>, cf_name: &str, deep_check: bool, quick: boo...
  function disk_revindex_index (line 582) | fn disk_revindex_index() -> Result<()> {
  function disk_revindex_update (line 622) | fn disk_revindex_update() -> Result<()> {
  function disk_revindex_load_and_gather (line 670) | fn disk_revindex_load_and_gather() -> Result<()> {
  function disk_revindex_load_and_gather_2 (line 715) | fn disk_revindex_load_and_gather_2() -> Result<()> {
  function disk_revindex_load_and_gather_3 (line 872) | fn disk_revindex_load_and_gather_3() -> Result<()> {
  function revindex_load_and_gather_picklist (line 955) | fn revindex_load_and_gather_picklist() -> Result<()> {
  function disk_revindex_find_signatures (line 1033) | fn disk_revindex_find_signatures() -> Result<()> {
  function disk_revindex_move (line 1082) | fn disk_revindex_move() -> Result<()> {
  function disk_revindex_internalize_storage (line 1143) | fn disk_revindex_internalize_storage() -> Result<()> {
  function rocksdb_storage_from_path (line 1200) | fn rocksdb_storage_from_path() -> Result<()> {
  function rocksdb_storage_fail_bad_directory (line 1271) | fn rocksdb_storage_fail_bad_directory() -> Result<()> {
  function countergather_basic (line 1281) | fn countergather_basic() -> Result<()> {

FILE: src/core/src/index/search.rs
  function search_minhashes (line 3) | pub fn search_minhashes<L>(node: &dyn Comparable<L>, query: &L, threshol...
  function search_minhashes_containment (line 7) | pub fn search_minhashes_containment<L>(
  function search_minhashes_find_best (line 15) | pub fn search_minhashes_find_best<L>() -> fn(&dyn Comparable<L>, &L, f64...

FILE: src/core/src/lib.rs
  type Result (line 24) | pub type Result<T> = std::result::Result<T, Error>;
  type HashIntoType (line 66) | type HashIntoType = u64;
  type ScaledType (line 67) | pub type ScaledType = u32;
  function _hash_murmur (line 69) | pub fn _hash_murmur(kmer: &[u8], seed: u64) -> u64 {

FILE: src/core/src/manifest.rs
  type Record (line 23) | pub struct Record {
    method fmt (line 86) | fn fmt(&self, fmt: &mut std::fmt::Formatter<'_>) -> std::result::Resul...
    method from_sig (line 100) | pub fn from_sig(sig: &Signature, path: &str) -> Vec<Self> {
    method moltype (line 152) | pub fn moltype(&self) -> HashFunctions {
    method check_compatible (line 156) | pub fn check_compatible(&self, other: &Record) -> Result<()> {
  function intbool (line 57) | fn intbool<S>(x: &bool, s: S) -> std::result::Result<S::Ok, S::Error>
  function to_bool (line 68) | fn to_bool<'de, D>(deserializer: D) -> std::result::Result<bool, D::Error>
  type Manifest (line 94) | pub struct Manifest {
    method from_reader (line 219) | pub fn from_reader<R: Read>(rdr: R) -> Result<Self> {
    method to_writer (line 232) | pub fn to_writer<W: Write>(&self, mut wtr: W) -> Result<()> {
    method internal_locations (line 244) | pub fn internal_locations(&self) -> impl Iterator<Item = &str> {
    method iter (line 248) | pub fn iter(&self) -> impl Iterator<Item = &Record> {
    method intersect_manifest (line 252) | pub fn intersect_manifest(&self, other: &Manifest) -> Self {
    method from (line 338) | fn from(records: Vec<Record>) -> Self {
    method from (line 344) | fn from(paths: &[PathBuf]) -> Self {
    method from (line 367) | fn from(pathlist: &PathBuf) -> Self {
  method eq (line 189) | fn eq(&self, other: &Self) -> bool {
  method hash (line 205) | fn hash<H: Hasher>(&self, state: &mut H) {
  method select (line 270) | fn select(self, selection: &Selection) -> Result<Self> {
  method select (line 320) | fn select(self, selection: &Selection) -> Result<Self> {
  type Target (line 382) | type Target = Vec<Record>;
  method deref (line 384) | fn deref(&self) -> &Self::Target {
  function manifest_from_pathlist (line 402) | fn manifest_from_pathlist() {
  function manifest_from_pathlist_nonexistent_file (line 434) | fn manifest_from_pathlist_nonexistent_file() {
  function manifest_from_pathlist_badfile (line 441) | fn manifest_from_pathlist_badfile() {
  function manifest_from_paths_badpath (line 459) | fn manifest_from_paths_badpath() {
  function manifest_to_writer_bools (line 476) | fn manifest_to_writer_bools() {
  function manifest_to_writer_moltype_dna (line 514) | fn manifest_to_writer_moltype_dna() {
  function manifest_selection (line 545) | fn manifest_selection() {
  function manifest_intersect (line 591) | fn manifest_intersect() {

FILE: src/core/src/prelude.rs
  type ToWriter (line 9) | pub trait ToWriter {
    method to_writer (line 10) | fn to_writer<W>(&self, writer: &mut W) -> Result<()>
  type Update (line 15) | pub trait Update<O> {
    method update (line 16) | fn update(&self, other: &mut O) -> Result<()>;
  type FromFactory (line 19) | pub trait FromFactory<N> {
    method factory (line 20) | fn factory(&self, name: &str) -> Result<N>;
  type ReadData (line 24) | pub trait ReadData<D> {
    method data (line 25) | fn data(&self) -> Result<&D>;
  type Comparable (line 29) | pub trait Comparable<O> {
    method similarity (line 30) | fn similarity(&self, other: &O) -> f64;
    method containment (line 31) | fn containment(&self, other: &O) -> f64;

FILE: src/core/src/selection.rs
  type Selection (line 9) | pub struct Selection {
    method ksize (line 66) | pub fn ksize(&self) -> Option<u32> {
    method set_ksize (line 70) | pub fn set_ksize(&mut self, ksize: u32) {
    method abund (line 74) | pub fn abund(&self) -> Option<bool> {
    method set_abund (line 78) | pub fn set_abund(&mut self, value: bool) {
    method num (line 82) | pub fn num(&self) -> Option<u32> {
    method set_num (line 86) | pub fn set_num(&mut self, num: u32) {
    method scaled (line 90) | pub fn scaled(&self) -> Option<ScaledType> {
    method set_scaled (line 94) | pub fn set_scaled(&mut self, scaled: ScaledType) {
    method containment (line 98) | pub fn containment(&self) -> Option<bool> {
    method set_containment (line 102) | pub fn set_containment(&mut self, containment: bool) {
    method moltype (line 106) | pub fn moltype(&self) -> Option<HashFunctions> {
    method set_moltype (line 110) | pub fn set_moltype(&mut self, value: HashFunctions) {
    method picklist (line 114) | pub fn picklist(&self) -> Option<Picklist> {
    method set_picklist (line 118) | pub fn set_picklist(&mut self, value: Picklist) {
    method from_record (line 122) | pub fn from_record(row: &Record) -> Result<Self> {
  type Picklist (line 33) | pub struct Picklist {
  type PickStyle (line 53) | pub enum PickStyle {
  type Select (line 59) | pub trait Select {
    method select (line 60) | fn select(self, selection: &Selection) -> Result<Self>

FILE: src/core/src/signature.rs
  type SigsTrait (line 29) | pub trait SigsTrait {
    method size (line 30) | fn size(&self) -> usize;
    method to_vec (line 31) | fn to_vec(&self) -> Vec<u64>;
    method ksize (line 32) | fn ksize(&self) -> usize;
    method check_compatible (line 33) | fn check_compatible(&self, other: &Self) -> Result<(), Error>;
    method seed (line 34) | fn seed(&self) -> u64;
    method hash_function (line 36) | fn hash_function(&self) -> HashFunctions;
    method add_hash (line 38) | fn add_hash(&mut self, hash: HashIntoType);
    method add_sequence (line 40) | fn add_sequence(&mut self, seq: &[u8], force: bool) -> Result<(), Erro...
    method add_protein (line 62) | fn add_protein(&mut self, seq: &[u8]) -> Result<(), Error> {
    method size (line 86) | fn size(&self) -> usize {
    method to_vec (line 94) | fn to_vec(&self) -> Vec<u64> {
    method ksize (line 102) | fn ksize(&self) -> usize {
    method seed (line 110) | fn seed(&self) -> u64 {
    method hash_function (line 118) | fn hash_function(&self) -> HashFunctions {
    method add_hash (line 126) | fn add_hash(&mut self, hash: HashIntoType) {
    method check_compatible (line 134) | fn check_compatible(&self, other: &Self) -> Result<(), Error> {
    method add_sequence (line 151) | fn add_sequence(&mut self, seq: &[u8], force: bool) -> Result<(), Erro...
    method add_protein (line 159) | fn add_protein(&mut self, seq: &[u8]) -> Result<(), Error> {
  type ReadingFrame (line 169) | pub enum ReadingFrame {
    method fmt (line 182) | fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
    method new_dna (line 201) | pub fn new_dna(sequence: &[u8]) -> Self {
    method new_protein (line 208) | pub fn new_protein(sequence: &[u8], dayhoff: bool, hp: bool) -> Self {
    method new_skipmer (line 222) | pub fn new_skipmer(
    method new_translated (line 246) | pub fn new_translated(
    method fw (line 279) | pub fn fw(&self) -> &[u8] {
    method rc (line 288) | pub fn rc(&self) -> &[u8] {
    method length (line 296) | pub fn length(&self) -> usize {
    method frame_type (line 304) | pub fn frame_type(&self) -> &'static str {
  type SeqToHashes (line 312) | pub struct SeqToHashes {
    method new (line 323) | pub fn new(
    method dna_frames (line 365) | fn dna_frames(seq: &[u8]) -> Vec<ReadingFrame> {
    method protein_frames (line 370) | fn protein_frames(seq: &[u8], hash_function: &HashFunctions) -> Vec<Re...
    method translated_frames (line 379) | fn translated_frames(
    method skipmer_frames (line 409) | fn skipmer_frames(
    method out_of_bounds (line 429) | fn out_of_bounds(&self, frame: &ReadingFrame) -> bool {
  type Item (line 435) | type Item = Result<u64, Error>;
  method next (line 437) | fn next(&mut self) -> Option<Self::Item> {
  type Signature (line 508) | pub struct Signature {
    method name (line 550) | pub fn name(&self) -> Option<String> {
    method name_str (line 555) | pub fn name_str(&self) -> String {
    method set_name (line 559) | pub fn set_name(&mut self, name: &str) {
    method filename (line 563) | pub fn filename(&self) -> String {
    method set_filename (line 571) | pub fn set_filename(&mut self, name: &str) {
    method size (line 575) | pub fn size(&self) -> usize {
    method sketches (line 579) | pub fn sketches(&self) -> Vec<Sketch> {
    method reset_sketches (line 583) | pub fn reset_sketches(&mut self) {
    method push (line 587) | pub fn push(&mut self, sketch: Sketch) {
    method license (line 591) | pub fn license(&self) -> String {
    method class (line 595) | pub fn class(&self) -> String {
    method hash_function (line 599) | pub fn hash_function(&self) -> String {
    method email (line 603) | pub fn email(&self) -> String {
    method md5sum (line 607) | pub fn md5sum(&self) -> String {
    method select_sketch (line 620) | pub fn select_sketch(&self, sketch: &Sketch) -> Option<&Sketch> {
    method get_sketch (line 638) | pub fn get_sketch(&self) -> Option<&Sketch> {
    method minhash (line 654) | pub fn minhash(&self) -> Option<&KmerMinHash> {
    method from_path (line 670) | pub fn from_path<P: AsRef<Path>>(path: P) -> Result<Vec<Signature>, Er...
    method from_reader (line 675) | pub fn from_reader<R>(rdr: R) -> Result<Vec<Signature>, Error>
    method load_signatures (line 685) | pub fn load_signatures<R>(
    method add_sequence (line 762) | pub fn add_sequence(&mut self, seq: &[u8], force: bool) -> Result<(), ...
    method add_protein (line 780) | pub fn add_protein(&mut self, seq: &[u8]) -> Result<(), Error> {
    method iter_mut (line 800) | pub fn iter_mut(&mut self) -> IterMut<'_> {
    method iter (line 808) | pub fn iter(&self) -> Iter<'_> {
    type Error (line 1002) | type Error = Error;
    method try_into (line 1004) | fn try_into(self) -> Result<KmerMinHash, Error> {
  function default_license (line 537) | fn default_license() -> String {
  function default_class (line 541) | fn default_class() -> String {
  function default_version (line 545) | fn default_version() -> f64 {
  type IterMut (line 817) | pub struct IterMut<'a> {
  type Item (line 823) | type Item = &'a mut Sketch;
  type IntoIter (line 824) | type IntoIter = IterMut<'a>;
  method into_iter (line 826) | fn into_iter(self) -> IterMut<'a> {
  type Item (line 832) | type Item = &'a mut Sketch;
  method next (line 834) | fn next(&mut self) -> Option<&'a mut Sketch> {
  method size_hint (line 843) | fn size_hint(&self) -> (usize, Option<usize>) {
  type Iter (line 848) | pub struct Iter<'a> {
  type Item (line 854) | type Item = &'a Sketch;
  method next (line 856) | fn next(&mut self) -> Option<&'a Sketch> {
  method size_hint (line 865) | fn size_hint(&self) -> (usize, Option<usize>) {
  method len (line 873) | fn len(&self) -> usize {
  method clone (line 879) | fn clone(&self) -> Self {
  method to_writer (line 888) | fn to_writer<W>(&self, writer: &mut W) -> Result<(), Error>
  method to_writer (line 898) | fn to_writer<W>(&self, writer: &mut W) -> Result<(), Error>
  method select (line 908) | fn select(mut self, selection: &Selection) -> Result<Self, Error> {
  method default (line 966) | fn default() -> Signature {
  method eq (line 981) | fn eq(&self, other: &Signature) -> bool {
  function load_sig (line 1043) | fn load_sig() {
  function load_signature (line 1060) | fn load_signature() {
  function signature_from_computeparams (line 1084) | fn signature_from_computeparams() {
  function signature_slow_path (line 1103) | fn signature_slow_path() {
  function signature_add_sequence_protein (line 1121) | fn signature_add_sequence_protein() {
  function signature_add_protein (line 1139) | fn signature_add_protein() {
  function signature_skipm2n3_add_sequence (line 1157) | fn signature_skipm2n3_add_sequence() {
  function signature_skipm1n3_add_sequence (line 1178) | fn signature_skipm1n3_add_sequence() {
  function signature_skipm2n3_add_sequence_too_small (line 1198) | fn signature_skipm2n3_add_sequence_too_small() {
  function signature_skipm1n3_add_sequence_too_small (line 1224) | fn signature_skipm1n3_add_sequence_too_small() {
  function signature_add_sequence_cp (line 1249) | fn signature_add_sequence_cp() {
  function load_minhash_from_signature (line 1275) | fn load_minhash_from_signature() {
  function load_single_sketch_from_signature (line 1291) | fn load_single_sketch_from_signature() {
  function get_sketch_multisketch_panic (line 1315) | fn get_sketch_multisketch_panic() {
  function load_minhash_multisketch_panic (line 1340) | fn load_minhash_multisketch_panic() {
  function selection_with_downsample (line 1364) | fn selection_with_downsample() {
  function selection_protein (line 1388) | fn selection_protein() {
  function selection_dayhoff (line 1408) | fn selection_dayhoff() {
  function selection_hp (line 1429) | fn selection_hp() {
  function selection_protein2 (line 1449) | fn selection_protein2() {
  function selection_scaled_too_low (line 1469) | fn selection_scaled_too_low() {
  function test_readingframe_dna (line 1488) | fn test_readingframe_dna() {
  function test_fw_dna (line 1497) | fn test_fw_dna() {
  function test_rc_dna (line 1507) | fn test_rc_dna() {
  function test_length_dna (line 1517) | fn test_length_dna() {
  function test_frame_type_dna (line 1527) | fn test_frame_type_dna() {
  function test_fw_protein (line 1537) | fn test_fw_protein() {
  function test_rc_protein_panics (line 1547) | fn test_rc_protein_panics() {
  function test_length_protein (line 1556) | fn test_length_protein() {
  function test_frame_type_protein (line 1565) | fn test_frame_type_protein() {
  function test_readingframe_display_protein (line 1574) | fn test_readingframe_display_protein() {
  function test_seqtohashes_frames_dna (line 1587) | fn test_seqtohashes_frames_dna() {
  function test_seqtohashes_frames_is_protein (line 1605) | fn test_seqtohashes_frames_is_protein() {
  function test_readingframe_protein (line 1622) | fn test_readingframe_protein() {
  function test_seqtohashes_frames_is_protein_try_access_rc (line 1633) | fn test_seqtohashes_frames_is_protein_try_access_rc() {
  function test_seqtohashes_frames_is_protein_dayhoff (line 1651) | fn test_seqtohashes_frames_is_protein_dayhoff() {
  function test_seqtohashes_frames_is_protein_hp (line 1669) | fn test_seqtohashes_frames_is_protein_hp() {
  function test_seqtohashes_frames_translate_protein (line 1687) | fn test_seqtohashes_frames_translate_protein() {
  function test_readingframe_translate (line 1708) | fn test_readingframe_translate() {
  function test_readingframe_skipmer (line 1725) | fn test_readingframe_skipmer() {
  function test_seqtohashes_frames_skipmer_m1n3 (line 1747) | fn test_seqtohashes_frames_skipmer_m1n3() {
  function test_seqtohashes_frames_skipmer_m2n3 (line 1775) | fn test_seqtohashes_frames_skipmer_m2n3() {
  function test_seqtohashes_dna (line 1802) | fn test_seqtohashes_dna() {
  function test_seqtohashes_dna_2 (line 1839) | fn test_seqtohashes_dna_2() {
  function test_seqtohashes_is_protein (line 1878) | fn test_seqtohashes_is_protein() {
  function test_seqtohashes_translate (line 1921) | fn test_seqtohashes_translate() {
  function test_seqtohashes_skipm1n3 (line 1961) | fn test_seqtohashes_skipm1n3() {
  function test_seq2hashes_skipm2n3 (line 1999) | fn test_seq2hashes_skipm2n3() {
  function test_seqtohashes_skipm2n3_2 (line 2037) | fn test_seqtohashes_skipm2n3_2() {

FILE: src/core/src/sketch/hyperloglog/estimators.rs
  type CounterType (line 6) | pub type CounterType = u8;
  type MultiplicityInteger (line 9) | pub trait MultiplicityInteger:
    constant ZERO (line 21) | const ZERO: Self;
    constant ONE (line 23) | const ONE: Self;
    method to_f64 (line 26) | fn to_f64(self) -> f64;
  function counts (line 46) | pub fn counts<M: MultiplicityInteger>(registers: &[CounterType], q: usiz...
  function mle (line 57) | pub fn mle<M: MultiplicityInteger>(counts: &[M], p: usize, q: usize, rel...
  function joint_mle (line 162) | pub fn joint_mle(
  function joint_mle_dispatch (line 181) | fn joint_mle_dispatch<M: MultiplicityInteger>(

FILE: src/core/src/sketch/hyperloglog/mod.rs
  type HyperLogLog (line 33) | pub struct HyperLogLog {
    method with_error_rate (line 41) | pub fn with_error_rate(error_rate: f64, ksize: usize) -> Result<HyperL...
    method new (line 46) | pub fn new(p: usize, ksize: usize) -> Result<HyperLogLog, Error> {
    method merge (line 62) | pub fn merge(&mut self, other: &HyperLogLog) -> Result<(), Error> {
    method add_word (line 71) | pub fn add_word(&mut self, word: &[u8]) {
    method add_many (line 76) | pub fn add_many(&mut self, hashes: &[HashIntoType]) -> Result<(), Erro...
    method cardinality (line 83) | pub fn cardinality(&self) -> usize {
    method union (line 109) | pub fn union(&self, other: &HyperLogLog) -> usize {
    method similarity (line 116) | pub fn similarity(&self, other: &HyperLogLog) -> f64 {
    method containment (line 123) | pub fn containment(&self, other: &HyperLogLog) -> f64 {
    method intersection (line 130) | pub fn intersection(&self, other: &HyperLogLog) -> usize {
    method save (line 138) | pub fn save<P: AsRef<Path>>(&self, path: P) -> Result<(), Error> {
    method save_to_writer (line 145) | pub fn save_to_writer<W>(&self, wtr: &mut W) -> Result<(), Error>
    method from_reader (line 159) | pub fn from_reader<R>(rdr: R) -> Result<HyperLogLog, Error>
    method from_path (line 188) | pub fn from_path<P: AsRef<Path>>(path: P) -> Result<HyperLogLog, Error> {
  method size (line 195) | fn size(&self) -> usize {
  method to_vec (line 199) | fn to_vec(&self) -> Vec<u64> {
  method ksize (line 203) | fn ksize(&self) -> usize {
  method seed (line 207) | fn seed(&self) -> u64 {
  method hash_function (line 212) | fn hash_function(&self) -> HashFunctions {
  method add_hash (line 217) | fn add_hash(&mut self, hash: HashIntoType) {
  method check_compatible (line 227) | fn check_compatible(&self, other: &HyperLogLog) -> Result<(), Error> {
  method update (line 243) | fn update(&self, other: &mut HyperLogLog) -> Result<(), Error> {
  function hll_add (line 267) | fn hll_add() {
  function hll_joint_mle (line 297) | fn hll_joint_mle() {
  function save_load_hll (line 388) | fn save_load_hll() {
  function test_mle_corner_cases (line 416) | fn test_mle_corner_cases() {

FILE: src/core/src/sketch/minhash.rs
  function max_hash_for_scaled (line 24) | pub fn max_hash_for_scaled(scaled: ScaledType) -> u64 {
  function scaled_for_max_hash (line 32) | pub fn scaled_for_max_hash(max_hash: u64) -> ScaledType {
  type KmerMinHash (line 44) | pub struct KmerMinHash {
    method deserialize (line 134) | fn deserialize<D>(deserializer: D) -> Result<Self, D::Error>
    method new (line 197) | pub fn new(
    method num (line 231) | pub fn num(&self) -> u32 {
    method is_protein (line 235) | pub fn is_protein(&self) -> bool {
    method max_hash (line 239) | pub fn max_hash(&self) -> u64 {
    method scaled (line 243) | pub fn scaled(&self) -> ScaledType {
    method clear (line 247) | pub fn clear(&mut self) {
    method is_empty (line 254) | pub fn is_empty(&self) -> bool {
    method set_hash_function (line 258) | pub fn set_hash_function(&mut self, h: HashFunctions) -> Result<(), Er...
    method track_abundance (line 273) | pub fn track_abundance(&self) -> bool {
    method enable_abundance (line 277) | pub fn enable_abundance(&mut self) -> Result<(), Error> {
    method disable_abundance (line 289) | pub fn disable_abundance(&mut self) {
    method reset_md5sum (line 293) | fn reset_md5sum(&self) {
    method md5sum (line 300) | pub fn md5sum(&self) -> String {
    method add_hash (line 319) | pub fn add_hash(&mut self, hash: u64) {
    method add_hash_with_abundance (line 323) | pub fn add_hash_with_abundance(&mut self, hash: u64, abundance: u64) {
    method set_hash_with_abundance (line 395) | pub fn set_hash_with_abundance(&mut self, hash: u64, abundance: u64) {
    method add_word (line 411) | pub fn add_word(&mut self, word: &[u8]) {
    method remove_hash (line 416) | pub fn remove_hash(&mut self, hash: u64) {
    method remove_from (line 428) | pub fn remove_from(&mut self, other: &KmerMinHash) -> Result<(), Error> {
    method remove_many (line 435) | pub fn remove_many<T: IntoIterator<Item = u64>>(&mut self, hashes: T) ...
    method merge (line 442) | pub fn merge(&mut self, other: &KmerMinHash) -> Result<(), Error> {
    method add_from (line 528) | pub fn add_from(&mut self, other: &KmerMinHash) -> Result<(), Error> {
    method add_many (line 535) | pub fn add_many(&mut self, hashes: &[u64]) -> Result<(), Error> {
    method add_many_with_abund (line 542) | pub fn add_many_with_abund(&mut self, hashes: &[(u64, u64)]) -> Result...
    method count_common (line 549) | pub fn count_common(&self, other: &KmerMinHash, downsample: bool) -> R...
    method intersection (line 570) | pub fn intersection(&self, other: &KmerMinHash) -> Result<(Vec<u64>, u...
    method intersection_size (line 603) | pub fn intersection_size(&self, other: &KmerMinHash) -> Result<(u64, u...
    method jaccard (line 634) | pub fn jaccard(&self, other: &KmerMinHash) -> Result<f64, Error> {
    method angular_similarity (line 645) | pub fn angular_similarity(&self, other: &KmerMinHash) -> Result<f64, E...
    method similarity (line 692) | pub fn similarity(
    method dayhoff (line 714) | pub fn dayhoff(&self) -> bool {
    method hp (line 718) | pub fn hp(&self) -> bool {
    method skipm1n3 (line 722) | pub fn skipm1n3(&self) -> bool {
    method skipm2n3 (line 726) | pub fn skipm2n3(&self) -> bool {
    method mins (line 730) | pub fn mins(&self) -> Vec<u64> {
    method iter_mins (line 734) | pub fn iter_mins(&self) -> impl Iterator<Item = &u64> {
    method abunds (line 738) | pub fn abunds(&self) -> Option<Vec<u64>> {
    method downsample_max_hash (line 743) | pub fn downsample_max_hash(self, max_hash: u64) -> Result<KmerMinHash,...
    method sum_abunds (line 753) | pub fn sum_abunds(&self) -> u64 {
    method to_vec_abunds (line 761) | pub fn to_vec_abunds(&self) -> Vec<(u64, u64)> {
    method as_hll (line 777) | pub fn as_hll(&self) -> HyperLogLog {
    method n_unique_kmers (line 790) | pub fn n_unique_kmers(&self) -> u64 {
    method downsample_scaled (line 795) | pub fn downsample_scaled(self, scaled: ScaledType) -> Result<KmerMinHa...
    method inflate (line 818) | pub fn inflate(&mut self, abunds_from: &KmerMinHash) -> Result<(), Err...
    method inflated_abundances (line 849) | pub fn inflated_abundances(&self, abunds_from: &KmerMinHash) -> Result...
    method from_reader (line 878) | pub fn from_reader<R>(rdr: R) -> Result<KmerMinHash, Error>
    method from (line 1699) | fn from(other: KmerMinHashBTree) -> KmerMinHash {
    method from (line 1724) | fn from(other: &KmerMinHashBTree) -> KmerMinHash {
  method eq (line 69) | fn eq(&self, other: &KmerMinHash) -> bool {
  method clone (line 76) | fn clone(&self) -> Self {
  method default (line 91) | fn default() -> KmerMinHash {
  method serialize (line 106) | fn serialize<S>(&self, serializer: S) -> Result<S::Ok, S::Error>
  method to_writer (line 187) | fn to_writer<W>(&self, writer: &mut W) -> Result<(), Error>
  method size (line 890) | fn size(&self) -> usize {
  method to_vec (line 894) | fn to_vec(&self) -> Vec<u64> {
  method ksize (line 898) | fn ksize(&self) -> usize {
  method seed (line 902) | fn seed(&self) -> u64 {
  method hash_function (line 906) | fn hash_function(&self) -> HashFunctions {
  method add_hash (line 910) | fn add_hash(&mut self, hash: u64) {
  method check_compatible (line 914) | fn check_compatible(&self, other: &KmerMinHash) -> Result<(), Error> {
  type Intersection (line 943) | struct Intersection<T, I: Iterator<Item = T>> {
  function new (line 949) | pub fn new(left: I, right: I) -> Self {
  type Item (line 958) | type Item = T;
  method next (line 960) | fn next(&mut self) -> Option<T> {
  type KmerMinHashBTree (line 991) | pub struct KmerMinHashBTree {
    method deserialize (line 1087) | fn deserialize<D>(deserializer: D) -> Result<Self, D::Error>
    method new (line 1154) | pub fn new(
    method num (line 1185) | pub fn num(&self) -> u32 {
    method is_protein (line 1189) | pub fn is_protein(&self) -> bool {
    method max_hash (line 1193) | pub fn max_hash(&self) -> u64 {
    method scaled (line 1197) | pub fn scaled(&self) -> ScaledType {
    method clear (line 1201) | pub fn clear(&mut self) {
    method is_empty (line 1209) | pub fn is_empty(&self) -> bool {
    method set_hash_function (line 1213) | pub fn set_hash_function(&mut self, h: HashFunctions) -> Result<(), Er...
    method track_abundance (line 1228) | pub fn track_abundance(&self) -> bool {
    method enable_abundance (line 1232) | pub fn enable_abundance(&mut self) -> Result<(), Error> {
    method disable_abundance (line 1244) | pub fn disable_abundance(&mut self) {
    method reset_md5sum (line 1248) | fn reset_md5sum(&self) {
    method md5sum (line 1255) | pub fn md5sum(&self) -> String {
    method add_hash_with_abundance (line 1274) | pub fn add_hash_with_abundance(&mut self, hash: u64, abundance: u64) {
    method add_word (line 1330) | pub fn add_word(&mut self, word: &[u8]) {
    method remove_hash (line 1335) | pub fn remove_hash(&mut self, hash: u64) {
    method remove_many (line 1347) | pub fn remove_many<T: IntoIterator<Item = u64>>(&mut self, hashes: T) ...
    method merge (line 1354) | pub fn merge(&mut self, other: &KmerMinHashBTree) -> Result<(), Error> {
    method add_from (line 1384) | pub fn add_from(&mut self, other: &KmerMinHashBTree) -> Result<(), Err...
    method add_many (line 1391) | pub fn add_many(&mut self, hashes: &[u64]) -> Result<(), Error> {
    method add_many_with_abund (line 1398) | pub fn add_many_with_abund(&mut self, hashes: &[(u64, u64)]) -> Result...
    method count_common (line 1405) | pub fn count_common(&self, other: &KmerMinHashBTree, downsample: bool)...
    method intersection (line 1427) | pub fn intersection(&self, other: &KmerMinHashBTree) -> Result<(Vec<u6...
    method intersection_size (line 1459) | pub fn intersection_size(&self, other: &KmerMinHashBTree) -> Result<(u...
    method jaccard (line 1490) | pub fn jaccard(&self, other: &KmerMinHashBTree) -> Result<f64, Error> {
    method angular_similarity (line 1501) | pub fn angular_similarity(&self, other: &KmerMinHashBTree) -> Result<f...
    method similarity (line 1532) | pub fn similarity(
    method dayhoff (line 1554) | pub fn dayhoff(&self) -> bool {
    method hp (line 1558) | pub fn hp(&self) -> bool {
    method hash_function (line 1562) | pub fn hash_function(&self) -> HashFunctions {
    method mins (line 1566) | pub fn mins(&self) -> Vec<u64> {
    method iter_mins (line 1570) | pub fn iter_mins(&self) -> impl Iterator<Item = &u64> {
    method abunds (line 1574) | pub fn abunds(&self) -> Option<Vec<u64>> {
    method downsample_max_hash (line 1581) | pub fn downsample_max_hash(self, max_hash: u64) -> Result<KmerMinHashB...
    method downsample_scaled (line 1592) | pub fn downsample_scaled(self, scaled: ScaledType) -> Result<KmerMinHa...
    method to_vec_abunds (line 1615) | pub fn to_vec_abunds(&self) -> Vec<(u64, u64)> {
    method sum_abunds (line 1627) | pub fn sum_abunds(&self) -> u64 {
    method from_reader (line 1635) | pub fn from_reader<R>(rdr: R) -> Result<KmerMinHashBTree, Error>
    method from (line 1750) | fn from(other: KmerMinHash) -> KmerMinHashBTree {
  method eq (line 1019) | fn eq(&self, other: &KmerMinHashBTree) -> bool {
  method clone (line 1026) | fn clone(&self) -> Self {
  method default (line 1042) | fn default() -> KmerMinHashBTree {
  method serialize (line 1058) | fn serialize<S>(&self, serializer: S) -> Result<S::Ok, S::Error>
  method to_writer (line 1144) | fn to_writer<W>(&self, writer: &mut W) -> Result<(), Error>
  method size (line 1647) | fn size(&self) -> usize {
  method to_vec (line 1651) | fn to_vec(&self) -> Vec<u64> {
  method ksize (line 1655) | fn ksize(&self) -> usize {
  method seed (line 1659) | fn seed(&self) -> u64 {
  method hash_function (line 1663) | fn hash_function(&self) -> HashFunctions {
  method add_hash (line 1667) | fn add_hash(&mut self, hash: u64) {
  method check_compatible (line 1671) | fn check_compatible(&self, other: &KmerMinHashBTree) -> Result<(), Error> {
  function intersection (line 1774) | fn intersection<'a>(
  function intersection_size (line 1818) | fn intersection_size<'a>(
  function test_deserialize_valid (line 1869) | fn test_deserialize_valid() {
  function test_deserialize_invalid_molecule (line 1896) | fn test_deserialize_invalid_molecule() {

FILE: src/core/src/sketch/mod.rs
  type Sketch (line 17) | pub enum Sketch {

FILE: src/core/src/sketch/nodegraph.rs
  type Nodegraph (line 15) | pub struct Nodegraph {
    method update (line 33) | fn update(&self, other: &mut Nodegraph) -> Result<(), Error> {
    method new (line 67) | pub fn new(tablesizes: &[usize], ksize: usize) -> Nodegraph {
    method with_tables (line 81) | pub fn with_tables(tablesize: usize, n_tables: usize, ksize: usize) ->...
    method count_kmer (line 102) | pub(crate) fn count_kmer(&mut self, kmer: &[u8]) -> bool {
    method count (line 107) | pub fn count(&mut self, hash: HashIntoType) -> bool {
    method get (line 126) | pub fn get(&self, hash: HashIntoType) -> usize {
    method get_kmer (line 136) | pub(crate) fn get_kmer(&self, kmer: &[u8]) -> usize {
    method expected_collisions (line 141) | pub fn expected_collisions(&self) -> f64 {
    method tablesize (line 150) | pub fn tablesize(&self) -> usize {
    method noccupied (line 154) | pub fn noccupied(&self) -> usize {
    method matches (line 158) | pub fn matches(&self, mh: &KmerMinHash) -> usize {
    method ntables (line 162) | pub fn ntables(&self) -> usize {
    method ksize (line 166) | pub fn ksize(&self) -> usize {
    method into_bitsets (line 170) | pub fn into_bitsets(self) -> Vec<FixedBitSet> {
    method save (line 175) | pub fn save<P: AsRef<Path>>(&self, path: P) -> Result<(), Error> {
    method save_to_writer (line 182) | pub fn save_to_writer<W>(&self, wtr: &mut W) -> Result<(), Error>
    method from_reader (line 222) | pub fn from_reader<R>(rdr: R) -> Result<Nodegraph, Error>
    method from_path (line 275) | pub fn from_path<P: AsRef<Path>>(path: P) -> Result<Nodegraph, Error> {
    method tablesizes (line 280) | pub fn tablesizes(&self) -> Vec<u64> {
    method n_occupied_bins (line 284) | pub fn n_occupied_bins(&self) -> usize {
    method unique_kmers (line 288) | pub fn unique_kmers(&self) -> usize {
    method similarity (line 292) | pub fn similarity(&self, other: &Nodegraph) -> f64 {
    method containment (line 308) | pub fn containment(&self, other: &Nodegraph) -> f64 {
  method eq (line 25) | fn eq(&self, other: &Nodegraph) -> bool {
  method update (line 49) | fn update(&self, other: &mut Nodegraph) -> Result<(), Error> {
  method update (line 58) | fn update(&self, other: &mut Nodegraph) -> Result<(), Error> {
  function twobit_repr (line 320) | fn twobit_repr(a: u8) -> HashIntoType {
  function twobit_comp (line 330) | fn twobit_comp(a: u8) -> HashIntoType {
  function uniqify_rc (line 340) | fn uniqify_rc(f: HashIntoType, r: HashIntoType) -> HashIntoType {
  function _hash (line 344) | fn _hash(kmer: &[u8]) -> HashIntoType {
  function load_compressed (line 416) | fn load_compressed() {
  function count_and_get_nodegraph (line 428) | fn count_and_get_nodegraph() {
  function containment (line 438) | fn containment() {
  function load_save_nodegraph (line 456) | fn load_save_nodegraph() {
  function binary_repr_load (line 484) | fn binary_repr_load() {
  function binary_repr_save (line 508) | fn binary_repr_save() {
  function update_nodegraph (line 532) | fn update_nodegraph() {
  function update_nodegraph_many (line 556) | fn update_nodegraph_many() -> Result<(), Box<dyn std::error::Error>> {
  function load_nodegraph (line 593) | fn load_nodegraph() {

FILE: src/core/src/storage/mod.rs
  type Storage (line 24) | pub trait Storage {
    method save (line 26) | fn save(&self, path: &str, content: &[u8]) -> Result<String>;
    method load (line 29) | fn load(&self, path: &str) -> Result<Vec<u8>>;
    method args (line 32) | fn args(&self) -> StorageArgs;
    method load_sig (line 35) | fn load_sig(&self, path: &str) -> Result<SigStore> {
    method spec (line 47) | fn spec(&self) -> String;
    method save_sig (line 50) | fn save_sig(&self, path: &str, sig: Signature) -> Result<String> {
    method save (line 195) | fn save(&self, path: &str, content: &[u8]) -> Result<String> {
    method load (line 199) | fn load(&self, path: &str) -> Result<Vec<u8>> {
    method args (line 203) | fn args(&self) -> StorageArgs {
    method load_sig (line 207) | fn load_sig(&self, path: &str) -> Result<SigStore> {
    method spec (line 213) | fn spec(&self) -> String {
    method save (line 239) | fn save(&self, path: &str, content: &[u8]) -> Result<String> {
    method load (line 243) | fn load(&self, path: &str) -> Result<Vec<u8>> {
    method args (line 247) | fn args(&self) -> StorageArgs {
    method load_sig (line 251) | fn load_sig(&self, path: &str) -> Result<SigStore> {
    method spec (line 255) | fn spec(&self) -> String {
    method save (line 281) | fn save(&self, path: &str, content: &[u8]) -> Result<String> {
    method load (line 297) | fn load(&self, path: &str) -> Result<Vec<u8>> {
    method args (line 306) | fn args(&self) -> StorageArgs {
    method load_sig (line 312) | fn load_sig(&self, path: &str) -> Result<SigStore> {
    method spec (line 324) | fn spec(&self) -> String {
    method save (line 354) | fn save(&self, _path: &str, _content: &[u8]) -> Result<String> {
    method load (line 358) | fn load(&self, path: &str) -> Result<Vec<u8>> {
    method args (line 381) | fn args(&self) -> StorageArgs {
    method load_sig (line 385) | fn load_sig(&self, path: &str) -> Result<SigStore> {
    method spec (line 396) | fn spec(&self) -> String {
    method save (line 666) | fn save(&self, _path: &str, _content: &[u8]) -> Result<String> {
    method load (line 670) | fn load(&self, path: &str) -> Result<Vec<u8>> {
    method args (line 682) | fn args(&self) -> StorageArgs {
    method load_sig (line 686) | fn load_sig(&self, path: &str) -> Result<SigStore> {
    method save_sig (line 690) | fn save_sig(&self, path: &str, sig: Signature) -> Result<String> {
    method spec (line 697) | fn spec(&self) -> String {
  type StorageError (line 61) | pub enum StorageError {
  type InnerStorage (line 86) | pub struct InnerStorage(Arc<RwLock<dyn Storage + Send + Sync + 'static>>);
    method new (line 163) | pub fn new(inner: impl Storage + Send + Sync + 'static) -> InnerStorage {
    method from_spec (line 167) | pub fn from_spec(spec: String) -> Result<Self> {
  type SigStore (line 89) | pub struct SigStore {
    method new_with_storage (line 468) | pub fn new_with_storage(sig: Signature, storage: InnerStorage) -> Self {
    method name (line 481) | pub fn name(&self) -> String {
    method fmt (line 496) | fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
    method data (line 506) | fn data(&self) -> Result<&Signature> {
    method save (line 526) | pub fn save(&self, path: &str) -> Result<String> {
    method from (line 557) | fn from(other: Signature) -> SigStore {
    type Error (line 572) | type Error = crate::Error;
    method try_into (line 574) | fn try_into(self) -> std::result::Result<KmerMinHash, Self::Error> {
    method similarity (line 581) | fn similarity(&self, other: &SigStore) -> f64 {
    method containment (line 596) | fn containment(&self, other: &SigStore) -> f64 {
    method from (line 620) | fn from(other: DatasetInfo) -> SigStore {
  method eq (line 106) | fn eq(&self, other: &Self) -> bool {
  type StorageArgs (line 116) | pub enum StorageArgs {
  type FSStorage (line 122) | pub struct FSStorage {
    method from (line 219) | fn from(other: &StorageArgs) -> FSStorage {
    method new (line 261) | pub fn new(location: &str, subdir: &str) -> FSStorage {
    method set_base (line 272) | pub fn set_base(&mut self, location: &str) {
  type ZipStorage (line 130) | pub struct ZipStorage {
    method from_file (line 402) | pub fn from_file<P: AsRef<Path>>(location: P) -> Result<Self> {
    method path (line 429) | pub fn path(&self) -> Option<PathBuf> {
    method subdir (line 433) | pub fn subdir(&self) -> Option<String> {
    method set_subdir (line 437) | pub fn set_subdir(&mut self, path: String) {
    method list_sbts (line 441) | pub fn list_sbts(&self) -> Result<Vec<String>> {
    method filenames (line 457) | pub fn filenames(&self) -> Result<Vec<String>> {
  type MemStorage (line 147) | pub struct MemStorage {
    method new (line 658) | pub fn new() -> Self {
  type Metadata (line 158) | pub type Metadata<'a> = BTreeMap<&'a OsStr, &'a piz::read::FileMetadata<...
  function lookup (line 329) | fn lookup<'a, P: AsRef<Path>>(
  function find_subdirs (line 340) | fn find_subdirs<'a>(archive: &'a piz::ZipArchive<'a>) -> Result<Option<S...
  method select (line 487) | fn select(mut self, selection: &Selection) -> Result<Self> {
  method from (line 543) | fn from(other: SigStore) -> Signature {
  type Target (line 549) | type Target = Signature;
  method deref (line 551) | fn deref(&self) -> &Signature {
  type DatasetInfo (line 614) | pub struct DatasetInfo {
  method similarity (line 632) | fn similarity(&self, other: &Signature) -> f64 {
  method containment (line 643) | fn containment(&self, other: &Signature) -> f64 {

FILE: src/core/src/storage/rocksdb.rs
  constant HASHES (line 9) | pub(crate) const HASHES: &str = "hashes";
  constant COLORS (line 10) | pub(crate) const COLORS: &str = "colors";
  constant METADATA (line 11) | pub(crate) const METADATA: &str = "metadata";
  constant STORAGE (line 14) | pub(crate) const STORAGE: &str = "storage";
  constant ALL_CFS (line 16) | pub(crate) const ALL_CFS: [&str; 3] = [HASHES, METADATA, STORAGE];
  type DB (line 18) | pub type DB = rocksdb::DBWithThreadMode<rocksdb::MultiThreaded>;
  type RocksDBStorage (line 22) | pub struct RocksDBStorage {
    method from_path (line 27) | pub fn from_path(path: &str) -> Self {
    method from_db (line 41) | pub fn from_db(db: Arc<DB>) -> Self {
  method save (line 47) | fn save(&self, path: &str, content: &[u8]) -> Result<String> {
  method load (line 54) | fn load(&self, path: &str) -> Result<Vec<u8>> {
  method args (line 60) | fn args(&self) -> StorageArgs {
  method spec (line 64) | fn spec(&self) -> String {
  function cf_descriptors (line 69) | pub(crate) fn cf_descriptors() -> Vec<ColumnFamilyDescriptor> {
  function db_options (line 110) | pub(crate) fn db_options() -> rocksdb::Options {

FILE: src/core/src/wasm.rs
  type KmerMinHash (line 13) | pub struct KmerMinHash(_KmerMinHash);
    method new_with_scaled (line 24) | pub fn new_with_scaled(
    method add_sequence_js (line 57) | pub fn add_sequence_js(&mut self, buf: &str) -> Result<(), JsErrors> {
    method to_json (line 63) | pub fn to_json(&mut self) -> Result<String, JsErrors> {
  type Signature (line 16) | pub struct Signature(_Signature);
    method new_from_params (line 121) | pub fn new_from_params(params: &ComputeParameters) -> Signature {
    method add_sequence_js (line 128) | pub fn add_sequence_js(&mut self, buf: &str) -> Result<(), JsErrors> {
    method add_from_file (line 135) | pub fn add_from_file(
    method to_json (line 158) | pub fn to_json(&mut self) -> Result<String, JsErrors> {
    method size (line 164) | pub fn size(&self) -> usize {
  type ComputeParameters (line 19) | pub struct ComputeParameters(_ComputeParameters);
    method new_with_params (line 73) | pub fn new_with_params() -> ComputeParameters {
    method set_ksizes (line 79) | pub fn set_ksizes(&mut self, ksizes: Vec<u32>) {
    method set_scaled (line 84) | pub fn set_scaled(&mut self, scaled: ScaledType) {
    method set_num (line 89) | pub fn set_num(&mut self, num: u32) {
    method set_protein (line 94) | pub fn set_protein(&mut self, is_protein: bool) {
    method set_dayhoff (line 99) | pub fn set_dayhoff(&mut self, dayhoff: bool) {
    method set_hp (line 104) | pub fn set_hp(&mut self, hp: bool) {
    method set_track_abundance (line 109) | pub fn set_track_abundance(&mut self, track: bool) {
    method set_seed (line 113) | pub fn set_seed(&mut self, seed: u32) {
  type JsErrors (line 170) | pub enum JsErrors {
    method into (line 185) | fn into(self) -> JsValue {
  function wasm_test (line 197) | fn wasm_test() {
  type SyncFile (line 219) | pub struct SyncFile {
    method new (line 230) | pub fn new(file: web_sys::File, cb: Option<js_sys::Function>) -> Self {
    method size (line 235) | pub fn size(&self) -> u64 {
    method set_pos (line 244) | fn set_pos(&mut self, pos: u64) {
    method progress (line 255) | pub fn progress(&self) -> f64 {
    method read (line 261) | fn read(&mut self, buf: &mut [u8]) -> Result<usize, std::io::Error> {

FILE: src/core/tests/minhash.rs
  constant EPSILON (line 19) | const EPSILON: f64 = 0.01;
  function throws_error (line 22) | fn throws_error() {
  function merge (line 32) | fn merge() {
  function invalid_dna (line 59) | fn invalid_dna() {
  function similarity (line 71) | fn similarity() -> Result<(), Box<dyn std::error::Error>> {
  function similarity_2 (line 86) | fn similarity_2() -> Result<(), Box<dyn std::error::Error>> {
  function similarity_3 (line 106) | fn similarity_3() -> Result<(), Box<dyn std::error::Error>> {
  function angular_similarity_requires_abundance (line 130) | fn angular_similarity_requires_abundance() -> Result<(), Box<dyn std::er...
  function angular_similarity_btree_requires_abundance (line 143) | fn angular_similarity_btree_requires_abundance() -> Result<(), Box<dyn s...
  function dayhoff (line 156) | fn dayhoff() {
  function hp (line 168) | fn hp() {
  function max_for_scaled (line 180) | fn max_for_scaled() {
  function load_save_minhash_sketches (line 383) | fn load_save_minhash_sketches() {
  function load_save_minhash_sketches_abund (line 484) | fn load_save_minhash_sketches_abund() {
  function merge_empty_scaled (line 585) | fn merge_empty_scaled() {
  function check_errors (line 611) | fn check_errors() {
  function test_inflate (line 801) | fn test_inflate() {
  function test_inflated_abundances (line 823) | fn test_inflated_abundances() {
  function test_inflate_noabund (line 845) | fn test_inflate_noabund() {
  function test_inflated_abunds_noabund (line 860) | fn test_inflated_abunds_noabund() {
  function test_sum_abunds (line 874) | fn test_sum_abunds() {
  function test_sum_abunds_noabund (line 883) | fn test_sum_abunds_noabund() {
  function test_n_unique_kmers (line 892) | fn test_n_unique_kmers() {
  function test_scaled_downsampling_kmerminhash (line 901) | fn test_scaled_downsampling_kmerminhash() {
  function test_scaled_downsampling_kmerminhashbtree (line 918) | fn test_scaled_downsampling_kmerminhashbtree() {

FILE: src/core/tests/node.rs
  function pass (line 6) | fn pass() {

FILE: src/core/tests/storage.rs
  function zipstorage_load_file (line 9) | fn zipstorage_load_file() -> Result<(), Box<dyn std::error::Error>> {
  function zipstorage_load_manifest (line 24) | fn zipstorage_load_manifest() -> Result<(), Box<dyn std::error::Error>> {
  function zipstorage_list_sbts (line 36) | fn zipstorage_list_sbts() -> Result<(), Box<dyn std::error::Error>> {
  function zipstorage_parallel_access (line 51) | fn zipstorage_parallel_access() -> Result<(), Box<dyn std::error::Error>> {
  function innerstorage_save_sig (line 85) | fn innerstorage_save_sig() -> Result<(), Box<dyn std::error::Error>> {
  function innerstorage_load (line 108) | fn innerstorage_load() -> Result<(), Box<dyn std::error::Error>> {
  function innerstorage_args (line 132) | fn innerstorage_args() -> Result<(), Box<dyn std::error::Error>> {
  function innerstorage_from_args (line 150) | fn innerstorage_from_args() -> Result<(), Box<dyn std::error::Error>> {

FILE: src/core/tests/test.rs
  function test_murmur (line 2) | fn test_murmur() {

FILE: src/sourmash/__init__.py
  function load_signatures (line 61) | def load_signatures(*args, **kwargs):
  function load_one_signature (line 82) | def load_one_signature(*args, **kwargs):
  function save_signatures (line 98) | def save_signatures(*args, **kwargs):
  function load_sbt_index (line 112) | def load_sbt_index(*args, **kwargs):
  function search_sbt_index (line 127) | def search_sbt_index(*args, **kwargs):

FILE: src/sourmash/__main__.py
  function main (line 8) | def main(arglist=None):

FILE: src/sourmash/cli/__init__.py
  class SourmashParser (line 44) | class SourmashParser(ArgumentParser):
    method __init__ (line 47) | def __init__(self, citation=True, **kwargs):
    method print_citation (line 52) | def print_citation(cls):
    method _subparser_from_name (line 61) | def _subparser_from_name(self, name):
    method print_help (line 72) | def print_help(self):
    method parse_args (line 76) | def parse_args(self, args=None, namespace=None):
  function get_parser (line 97) | def get_parser():
  function parse_args (line 165) | def parse_args(arglist=None):

FILE: src/sourmash/cli/categorize.py
  function subparser (line 6) | def subparser(subparsers):
  function main (line 36) | def main(args):

FILE: src/sourmash/cli/compare.py
  function subparser (line 39) | def subparser(subparsers):
  function main (line 128) | def main(args):

FILE: src/sourmash/cli/compute.py
  function ksize_parser (line 36) | def ksize_parser(ksizes):
  function subparser (line 47) | def subparser(subparsers):
  function main (line 143) | def main(args):

FILE: src/sourmash/cli/gather.py
  function subparser (line 74) | def subparser(subparsers):
  function main (line 200) | def main(args):

FILE: src/sourmash/cli/import_csv.py
  function subparser (line 6) | def subparser(subparsers):
  function main (line 16) | def main(args):

FILE: src/sourmash/cli/index.py
  function subparser (line 30) | def subparser(subparsers):
  function main (line 95) | def main(args):

FILE: src/sourmash/cli/info.py
  function subparser (line 10) | def subparser(subparsers):
  function info (line 20) | def info(verbose=False):
  function main (line 36) | def main(args):

FILE: src/sourmash/cli/lca/__init__.py
  function subparser (line 18) | def subparser(subparsers):

FILE: src/sourmash/cli/lca/classify.py
  function subparser (line 4) | def subparser(subparsers):
  function main (line 47) | def main(args):

FILE: src/sourmash/cli/lca/compare_csv.py
  function subparser (line 4) | def subparser(subparsers):
  function main (line 38) | def main(args):

FILE: src/sourmash/cli/lca/index.py
  function subparser (line 6) | def subparser(subparsers):
  function main (line 79) | def main(args):

FILE: src/sourmash/cli/lca/rankinfo.py
  function subparser (line 4) | def subparser(subparsers):
  function main (line 22) | def main(args):

FILE: src/sourmash/cli/lca/summarize.py
  function subparser (line 4) | def subparser(subparsers):
  function main (line 50) | def main(args):

FILE: src/sourmash/cli/migrate.py
  function subparser (line 4) | def subparser(subparsers):
  function main (line 9) | def main(args):

FILE: src/sourmash/cli/multigather.py
  function subparser (line 42) | def subparser(subparsers):
  function main (line 119) | def main(args):

FILE: src/sourmash/cli/plot.py
  function subparser (line 4) | def subparser(subparsers):
  function main (line 82) | def main(args):

FILE: src/sourmash/cli/prefetch.py
  function subparser (line 12) | def subparser(subparsers):
  function main (line 83) | def main(args):

FILE: src/sourmash/cli/sbt_combine.py
  function subparser (line 4) | def subparser(subparsers):
  function main (line 11) | def main(args):

FILE: src/sourmash/cli/scripts/__init__.py
  function __getattr__ (line 25) | def __getattr__(name):
  function subparser (line 31) | def subparser(subparsers):

FILE: src/sourmash/cli/search.py
  function subparser (line 53) | def subparser(subparsers):
  function main (line 143) | def main(args):

FILE: src/sourmash/cli/sig/__init__.py
  function subparser (line 35) | def subparser(subparsers):

FILE: src/sourmash/cli/sig/cat.py
  function subparser (line 26) | def subparser(subparsers):
  function main (line 62) | def main(args):

FILE: src/sourmash/cli/sig/check.py
  function subparser (line 27) | def subparser(subparsers):
  function main (line 104) | def main(args):

FILE: src/sourmash/cli/sig/collect.py
  function subparser (line 25) | def subparser(subparsers):
  function main (line 88) | def main(args):

FILE: src/sourmash/cli/sig/describe.py
  function subparser (line 33) | def subparser(subparsers):
  function main (line 58) | def main(args):

FILE: src/sourmash/cli/sig/downsample.py
  function subparser (line 37) | def subparser(subparsers):
  function main (line 66) | def main(args):

FILE: src/sourmash/cli/sig/export.py
  function subparser (line 19) | def subparser(subparsers):
  function main (line 38) | def main(args):

FILE: src/sourmash/cli/sig/extract.py
  function subparser (line 48) | def subparser(subparsers):
  function main (line 84) | def main(args):

FILE: src/sourmash/cli/sig/fileinfo.py
  function subparser (line 17) | def subparser(subparsers):
  function main (line 37) | def main(args):

FILE: src/sourmash/cli/sig/filter.py
  function subparser (line 27) | def subparser(subparsers):
  function main (line 70) | def main(args):

FILE: src/sourmash/cli/sig/flatten.py
  function subparser (line 24) | def subparser(subparsers):
  function main (line 59) | def main(args):

FILE: src/sourmash/cli/sig/grep.py
  function subparser (line 32) | def subparser(subparsers):
  function main (line 105) | def main(args):

FILE: src/sourmash/cli/sig/inflate.py
  function subparser (line 6) | def subparser(subparsers):
  function main (line 28) | def main(args):

FILE: src/sourmash/cli/sig/ingest.py
  function subparser (line 16) | def subparser(subparsers):
  function main (line 37) | def main(args):

FILE: src/sourmash/cli/sig/intersect.py
  function subparser (line 28) | def subparser(subparsers):
  function main (line 60) | def main(args):

FILE: src/sourmash/cli/sig/kmers.py
  function subparser (line 54) | def subparser(subparsers):
  function main (line 96) | def main(args):

FILE: src/sourmash/cli/sig/manifest.py
  function subparser (line 20) | def subparser(subparsers):
  function main (line 64) | def main(args):

FILE: src/sourmash/cli/sig/merge.py
  function subparser (line 30) | def subparser(subparsers):
  function main (line 59) | def main(args):

FILE: src/sourmash/cli/sig/overlap.py
  function subparser (line 30) | def subparser(subparsers):
  function main (line 41) | def main(args):

FILE: src/sourmash/cli/sig/rename.py
  function subparser (line 28) | def subparser(subparsers):
  function main (line 58) | def main(args):

FILE: src/sourmash/cli/sig/split.py
  function subparser (line 42) | def subparser(subparsers):
  function main (line 72) | def main(args):

FILE: src/sourmash/cli/sig/subtract.py
  function subparser (line 28) | def subparser(subparsers):
  function main (line 58) | def main(args):

FILE: src/sourmash/cli/sketch/__init__.py
  function subparser (line 20) | def subparser(subparsers):

FILE: src/sourmash/cli/sketch/dna.py
  function subparser (line 32) | def subparser(subparsers):
  function main (line 103) | def main(args):

FILE: src/sourmash/cli/sketch/fromfile.py
  function subparser (line 30) | def subparser(subparsers):
  function main (line 90) | def main(args):

FILE: src/sourmash/cli/sketch/protein.py
  function subparser (line 33) | def subparser(subparsers):
  function main (line 107) | def main(args):

FILE: src/sourmash/cli/sketch/translate.py
  function subparser (line 34) | def subparser(subparsers):
  function main (line 113) | def main(args):

FILE: src/sourmash/cli/storage/__init__.py
  function subparser (line 14) | def subparser(subparsers):

FILE: src/sourmash/cli/storage/convert.py
  function subparser (line 4) | def subparser(subparsers):
  function main (line 10) | def main(args):

FILE: src/sourmash/cli/tax/__init__.py
  function subparser (line 20) | def subparser(subparsers):

FILE: src/sourmash/cli/tax/annotate.py
  function subparser (line 21) | def subparser(subparsers):
  function main (line 90) | def main(args):

FILE: src/sourmash/cli/tax/genome.py
  function subparser (line 46) | def subparser(subparsers):
  function main (line 140) | def main(args):

FILE: src/sourmash/cli/tax/grep.py
  function subparser (line 23) | def subparser(subparsers):
  function main (line 88) | def main(args):

FILE: src/sourmash/cli/tax/metagenome.py
  function subparser (line 34) | def subparser(subparsers):
  function main (line 151) | def main(args):

FILE: src/sourmash/cli/tax/prepare.py
  function subparser (line 19) | def subparser(subparsers):
  function main (line 70) | def main(args):

FILE: src/sourmash/cli/tax/summarize.py
  function subparser (line 20) | def subparser(subparsers):
  function main (line 69) | def main(args):

FILE: src/sourmash/cli/utils.py
  function add_moltype_args (line 8) | def add_moltype_args(parser):
  function add_construct_moltype_args (line 106) | def add_construct_moltype_args(parser):
  function add_ksize_arg (line 111) | def add_ksize_arg(parser, *, default=None):
  function add_v5_args (line 128) | def add_v5_args(parser):
  function range_limited_float_type (line 147) | def range_limited_float_type(arg):
  function add_tax_threshold_arg (line 162) | def add_tax_threshold_arg(parser, containment_default=0.1, ani_default=N...
  function add_picklist_args (line 178) | def add_picklist_args(parser):
  function add_pattern_args (line 192) | def add_pattern_args(parser):
  function opfilter (line 205) | def opfilter(path):
  function command_list (line 209) | def command_list(dirpath):
  function add_scaled_arg (line 219) | def add_scaled_arg(parser, default=None):
  function add_num_arg (line 229) | def add_num_arg(parser, default=0):
  function check_rank (line 241) | def check_rank(args):
  function add_rank_arg (line 267) | def add_rank_arg(parser):
  function check_tax_outputs (line 279) | def check_tax_outputs(

FILE: src/sourmash/cli/watch.py
  function subparser (line 6) | def subparser(subparsers):
  function main (line 36) | def main(args):

FILE: src/sourmash/command_compute.py
  function compute (line 28) | def compute(args):
  class _signatures_for_compute_factory (line 140) | class _signatures_for_compute_factory:
    method __init__ (line 143) | def __init__(self, args):
    method __call__ (line 146) | def __call__(self):
  function _compute_individual (line 163) | def _compute_individual(args, signatures_factory):
  function _compute_merged (line 292) | def _compute_merged(args, signatures_factory):
  function add_seq (line 328) | def add_seq(sigs, seq, input_is_protein, check_sequence):
  function set_sig_name (line 336) | def set_sig_name(sigs, filename, name=None):
  function save_siglist (line 346) | def save_siglist(siglist, sigfile_name):
  function save_sigs_to_location (line 357) | def save_sigs_to_location(siglist, save_sig):
  class ComputeParameters (line 365) | class ComputeParameters(RustObject):
    method __init__ (line 368) | def __init__(
    method from_manifest_row (line 394) | def from_manifest_row(cls, row):
    method to_param_str (line 427) | def to_param_str(self):
    method __repr__ (line 467) | def __repr__(self):
    method __eq__ (line 470) | def __eq__(self, other):
    method from_args (line 484) | def from_args(args):
    method seed (line 497) | def seed(self):
    method seed (line 501) | def seed(self, v):
    method ksizes (line 505) | def ksizes(self):
    method ksizes (line 514) | def ksizes(self, v):
    method protein (line 518) | def protein(self):
    method protein (line 522) | def protein(self, v):
    method dayhoff (line 526) | def dayhoff(self):
    method dayhoff (line 530) | def dayhoff(self, v):
    method hp (line 534) | def hp(self):
    method hp (line 538) | def hp(self, v):
    method dna (line 542) | def dna(self):
    method dna (line 546) | def dna(self, v):
    method moltype (line 550) | def moltype(self):
    method num_hashes (line 565) | def num_hashes(self):
    method num_hashes (line 569) | def num_hashes(self, v):
    method track_abundance (line 573) | def track_abundance(self):
    method track_abundance (line 577) | def track_abundance(self, v):
    method scaled (line 581) | def scaled(self):
    method scaled (line 585) | def scaled(self, v):

FILE: src/sourmash/command_sketch.py
  function _parse_params_str (line 35) | def _parse_params_str(params_str):
  class _signatures_for_sketch_factory (line 94) | class _signatures_for_sketch_factory:
    method __init__ (line 97) | def __init__(self, params_str_list, default_moltype):
    method get_compute_params (line 147) | def get_compute_params(self, *, split_ksizes=False):
    method __call__ (line 195) | def __call__(self, *, split_ksizes=False):
  function _add_from_file_to_filenames (line 205) | def _add_from_file_to_filenames(args):
  function _execute_sketch (line 214) | def _execute_sketch(args, signatures_factory):
  function dna (line 250) | def dna(args):
  function protein (line 268) | def protein(args):
  function translate (line 297) | def translate(args):
  function _compute_sigs (line 325) | def _compute_sigs(to_build, output, *, check_sequence=False):
  function _output_csv_info (line 381) | def _output_csv_info(filename, sigs_to_build):
  function fromfile (line 419) | def fromfile(args):
  class _signatures_for_compute_factory (line 655) | class _signatures_for_compute_factory:
    method __init__ (line 658) | def __init__(self, args):
    method __call__ (line 661) | def __call__(self):
  function _compute_individual (line 680) | def _compute_individual(args, signatures_factory):
  function _compute_merged (line 809) | def _compute_merged(args, signatures_factory):
  function add_seq (line 845) | def add_seq(sigs, seq, input_is_protein, check_sequence):
  function set_sig_name (line 853) | def set_sig_name(sigs, filename, name=None):
  function save_siglist (line 863) | def save_siglist(siglist, sigfile_name):
  function save_sigs_to_location (line 874) | def save_sigs_to_location(siglist, save_sig):
  class ComputeParameters (line 882) | class ComputeParameters(RustObject):
    method __init__ (line 885) | def __init__(
    method from_manifest_row (line 915) | def from_manifest_row(cls, row):
    method to_param_str (line 956) | def to_param_str(self):
    method __repr__ (line 1000) | def __repr__(self):
    method __eq__ (line 1003) | def __eq__(self, other):
    method from_args (line 1019) | def from_args(args):
    method seed (line 1032) | def seed(self):
    method seed (line 1036) | def seed(self, v):
    method ksizes (line 1040) | def ksizes(self):
    method ksizes (line 1049) | def ksizes(self, v):
    method protein (line 1053) | def protein(self):
    method protein (line 1057) | def protein(self, v):
    method dayhoff (line 1061) | def dayhoff(self):
    method dayhoff (line 1065) | def dayhoff(self, v):
    method hp (line 1069) | def hp(self):
    method hp (line 1073) | def hp(self, v):
    method dna (line 1077) | def dna(self):
    method dna (line 1081) | def dna(self, v):
    method skipm1n3 (line 1085) | def skipm1n3(self):
    method skipm1n3 (line 1089) | def skipm1n3(self, v):
    method skipm2n3 (line 1093) | def skipm2n3(self):
    method skipm2n3 (line 1097) | def skipm2n3(self, v):
    method moltype (line 1101) | def moltype(self):
    method num_hashes (line 1120) | def num_hashes(self):
    method num_hashes (line 1124) | def num_hashes(self, v):
    method track_abundance (line 1128) | def track_abundance(self):
    method track_abundance (line 1132) | def track_abundance(self, v):
    method scaled (line 1136) | def scaled(self):
    method scaled (line 1140) | def scaled(self, v):

FILE: src/sourmash/commands.py
  class EnumIndexType (line 34) | class EnumIndexType(enum.StrEnum):  # used in 'index'
  function _get_screen_width (line 40) | def _get_screen_width():
  function compare (line 47) | def compare(args):
  function plot (line 315) | def plot(args):
  function import_csv (line 464) | def import_csv(args):
  function sbt_combine (line 495) | def sbt_combine(args):
  function index (line 510) | def index(args):
  function search (line 659) | def search(args):
  function categorize (line 811) | def categorize(args):
  function gather (line 889) | def gather(args):
  function multigather (line 1180) | def multigather(args):
  function watch (line 1456) | def watch(args):
  function migrate (line 1553) | def migrate(args):
  function prefetch (line 1561) | def prefetch(args):

FILE: src/sourmash/compare.py
  function compare_serial (line 14) | def compare_serial(siglist, ignore_abundance, *, downsample=False, retur...
  function compare_serial_containment (line 67) | def compare_serial_containment(siglist, *, downsample=False, return_ani=...
  function compare_serial_max_containment (line 109) | def compare_serial_max_containment(siglist, *, downsample=False, return_...
  function compare_serial_avg_containment (line 150) | def compare_serial_avg_containment(siglist, *, downsample=False, return_...
  function similarity_args_unpack (line 190) | def similarity_args_unpack(args, ignore_abundance, *, downsample, return...
  function get_similarities_at_index (line 205) | def get_similarities_at_index(
  function compare_parallel (line 241) | def compare_parallel(
  function compare_all_pairs (line 328) | def compare_all_pairs(

FILE: src/sourmash/distance_utils.py
  function check_distance (line 17) | def check_distance(dist):
  function check_prob_threshold (line 24) | def check_prob_threshold(val, threshold=1e-3):
  function check_jaccard_error (line 36) | def check_jaccard_error(val, threshold=1e-4):
  class ANIResult (line 44) | class ANIResult:
    method check_dist_and_p_threshold (line 53) | def check_dist_and_p_threshold(self):
    method __post_init__ (line 60) | def __post_init__(self):
    method ani (line 64) | def ani(self):
  class jaccardANIResult (line 71) | class jaccardANIResult(ANIResult):
    method __post_init__ (line 77) | def __post_init__(self):
    method ani (line 89) | def ani(self):
  class ciANIResult (line 97) | class ciANIResult(ANIResult):
    method __post_init__ (line 107) | def __post_init__(self):
    method ani_low (line 116) | def ani_low(self):
    method ani_high (line 122) | def ani_high(self):
  function r1_to_q (line 128) | def r1_to_q(k, r1):
  function var_n_mutated (line 134) | def var_n_mutated(L, k, r1, *, q=None):
  function exp_n_mutated (line 155) | def exp_n_mutated(L, k, r1):
  function exp_n_mutated_squared (line 160) | def exp_n_mutated_squared(L, k, p):
  function probit (line 164) | def probit(p):
  function handle_seqlen_nkmers (line 168) | def handle_seqlen_nkmers(ksize, *, sequence_len_bp=None, n_unique_kmers=...
  function set_size_chernoff (line 181) | def set_size_chernoff(set_size, scaled, *, relative_error=0.05):
  function set_size_exact_prob (line 196) | def set_size_exact_prob(set_size, scaled, *, relative_error=0.05):
  function get_expected_log_probability (line 221) | def get_expected_log_probability(n_unique_kmers, ksize, mutation_rate, s...
  function get_exp_probability_nothing_common (line 233) | def get_exp_probability_nothing_common(
  function containment_to_distance (line 258) | def containment_to_distance(
  function jaccard_to_distance (line 349) | def jaccard_to_distance(

FILE: src/sourmash/exceptions.py
  class SourmashError (line 8) | class SourmashError(Exception):
    method __init__ (line 11) | def __init__(self, msg):
    method __str__ (line 16) | def __str__(self):
  class IndexNotSupported (line 23) | class IndexNotSupported(SourmashError):
    method __init__ (line 24) | def __init__(self):
  class IndexNotLoaded (line 30) | class IndexNotLoaded(SourmashError):
    method __init__ (line 31) | def __init__(self, msg):
  function _make_error (line 35) | def _make_error(error_name, base=SourmashError, code=None):
  function _get_error_base (line 47) | def _get_error_base(error_name):
  function _make_exceptions (line 58) | def _make_exceptions():

FILE: src/sourmash/fig.py
  function load_matrix_and_labels (line 16) | def load_matrix_and_labels(basefile):
  function plot_composite_matrix (line 26) | def plot_composite_matrix(

FILE: src/sourmash/hll.py
  class HLL (line 12) | class HLL(RustObject):
    method __init__ (line 15) | def __init__(self, error_rate, ksize):
    method __len__ (line 18) | def __len__(self):
    method cardinality (line 21) | def cardinality(self):
    method ksize (line 25) | def ksize(self):
    method add_sequence (line 28) | def add_sequence(self, sequence, force=False):
    method add_kmer (line 32) | def add_kmer(self, kmer):
    method add (line 38) | def add(self, h):
    method update (line 43) | def update(self, other):
    method similarity (line 53) | def similarity(self, other):
    method containment (line 61) | def containment(self, other):
    method intersection (line 69) | def intersection(self, other):
    method load (line 78) | def load(filename):
    method from_buffer (line 83) | def from_buffer(buf):
    method save (line 87) | def save(self, filename):
    method to_bytes (line 90) | def to_bytes(self, compression=1):
    method count (line 100) | def count(self, h):
    method get (line 103) | def get(self, h):
    method matches (line 106) | def matches(self, mh):

FILE: src/sourmash/index/__init__.py
  class Index (line 61) | class Index(ABC):
    method __len__ (line 71) | def __len__(self):
    method location (line 75) | def location(self):
    method signatures (line 80) | def signatures(self):
    method signatures_with_location (line 83) | def signatures_with_location(self):
    method _signatures_with_internal (line 88) | def _signatures_with_internal(self):
    method insert (line 103) | def insert(self, signature):
    method save (line 107) | def save(self, path, storage=None, sparseness=0.0, structure_only=False):
    method load (line 112) | def load(cls, location, leaf_loader=None, storage=None, print_version_...
    method find (line 115) | def find(self, search_fn, query, **kwargs):
    method search_abund (line 172) | def search_abund(self, query, *, threshold=None, **kwargs):
    method search (line 202) | def search(
    method prefetch (line 241) | def prefetch(self, query, threshold_bp, **kwargs):
    method best_containment (line 258) | def best_containment(self, query, threshold_bp=None, **kwargs):
    method peek (line 272) | def peek(self, query_mh, *, threshold_bp=0):
    method consume (line 298) | def consume(self, intersect_mh):
    method counter_gather (line 302) | def counter_gather(self, query, threshold_bp, **kwargs):
    method select (line 323) | def select(
  function select_signature (line 349) | def select_signature(
  class LinearIndex (line 397) | class LinearIndex(Index):
    method __init__ (line 405) | def __init__(self, _signatures=None, filename=None):
    method location (line 412) | def location(self):
    method signatures (line 415) | def signatures(self):
    method __bool__ (line 418) | def __bool__(self):
    method __len__ (line 421) | def __len__(self):
    method insert (line 424) | def insert(self, node):
    method save (line 427) | def save(self, path):
    method load (line 432) | def load(cls, location, filename=None):
    method select (line 441) | def select(self, **kwargs):
  class LazyLinearIndex (line 456) | class LazyLinearIndex(Index):
    method __init__ (line 477) | def __init__(self, db, selection_dict={}):
    method signatures (line 481) | def signatures(self):
    method signatures_with_location (line 486) | def signatures_with_location(self):
    method __bool__ (line 491) | def __bool__(self):
    method __len__ (line 498) | def __len__(self):
    method insert (line 502) | def insert(self, node):
    method save (line 505) | def save(self, path):
    method load (line 509) | def load(cls, path):
    method select (line 512) | def select(self, **kwargs):
  class ZipFileLinearIndex (line 529) | class ZipFileLinearIndex(Index):
    method __init__ (line 540) | def __init__(
    method _load_manifest (line 569) | def _load_manifest(self):
    method __bool__ (line 585) | def __bool__(self):
    method __len__ (line 594) | def __len__(self):
    method location (line 609) | def location(self):
    method insert (line 612) | def insert(self, signature):
    method save (line 615) | def save(self, path):
    method load (line 619) | def load(cls, location, traverse_yield_all=False, use_manifest=True):
    method _signatures_with_internal (line 632) | def _signatures_with_internal(self):
    method signatures (line 650) | def signatures(self):
    method select (line 694) | def select(self, **kwargs):
  class CounterGather (line 735) | class CounterGather:
    method __init__ (line 757) | def __init__(self, query):
    method add (line 777) | def add(self, ss, *, location=None, require_overlap=True):
    method downsample (line 796) | def downsample(self, scaled):
    method __len__ (line 802) | def __len__(self):
    method signatures (line 805) | def signatures(self):
    method union_found (line 810) | def union_found(self):
    method peek (line 828) | def peek(self, cur_query_mh, *, threshold_bp=0):
    method consume (line 885) | def consume(self, intersect_mh):
  class MultiIndex (line 915) | class MultiIndex(Index):
    method __init__ (line 940) | def __init__(self, manifest, parent, *, prepend_location=False):
    method location (line 952) | def location(self):
    method signatures (line 955) | def signatures(self):
    method signatures_with_location (line 959) | def signatures_with_location(self):
    method _signatures_with_internal (line 968) | def _signatures_with_internal(self):
    method __len__ (line 977) | def __len__(self):
    method insert (line 983) | def insert(self, *args):
    method load (line 987) | def load(cls, index_list, source_list, parent, *, prepend_location=Fal...
    method load_from_directory (line 1019) | def load_from_directory(cls, pathname, *, force=False):
    method load_from_path (line 1057) | def load_from_path(cls, pathname, force=False):
    method load_from_pathlist (line 1085) | def load_from_pathlist(cls, filename):
    method save (line 1107) | def save(self, *args):
    method select (line 1110) | def select(self, **kwargs):
  class StandaloneManifestIndex (line 1119) | class StandaloneManifestIndex(Index):
    method __init__ (line 1150) | def __init__(self, manifest, location, *, prefix=None):
    method load (line 1159) | def load(cls, location, *, prefix=None):
    method location (line 1177) | def location(self):
    method signatures_with_location (line 1181) | def signatures_with_location(self):
    method signatures (line 1185) | def signatures(self):
    method _signatures_with_internal (line 1190) | def _signatures_with_internal(self):
    method __len__ (line 1211) | def __len__(self):
    method __bool__ (line 1215) | def __bool__(self):
    method save (line 1219) | def save(self, *args):
    method insert (line 1222) | def insert(self, *args):
    method select (line 1225) | def select(self, **kwargs):
  function _check_select_parameters (line 1232) | def _check_select_parameters(**kw):

FILE: src/sourmash/index/revindex.py
  class RevIndex (line 18) | class RevIndex(RustObject, Index):
    method __init__ (line 30) | def __init__(self):
    method _ffi_idx_picklist (line 35) | def _ffi_idx_picklist(self):
    method manifest (line 41) | def manifest(self):
    method _generate_idx_picklist_from_manifest (line 46) | def _generate_idx_picklist_from_manifest(self, mf):
    method signatures (line 51) | def signatures(self, *, use_picklist=True):
    method signatures_with_location (line 68) | def signatures_with_location(self):
    method _signatures_with_internal (line 72) | def _signatures_with_internal(self):
    method __len__ (line 78) | def __len__(self):
    method scaled (line 83) | def scaled(self):
    method save (line 87) | def save(self, path):
    method load (line 91) | def load(cls, location):
    method search (line 94) | def search(
    method best_containment (line 159) | def best_containment(self, query_ss, *, threshold_bp=0, **kwargs):
    method peek (line 186) | def peek(self, query_mh, *, threshold_bp=0):
    method consume (line 215) | def consume(self, intersect_mh):
    method counter_gather (line 221) | def counter_gather(self, query_ss, threshold_bp=0, **kwargs):
    method prefetch (line 238) | def prefetch(self, query_ss, threshold_bp=0, **kwargs):
    method select (line 264) | def select(
  class SearchResult (line 325) | class SearchResult(RustObject):
    method __repr__ (line 332) | def __repr__(self):
    method __iter__ (line 335) | def __iter__(self):
    method __getitem__ (line 338) | def __getitem__(self, i):
    method score (line 342) | def score(self):
    method signature (line 346) | def signature(self):
    method location (line 351) | def location(self):
  class MemRevIndex (line 358) | class MemRevIndex(RevIndex):
    method __init__ (line 363) | def __init__(self, *, template=None):
    method _check_not_init (line 377) | def _check_not_init(self, *, do_raise=True):
    method _init_inner (line 385) | def _init_inner(self):
    method insert (line 425) | def insert(self, sig):
    method search (line 433) | def search(self, *args, **kwargs):
  class DiskRevIndex (line 449) | class DiskRevIndex(RevIndex):
    method __init__ (line 457) | def __init__(self, path):
    method _init_inner (line 473) | def _init_inner(self):
    method location (line 477) | def location(self):
    method insert (line 480) | def insert(self, *args, **kwargs):
    method create_from_sigs (line 484) | def create_from_sigs(self, siglist, path):
  class RevIndex_CounterGather (line 503) | class RevIndex_CounterGather:
    method __init__ (line 512) | def __init__(self, query, db, threshold_bp, *, allow_insert=False):
    method __len__ (line 526) | def __len__(self):
    method scaled (line 530) | def scaled(self):
    method add (line 533) | def add(self, match_ss, *, location=None, require_overlap=True):
    method peek (line 553) | def peek(self, query_mh, *, threshold_bp=0):
    method consume (line 574) | def consume(self, intersect_mh):
    method union_found (line 587) | def union_found(self):
    method signatures (line 591) | def signatures(self):
  class RevIndex_CounterGather_Colors (line 598) | class RevIndex_CounterGather_Colors(RustObject):
    method __init__ (line 605) | def __init__(self, objptr, query_ss, db):
    method scaled (line 628) | def scaled(self):
    method add (line 631) | def add(self, match_ss, *, location=None, require_overlap=True):
    method peek (line 634) | def peek(self, query_mh, *, threshold_bp=0):
    method consume (line 659) | def consume(self, intersect_mh):
    method union_found (line 664) | def union_found(self):
    method __len__ (line 668) | def __len__(self):
    method signatures (line 672) | def signatures(self):
  class RevIndex_DatasetPicklist (line 685) | class RevIndex_DatasetPicklist(RustObject):
    method __init__ (line 693) | def __init__(self, idxs):
    method from_manifest (line 703) | def from_manifest(cls, mf):

FILE: src/sourmash/index/sqlite_index.py
  function convert_hash_to (line 102) | def convert_hash_to(x):
  function convert_hash_from (line 106) | def convert_hash_from(x):
  function load_sqlite_index (line 110) | def load_sqlite_index(filename, *, request_manifest=False):
  class SqliteIndex (line 188) | class SqliteIndex(Index):
    method __init__ (line 194) | def __init__(self, dbfile, *, sqlite_manifest=None, conn=None):
    method _open (line 223) | def _open(cls, dbfile, *, empty_ok=True):
    method load (line 243) | def load(self, dbfile):
    method create (line 248) | def create(cls, dbfile, *, append=False):
    method _create_tables (line 257) | def _create_tables(cls, c, *, ignore_exists=False):
    method cursor (line 300) | def cursor(self):
    method close (line 303) | def close(self):
    method commit (line 306) | def commit(self):
    method __len__ (line 309) | def __len__(self):
    method insert (line 312) | def insert(self, ss, *, cursor=None, commit=True):
    method location (line 363) | def location(self):
    method signatures (line 366) | def signatures(self):
    method signatures_with_location (line 371) | def signatures_with_location(self):
    method save (line 378) | def save(self, *args, **kwargs):
    method find (line 381) | def find(self, search_fn, query, **kwargs):
    method _select (line 431) | def _select(self, *, num=0, track_abundance=False, **kwargs):
    method select (line 450) | def select(self, *args, **kwargs):
    method _load_sketch_size (line 460) | def _load_sketch_size(self, c1, sketch_id, max_hash):
    method _load_sketch (line 478) | def _load_sketch(self, c, sketch_id, *, match_scaled=None):
    method _load_sketches (line 541) | def _load_sketches(self, c):
    method _get_matching_sketches (line 576) | def _get_matching_sketches(self, c, hashes, max_hash):
  class SqliteCollectionManifest (line 625) | class SqliteCollectionManifest(BaseCollectionManifest):
    method __init__ (line 641) | def __init__(self, conn, *, selection_dict=None, managed_by_index=False):
    method create (line 659) | def create(cls, filename):
    method create_or_open (line 667) | def create_or_open(cls, filename):
    method load_from_manifest (line 678) | def load_from_manifest(cls, manifest, *, dbfile=":memory:", append=Fal...
    method create_manifest (line 685) | def create_manifest(cls, locations_iter, *, include_signature=False):
    method _create_tables (line 702) | def _create_tables(cls, cursor):
    method add_row (line 728) | def add_row(self, row):
    method _insert_row (line 732) | def _insert_row(self, cursor, row, *, call_is_from_index=False):
    method __bool__ (line 756) | def __bool__(self):
    method __eq__ (line 767) | def __eq__(self, other):
    method __len__ (line 777) | def __len__(self):
    method __iadd__ (line 788) | def __iadd__(self, other):
    method __add__ (line 794) | def __add__(self, other):
    method close (line 800) | def close(self):
    method _make_select (line 803) | def _make_select(self):
    method select_to_manifest (line 836) | def select_to_manifest(self, **kwargs):
    method rows (line 861) | def rows(self):
    method filter_rows (line 912) | def filter_rows(self, row_filter_fn):
    method filter_on_columns (line 925) | def filter_on_columns(self, col_filter_fn, col_names):
    method locations (line 934) | def locations(self):
    method __contains__ (line 961) | def __contains__(self, ss):
    method picklist (line 975) | def picklist(self):
    method to_picklist (line 981) | def to_picklist(self):
    method _create_manifest_from_rows (line 988) | def _create_manifest_from_rows(
  class LCA_SqliteDatabase (line 1017) | class LCA_SqliteDatabase(SqliteIndex):
    method __init__ (line 1024) | def __init__(self, dbfile, *, lineage_db=None, sqlite_manifest=None):
    method load (line 1051) | def load(cls, filename):
    method create (line 1070) | def create(cls, filename, idx, lineage_db):
    method _build_index (line 1088) | def _build_index(self):
    method insert (line 1135) | def insert(self, *args, **kwargs):
    method select (line 1139) | def select(self, *args, **kwargs):
    method downsample_scaled (line 1148) | def downsample_scaled(self, scaled):
    method get_lineage_assignments (line 1157) | def get_lineage_assignments(self, hashval, *, min_num=None):
    method idx_to_ident (line 1174) | def idx_to_ident(self):
    method hashval_to_idx (line 1183) | def hashval_to_idx(self):
    method hashvals (line 1188) | def hashvals(self):
    method get_identifiers_for_hashval (line 1192) | def get_identifiers_for_hashval(self, hashval):
  class _SqliteIndexHashvalToIndex (line 1199) | class _SqliteIndexHashvalToIndex:
    method __init__ (line 1205) | def __init__(self, sqlidx):
    method __iter__ (line 1208) | def __iter__(self):
    method get (line 1215) | def get(self, key, dv=None):
    method __getitem__ (line 1227) | def __getitem__(self, key):

FILE: src/sourmash/lca/__main__.py
  function main (line 29) | def main(arglist=None):

FILE: src/sourmash/lca/command_classify.py
  function classify_signature (line 18) | def classify_signature(query_sig, dblist, threshold, majority):
  function classify (line 80) | def classify(args):

FILE: src/sourmash/lca/command_compare_csv.py
  function compare_csv (line 15) | def compare_csv(args):

FILE: src/sourmash/lca/command_index.py
  function load_taxonomy_assignments (line 19) | def load_taxonomy_assignments(
  function generate_report (line 130) | def generate_report(
  function index (line 166) | def index(args):

FILE: src/sourmash/lca/command_rankinfo.py
  function make_lca_counts (line 13) | def make_lca_counts(dblist, min_num=0):
  function rankinfo_main (line 44) | def rankinfo_main(args):

FILE: src/sourmash/lca/command_summarize.py
  function summarize (line 20) | def summarize(hashvals, dblist, threshold, ignore_abundance):
  function load_singletons_and_count (line 61) | def load_singletons_and_count(filenames, ksize, scaled, ignore_abundance):
  function count_signature (line 91) | def count_signature(sig, scaled, hashvals):
  function output_results (line 104) | def output_results(lineage_counts, total_counts, filename=None, sig=None):
  function output_csv (line 124) | def output_csv(lineage_counts, total_counts, csv_fp, filename, sig, writ...
  function summarize_main (line 142) | def summarize_main(args):

FILE: src/sourmash/lca/lca_db.py
  function cached_property (line 16) | def cached_property(fun):
  class LCA_Database (line 33) | class LCA_Database(Index):
    method __init__ (line 69) | def __init__(self, ksize, scaled, moltype="DNA"):
    method location (line 86) | def location(self):
    method __len__ (line 93) | def __len__(self):
    method _invalidate_cache (line 100) | def _invalidate_cache(self):
    method _get_ident_index (line 108) | def _get_ident_index(self, ident, fail_on_duplicate=False):
    method _get_lineage_id (line 125) | def _get_lineage_id(self, lineage):
    method insert (line 145) | def insert(self, sig, ident=None, lineage=None):
    method __repr__ (line 207) | def __repr__(self):
    method signatures (line 212) | def signatures(self):
    method _signatures_with_internal (line 228) | def _signatures_with_internal(self):
    method select (line 237) | def select(
    method load (line 298) | def load(cls, db_name):
    method save (line 415) | def save(self, db_name, *, format="json"):
    method save_to_json (line 422) | def save_to_json(self, db_name):
    method save_to_sql (line 469) | def save_to_sql(self, dbname):
    method downsample_scaled (line 495) | def downsample_scaled(self, scaled):
    method hashvals (line 522) | def hashvals(self):
    method get_lineage_assignments (line 526) | def get_lineage_assignments(self, hashval, min_num=None):
    method get_identifiers_for_hashval (line 546) | def get_identifiers_for_hashval(self, hashval):
    method _signatures (line 556) | def _signatures(self):
    method find (line 621) | def find(self, search_fn, query, **kwargs):
    method _lid_to_idx (line 694) | def _lid_to_idx(self):
    method _idx_to_ident (line 705) | def _idx_to_ident(self):
  function load_single_database (line 717) | def load_single_database(filename, verbose=False):
  function load_databases (line 723) | def load_databases(filenames, scaled=None, verbose=True):

FILE: src/sourmash/lca/lca_utils.py
  function check_files_exist (line 38) | def check_files_exist(*files):
  function taxlist (line 58) | def taxlist(include_strain=True):
  function zip_lineage (line 76) | def zip_lineage(lineage, include_strain=True, truncate_empty=False):
  function display_lineage (line 119) | def display_lineage(lineage, include_strain=True, truncate_empty=True):
  function filter_null (line 128) | def filter_null(x):
  function build_tree (line 137) | def build_tree(assignments, initial=None):
  function find_lca (line 165) | def find_lca(tree):
  function gather_assignments (line 186) | def gather_assignments(hashvals, dblist):
  function count_lca_for_assignments (line 202) | def count_lca_for_assignments(assignments, hashval_counts=None):
  function is_lineage_match (line 228) | def is_lineage_match(lin_a, lin_b, rank):
  function pop_to_rank (line 243) | def pop_to_rank(lin, rank):
  function make_lineage (line 265) | def make_lineage(lineage):

FILE: src/sourmash/logging.py
  function set_quiet (line 8) | def set_quiet(val, print_debug=False):
  function print_results (line 14) | def print_results(s, *args, **kwargs):
  function notify (line 22) | def notify(s, *args, **kwargs):
  function debug (line 33) | def debug(s, *args, **kwargs):
  function debug_literal (line 44) | def debug_literal(s, *args, **kwargs):
  function error (line 55) | def error(s, *args, **kwargs):
  function test_notify (line 63) | def test_notify():
  function test_notify_flush (line 79) | def test_notify_flush():
  function test_notify_end (line 95) | def test_notify_end():
  function test_notify_quiet (line 111) | def test_notify_quiet():
  function test_error (line 127) | def test_error():
  function test_error_flush (line 143) | def test_error_flush():
  function test_error_quiet (line 159) | def test_error_quiet():

FILE: src/sourmash/manifest.py
  class BaseCollectionManifest (line 15) | class BaseCollectionManifest:
    method load_from_manifest (line 47) | def load_from_manifest(cls, manifest, **kwargs):
    method load_from_filename (line 51) | def load_from_filename(cls, filename):
    method load_from_csv (line 67) | def load_from_csv(cls, fp):
    method load_from_sql (line 103) | def load_from_sql(cls, filename):
    method write_to_filename (line 112) | def write_to_filename(self, filename, *, database_format="csv", ok_if_...
    method write_csv_header (line 130) | def write_csv_header(cls, fp):
    method write_to_csv (line 136) | def write_to_csv(self, fp, write_header=False):
    method make_manifest_row (line 150) | def make_manifest_row(cls, ss, location, *, include_signature=True):
    method create_manifest (line 175) | def create_manifest(cls, locations_iter, *, include_signature=True):
    method __add__ (line 193) | def __add__(self, other):
    method __bool__ (line 197) | def __bool__(self):
    method __len__ (line 201) | def __len__(self):
    method __eq__ (line 205) | def __eq__(self, other):
    method select_to_manifest (line 209) | def select_to_manifest(self, **kwargs):
    method filter_rows (line 213) | def filter_rows(self, row_filter_fn):
    method filter_on_columns (line 217) | def filter_on_columns(self, col_filter_fn, col_names):
    method locations (line 221) | def locations(self):
    method __contains__ (line 225) | def __contains__(self, ss):
    method to_picklist (line 229) | def to_picklist(self):
    method _check_row_values (line 232) | def _check_row_values(self):
  class CollectionManifest (line 244) | class CollectionManifest(BaseCollectionManifest):
    method __init__ (line 249) | def __init__(self, rows=[]):
    method load_from_manifest (line 257) | def load_from_manifest(cls, manifest, **kwargs):
    method _from_rust (line 262) | def _from_rust(value):
    method add_row (line 301) | def add_row(self, row):
    method _add_rows (line 304) | def _add_rows(self, rows):
    method __iadd__ (line 312) | def __iadd__(self, other):
    method __add__ (line 318) | def __add__(self, other):
    method __bool__ (line 323) | def __bool__(self):
    method __len__ (line 326) | def __len__(self):
    method __eq__ (line 329) | def __eq__(self, other):
    method _select (line 342) | def _select(
    method select_to_manifest (line 387) | def select_to_manifest(self, **kwargs):
    method filter_rows (line 392) | def filter_rows(self, row_filter_fn):
    method filter_on_columns (line 398) | def filter_on_columns(self, col_filter_fn, col_names):
    method locations (line 407) | def locations(self):
    method __contains__ (line 418) | def __contains__(self, ss):
    method to_picklist (line 423) | def to_picklist(self):

FILE: src/sourmash/minhash.py
  function get_minhash_default_seed (line 38) | def get_minhash_default_seed():
  function get_minhash_max_hash (line 48) | def get_minhash_max_hash():
  function _get_max_hash_for_scaled (line 53) | def _get_max_hash_for_scaled(scaled):
  function _get_scaled_for_max_hash (line 63) | def _get_scaled_for_max_hash(max_hash):
  function to_bytes (line 70) | def to_bytes(s):
  function hash_murmur (line 88) | def hash_murmur(kmer, seed=MINHASH_DEFAULT_SEED):
  function translate_codon (line 96) | def translate_codon(codon):
  function flatten_and_downsample_scaled (line 104) | def flatten_and_downsample_scaled(mh, *scaled_vals):
  function flatten_and_downsample_num (line 116) | def flatten_and_downsample_num(mh, *num_vals):
  function flatten_and_intersect_scaled (line 128) | def flatten_and_intersect_scaled(mh1, mh2):
  class _HashesWrapper (line 137) | class _HashesWrapper(Mapping):
    method __init__ (line 140) | def __init__(self, h):
    method __getitem__ (line 143) | def __getitem__(self, key):
    method __repr__ (line 146) | def __repr__(self):
    method __len__ (line 149) | def __len__(self):
    method __iter__ (line 152) | def __iter__(self):
    method __eq__ (line 155) | def __eq__(self, other):
    method __setitem__ (line 158) | def __setitem__(self, k, v):
  class MinHash (line 162) | class MinHash(RustObject):
    method __init__ (line 191) | def __init__(
    method __copy__ (line 267) | def __copy__(self):
    method __getstate__ (line 286) | def __getstate__(self):
    method __setstate__ (line 313) | def __setstate__(self, tup):
    method __eq__ (line 355) | def __eq__(self, other):
    method copy_and_clear (line 359) | def copy_and_clear(self):
    method add_sequence (line 375) | def add_sequence(self, sequence, force=False):
    method seq_to_hashes (line 379) | def seq_to_hashes(
    method kmers_and_hashes (line 419) | def kmers_and_hashes(self, sequence, *, force=False, is_protein=False):
    method add_kmer (line 488) | def add_kmer(self, kmer):
    method add_many (line 498) | def add_many(self, hashes):
    method remove_many (line 509) | def remove_many(self, hashes):
    method __len__ (line 520) | def __len__(self):
    method get_mins (line 530) | def get_mins(self, with_abundance=False):
    method get_hashes (line 545) | def get_hashes(self):
    method hashes (line 550) | def hashes(self):
    method seed (line 574) | def seed(self):
    method num (line 578) | def num(self):
    method scaled (line 582) | def scaled(self):
    method is_dna (line 589) | def is_dna(self):
    method is_protein (line 595) | def is_protein(self):
    method dayhoff (line 599) | def dayhoff(self):
    method hp (line 603) | def hp(self):
    method skipm1n3 (line 607) | def skipm1n3(self):
    method skipm2n3 (line 611) | def skipm2n3(self):
    method ksize (line 615) | def ksize(self):
    method max_hash (line 629) | def max_hash(self):
    method _max_hash (line 634) | def _max_hash(self):
    method track_abundance (line 638) | def track_abundance(self):
    method track_abundance (line 642) | def track_abundance(self, b):
    method add_hash (line 655) | def add_hash(self, h):
    method add_hash_with_abundance (line 659) | def add_hash_with_abundance(self, h, a):
    method clear (line 669) | def clear(self):
    method count_common (line 673) | def count_common(self, other, downsample=False):
    method intersection_and_union_size (line 685) | def intersection_and_union_size(self, other):
    method downsample (line 700) | def downsample(self, *, num=None, scaled=None):
    method flatten (line 759) | def flatten(self):
    method jaccard (line 780) | def jaccard(self, other, downsample=False):
    method jaccard_ani (line 789) | def jaccard_ani(
    method similarity (line 827) | def similarity(self, other, ignore_abundance=False, downsample=False):
    method angular_similarity (line 848) | def angular_similarity(self, other, downsample=False):
    method is_compatible (line 860) | def is_compatible(self, other):
    method contained_by (line 863) | def contained_by(self, other, downsample=False):
    method contained_by_weighted (line 887) | def contained_by_weighted(self, other):
    method containment_ani (line 907) | def containment_ani(
    method max_containment (line 945) | def max_containment(self, other, downsample=False):
    method max_containment_ani (line 971) | def max_containment_ani(
    method avg_containment (line 1010) | def avg_containment(self, other, *, downsample=False):
    method avg_containment_ani (line 1025) | def avg_containment_ani(self, other, *, downsample=False, prob_thresho...
    method __add__ (line 1042) | def __add__(self, other):
    method __iadd__ (line 1058) | def __iadd__(self, other):
    method merge (line 1064) | def merge(self, other):
    method intersection (line 1069) | def intersection(self, other):
    method set_abundances (line 1080) | def set_abundances(self, values, clear=True):
    method add_protein (line 1106) | def add_protein(self, sequence):
    method moltype (line 1111) | def moltype(self):  # TODO: test in minhash tests
    method to_mutable (line 1125) | def to_mutable(self):
    method to_frozen (line 1129) | def to_frozen(self):
    method into_frozen (line 1135) | def into_frozen(self):
    method inflate (line 1139) | def inflate(self, from_mh):
    method sum_abundances (line 1162) | def sum_abundances(self):
    method mean_abundance (line 1168) | def mean_abundance(self):
    method median_abundance (line 1174) | def median_abundance(self):
    method std_abundance (line 1180) | def std_abundance(self):
    method unique_dataset_hashes (line 1186) | def unique_dataset_hashes(self):
    method size_is_accurate (line 1197) | def size_is_accurate(self, relative_error=0.20, confidence=0.95):
  class FrozenMinHash (line 1220) | class FrozenMinHash(MinHash):
    method add_sequence (line 1221) | def add_sequence(self, *args, **kwargs):
    method add_kmer (line 1224) | def add_kmer(self, *args, **kwargs):
    method add_many (line 1227) | def add_many(self, *args, **kwargs):
    method remove_many (line 1230) | def remove_many(self, *args, **kwargs):
    method add_hash (line 1233) | def add_hash(self, *args, **kwargs):
    method add_hash_with_abundance (line 1236) | def add_hash_with_abundance(self, *args, **kwargs):
    method clear (line 1239) | def clear(self, *args, **kwargs):
    method set_abundances (line 1242) | def set_abundances(self, *args, **kwargs):
    method add_protein (line 1245) | def add_protein(self, *args, **kwargs):
    method downsample (line 1248) | def downsample(self, *, num=None, scaled=None):
    method flatten (line 1258) | def flatten(self):
    method __iadd__ (line 1265) | def __iadd__(self, *args, **kwargs):
    method merge (line 1268) | def merge(self, *args, **kwargs):
    method to_mutable (line 1271) | def to_mutable(self):
    method to_frozen (line 1279) | def to_frozen(self):
    method into_frozen (line 1283) | def into_frozen(self):
    method __setstate__ (line 1287) | def __setstate__(self, tup):
    method __copy__ (line 1329) | def __copy__(self):

FILE: src/sourmash/nodegraph.py
  class Nodegraph (line 13) | class Nodegraph(RustObject):
    method __init__ (line 16) | def __init__(self, ksize, starting_size, n_tables):
    method load (line 20) | def load(filename):
    method from_buffer (line 25) | def from_buffer(buf):
    method save (line 29) | def save(self, filename):
    method to_bytes (line 32) | def to_bytes(self, compression=1):
    method update (line 42) | def update(self, other):
    method count (line 52) | def count(self, h):
    method get (line 57) | def get(self, h):
    method n_occupied (line 62) | def n_occupied(self):
    method ksize (line 65) | def ksize(self):
    method hashsizes (line 68) | def hashsizes(self):
    method expected_collisions (line 78) | def expected_collisions(self):
    method matches (line 81) | def matches(self, mh):
    method to_khmer_nodegraph (line 90) | def to_khmer_nodegraph(self):
  function extract_nodegraph_info (line 105) | def extract_nodegraph_info(filename):
  function calc_expected_collisions (line 146) | def calc_expected_collisions(graph, force=False, max_false_pos=0.2):

FILE: src/sourmash/np_utils.py
  function to_memmap (line 4) | def to_memmap(array):

FILE: src/sourmash/picklist.py
  function combine_ident_md5 (line 35) | def combine_ident_md5(x):
  class PickStyle (line 49) | class PickStyle(Enum):
  class SignaturePicklist (line 54) | class SignaturePicklist:
    method __init__ (line 92) | def __init__(
    method from_picklist_args (line 127) | def from_picklist_args(cls, argstr):
    method _get_sig_attribute (line 152) | def _get_sig_attribute(self, ss):
    method _get_value_for_manifest_row (line 168) | def _get_value_for_manifest_row(self, row):
    method _get_value_for_csv_row (line 191) | def _get_value_for_csv_row(self, row):
    method init (line 209) | def init(self, values=[]):
    method load (line 216) | def load(self, *, allow_empty=False):
    method add (line 261) | def add(self, value):
    method __contains__ (line 265) | def __contains__(self, ss):
    method matches_manifest_row (line 287) | def matches_manifest_row(self, row):
    method matched_csv_row (line 302) | def matched_csv_row(self, row):
    method filter (line 314) | def filter(self, it):
  function passes_all_picklists (line 321) | def passes_all_picklists(ss, picklists):

FILE: src/sourmash/plugins.py
  function get_load_from_functions (line 45) | def get_load_from_functions():
  function get_save_to_functions (line 68) | def get_save_to_functions():
  class CommandLinePlugin (line 91) | class CommandLinePlugin:
    method __init__ (line 101) | def __init__(self, parser):
    method main (line 109) | def main(self, args):
  function get_cli_script_plugins (line 113) | def get_cli_script_plugins():
  function get_cli_scripts_descriptions (line 143) | def get_cli_scripts_descriptions():
  function add_cli_scripts (line 159) | def add_cli_scripts(parser):
  function list_all_plugins (line 188) | def list_all_plugins():

FILE: src/sourmash/save_load.py
  function load_file_as_index (line 52) | def load_file_as_index(filename, *, yield_all_files=False):
  function SaveSignaturesToLocation (line 70) | def SaveSignaturesToLocation(location):
  function _load_database (line 95) | def _load_database(filename, traverse_yield_all, *, cache_size=None):
  function add_loader (line 141) | def add_loader(name, priority):
  function _load_stdin (line 152) | def _load_stdin(filename, **kwargs):
  function _load_standalone_manifest (line 165) | def _load_standalone_manifest(filename, **kwargs):
  function _multiindex_load_from_pathlist (line 177) | def _multiindex_load_from_pathlist(filename, **kwargs):
  function _multiindex_load_from_path (line 185) | def _multiindex_load_from_path(filename, **kwargs):
  function _load_sbt (line 194) | def _load_sbt(filename, **kwargs):
  function _load_revindex (line 207) | def _load_revindex(filename, **kwargs):
  function _load_sqlite_db (line 214) | def _load_sqlite_db(filename, **kwargs):
  function _load_disk_revindex (line 219) | def _load_disk_revindex(filename, **kwargs):
  function _load_zipfile (line 224) | def _load_zipfile(filename, **kwargs):
  function _error_on_fastaq (line 242) | def _error_on_fastaq(filename, **kwargs):
  class Base_SaveSignaturesToLocation (line 262) | class Base_SaveSignaturesToLocation:
    method __init__ (line 265) | def __init__(self, location):
    method matches (line 270) | def matches(cls, location):
    method __repr__ (line 274) | def __repr__(self):
    method __len__ (line 277) | def __len__(self):
    method open (line 280) | def open(self):
    method close (line 283) | def close(self):
    method __enter__ (line 286) | def __enter__(self):
    method __exit__ (line 291) | def __exit__(self, type, value, traceback):
    method add (line 295) | def add(self, ss):
    method add_many (line 298) | def add_many(self, sslist):
  function _get_signatures_from_rust (line 303) | def _get_signatures_from_rust(siglist):
  class SaveSignatures_NoOutput (line 313) | class SaveSignatures_NoOutput(Base_SaveSignaturesToLocation):
    method __repr__ (line 316) | def __repr__(self):
    method matches (line 320) | def matches(cls, location):
    method open (line 323) | def open(self):
    method close (line 326) | def close(self):
  class SaveSignatures_Directory (line 330) | class SaveSignatures_Directory(Base_SaveSignaturesToLocation):
    method __init__ (line 333) | def __init__(self, location):
    method __repr__ (line 336) | def __repr__(self):
    method matches (line 340) | def matches(cls, location):
    method close (line 345) | def close(self):
    method open (line 348) | def open(self):
    method add (line 357) | def add(self, ss):
  class SaveSignatures_SqliteIndex (line 375) | class SaveSignatures_SqliteIndex(Base_SaveSignaturesToLocation):
    method __init__ (line 378) | def __init__(self, location):
    method matches (line 385) | def matches(cls, location):
    method __repr__ (line 390) | def __repr__(self):
    method close (line 393) | def close(self):
    method open (line 398) | def open(self):
    method add (line 402) | def add(self, add_sig):
  class SaveSignatures_SigFile (line 412) | class SaveSignatures_SigFile(Base_SaveSignaturesToLocation):
    method __init__ (line 415) | def __init__(self, location):
    method matches (line 423) | def matches(cls, location):
    method __repr__ (line 427) | def __repr__(self):
    method open (line 430) | def open(self):
    method close (line 433) | def close(self):
    method add (line 449) | def add(self, ss):
  class SaveSignatures_ZipFile (line 454) | class SaveSignatures_ZipFile(Base_SaveSignaturesToLocation):
    method __init__ (line 457) | def __init__(self, location):
    method matches (line 462) | def matches(cls, location):
    method __repr__ (line 467) | def __repr__(self):
    method close (line 470) | def close(self):
    method open (line 484) | def open(self):
    method _exists (line 522) | def _exists(self, name):
    method add (line 529) | def add(self, add_sig):

FILE: src/sourmash/sbt.py
  class GraphFactory (line 43) | class GraphFactory:
    method __init__ (line 56) | def __init__(self, ksize, starting_size, n_tables):
    method __call__ (line 61) | def __call__(self):
    method init_args (line 64) | def init_args(self):
  class _NodesCache (line 68) | class _NodesCache(Cache):
    method __init__ (line 76) | def __init__(self, maxsize, getsizeof=None):
    method __getitem__ (line 80) | def __getitem__(self, key, cache_getitem=Cache.__getitem__):
    method __setitem__ (line 85) | def __setitem__(self, key, value, cache_setitem=Cache.__setitem__):
    method __delitem__ (line 89) | def __delitem__(self, key, cache_delitem=Cache.__delitem__):
    method popitem (line 93) | def popitem(self):
  class SBT (line 118) | class SBT(Index):
    method __init__ (line 146) | def __init__(self, factory, *, d=2, storage=None, cache_size=None):
    method location (line 162) | def location(self):
    method signatures (line 165) | def signatures(self):
    method _signatures_with_internal (line 191) | def _signatures_with_internal(self):
    method select (line 200) | def select(
    method new_node_pos (line 293) | def new_node_pos(self, node):
    method insert (line 325) | def insert(self, signature):
    method add_node (line 332) | def add_node(self, node):
    method _find_nodes (line 383) | def _find_nodes(self, search_fn, *args, **kwargs):
    method find (line 434) | def find(self, search_fn, query, **kwargs):
    method _rebuild_node (line 545) | def _rebuild_node(self, pos=0):
    method parent (line 571) | def parent(self, pos):
    method children (line 596) | def children(self, pos):
    method child (line 612) | def child(self, parent, pos):
    method save (line 637) | def save(self, path, storage=None, sparseness=0.0, structure_only=False):
    method load (line 825) | def load(
    method _load_v1 (line 952) | def _load_v1(
    method _load_v2 (line 992) | def _load_v2(
    method _load_v3 (line 1035) | def _load_v3(
    method _load_v4 (line 1090) | def _load_v4(
    method _load_v5 (line 1134) | def _load_v5(
    method _load_v6 (line 1185) | def _load_v6(
    method _fill_min_n_below (line 1235) | def _fill_min_n_below(self):
    method _fill_internal (line 1262) | def _fill_internal(self):
    method _fill_up (line 1272) | def _fill_up(self, search_fn, *args, **kwargs):
    method __len__ (line 1312) | def __len__(self):
    method print_dot (line 1315) | def print_dot(self):
    method print (line 1335) | def print(self):
    method __iter__ (line 1349) | def __iter__(self):
    method _parents (line 1355) | def _parents(self, pos=0):
    method leaves (line 1364) | def leaves(self, with_pos=False, unload_data=True):
    method combine (line 1373) | def combine(self, other):
  class Node (line 1411) | class Node:
    method __init__ (line 1414) | def __init__(self, factory, name=None, path=None, storage=None):
    method __str__ (line 1422) | def __str__(self):
    method save (line 1425) | def save(self, path):
    method data (line 1430) | def data(self):
    method data (line 1440) | def data(self, new_data):
    method unload (line 1443) | def unload(self):
    method load (line 1450) | def load(info, storage=None):
    method update (line 1457) | def update(self, parent):
  class Leaf (line 1469) | class Leaf:
    method __init__ (line 1470) | def __init__(self, metadata, data=None, name=None, storage=None, path=...
    method __str__ (line 1482) | def __str__(self):
    method make_manifest_row (line 1485) | def make_manifest_row(self, location):
    method data (line 1489) | def data(self):
    method data (line 1496) | def data(self, new_data):
    method unload (line 1499) | def unload(self):
    method save (line 1505) | def save(self, path):
    method update (line 1509) | def update(self, parent):
    method load (line 1513) | def load(cls, info, storage=None):
  function filter_distance (line 1519) | def filter_distance(filter_a, filter_b, n=1000):
  function convert_cmd (line 1556) | def convert_cmd(name, backend):

FILE: src/sourmash/sbt_storage.py
  class Storage (line 18) | class Storage(ABC):
    method save (line 20) | def save(self, path, content, *, overwrite=False):
    method load (line 24) | def load(self, path):
    method list_sbts (line 27) | def list_sbts(self):
    method init_args (line 30) | def init_args(self):
    method __enter__ (line 33) | def __enter__(self):
    method __exit__ (line 36) | def __exit__(self, type, value, traceback):
    method close (line 39) | def close(self):
    method can_open (line 42) | def can_open(self, location):
  class FSStorage (line 46) | class FSStorage(Storage):
    method __init__ (line 47) | def __init__(self, location, subdir, make_dirs=True):
    method init_args (line 56) | def init_args(self):
    method save (line 59) | def save(self, path, content, overwrite=False):
    method load (line 91) | def load(self, path):
  class ZipStorage (line 96) | class ZipStorage(RustObject, Storage):
    method __init__ (line 99) | def __init__(self, path, *, mode="r"):
    method can_open (line 108) | def can_open(location):
    method path (line 112) | def path(self):
    method subdir (line 118) | def subdir(self):
    method subdir (line 124) | def subdir(self, value):
    method _filenames (line 130) | def _filenames(self):
    method save (line 145) | def save(self, path, content, *, overwrite=False, compress=False):
    method load (line 152) | def load(self, path):
    method list_sbts (line 171) | def list_sbts(self):
    method init_args (line 186) | def init_args(self):
    method flush (line 189) | def flush(self):
    method close (line 193) | def close(self):
    method can_open (line 198) | def can_open(location):
  class _RwZipStorage (line 202) | class _RwZipStorage(Storage):
    method __init__ (line 203) | def __init__(self, path):
    method _filenames (line 232) | def _filenames(self):
    method _content_matches (line 235) | def _content_matches(self, zf, path, content):
    method _generate_filename (line 242) | def _generate_filename(self, zf, path, content):
    method _write_to_zf (line 267) | def _write_to_zf(self, zf, path, content, *, compress=False):
    method save (line 282) | def save(self, path, content, *, overwrite=False, compress=False):
    method _load_from_zf (line 311) | def _load_from_zf(self, zf, path):
    method load (line 320) | def load(self, path):
    method close (line 329) | def close(self):
    method flush (line 341) | def flush(self, *, keep_closed=False):
    method list_sbts (line 411) | def list_sbts(self):
    method __del__ (line 414) | def __del__(self):
  class IPFSStorage (line 418) | class IPFSStorage(Storage):
    method __init__ (line 419) | def __init__(self, pin_on_add=True, **kwargs):
    method save (line 426) | def save(self, path, content, *, overwrite=False):
    method load (line 441) | def load(self, path):
    method init_args (line 444) | def init_args(self):
    method __exit__ (line 447) | def __exit__(self, type, value, traceback):
  class RedisStorage (line 457) | class RedisStorage(Storage):
    method __init__ (line 458) | def __init__(self, **kwargs):
    method save (line 464) | def save(self, path, content, *, overwrite=False):
    method load (line 470) | def load(self, path):
    method init_args (line 473) | def init_args(self):
    method __exit__ (line 477) | def __exit__(self, type, value, traceback):

FILE: src/sourmash/sbtmh.py
  function load_sbt_index (line 8) | def load_sbt_index(filename, *, print_version_warning=True, cache_size=N...
  function create_sbt_index (line 18) | def create_sbt_index(bloom_filter_size=1e5, n_children=2):
  function search_sbt_index (line 25) | def search_sbt_index(tree, query, threshold):
  class SigLeaf (line 39) | class SigLeaf(Leaf):
    method __str__ (line 40) | def __str__(self):
    method make_manifest_row (line 43) | def make_manifest_row(self, loc):
    method save (line 49) | def save(self, path):
    method update (line 58) | def update(self, parent):
    method data (line 70) | def data(self):
    method data (line 77) | def data(self, new_data):

FILE: src/sourmash/search.py
  function calc_threshold_from_bp (line 15) | def calc_threshold_from_bp(threshold_bp, scaled, query_size):
  class SearchType (line 40) | class SearchType(Enum):
  function make_jaccard_search_query (line 46) | def make_jaccard_search_query(
  function make_containment_query (line 70) | def make_containment_query(query_mh, threshold_bp, *, best_only=True):
  class JaccardSearch (line 90) | class JaccardSearch:
    method __init__ (line 95) | def __init__(self, search_type, threshold=None):
    method check_is_compatible (line 115) | def check_is_compatible(self, sig):
    method passes (line 127) | def passes(self, score):
    method collect (line 139) | def collect(self, score, match_sig):
    method score_jaccard (line 143) | def score_jaccard(self, query_size, shared_size, subject_size, total_s...
    method score_containment (line 149) | def score_containment(self, query_size, shared_size, subject_size, tot...
    method score_max_containment (line 155) | def score_max_containment(self, query_size, shared_size, subject_size,...
  class JaccardSearchBestOnly (line 163) | class JaccardSearchBestOnly(JaccardSearch):
    method collect (line 166) | def collect(self, score, match):
  class BaseResult (line 173) | class BaseResult:
    method init_result (line 193) | def init_result(self):
    method build_fracminhashcomparison (line 197) | def build_fracminhashcomparison(self):
    method build_numminhashcomparison (line 212) | def build_numminhashcomparison(self, cmp_num=None):
    method get_cmpinfo (line 221) | def get_cmpinfo(self):
    method pass_threshold (line 247) | def pass_threshold(self):
    method shorten_md5 (line 250) | def shorten_md5(self, md5):
    method to_write (line 253) | def to_write(self, columns=[]):
    method init_dictwriter (line 261) | def init_dictwriter(self, csv_handle):
    method prep_result (line 267) | def prep_result(self):
    method write (line 271) | def write(self, w):
    method resultdict (line 277) | def resultdict(self):
  class SearchResult (line 284) | class SearchResult(BaseResult):
    method init_sigcomparison (line 309) | def init_sigcomparison(self):
    method __post_init__ (line 317) | def __post_init__(self):
    method check_similarity (line 327) | def check_similarity(self):
    method estimate_search_ani (line 334) | def estimate_search_ani(self):
  class PrefetchResult (line 361) | class PrefetchResult(BaseResult):
    method init_sigcomparison (line 402) | def init_sigcomparison(self):
    method estimate_containment_ani (line 419) | def estimate_containment_ani(self):
    method handle_ani_ci (line 429) | def handle_ani_ci(self):
    method build_prefetch_result (line 435) | def build_prefetch_result(self):
    method __post_init__ (line 449) | def __post_init__(self):
    method prep_prefetch_result (line 453) | def prep_prefetch_result(self):
    method prep_result (line 461) | def prep_result(self):
    method prefetchresultdict (line 466) | def prefetchresultdict(self):
  class GatherResult (line 473) | class GatherResult(PrefetchResult):
    method init_gathersketchcomparison (line 526) | def init_gathersketchcomparison(self):
    method check_gatherresult_input (line 532) | def check_gatherresult_input(self):
    method build_gather_result (line 553) | def build_gather_result(self):
    method __post_init__ (line 625) | def __post_init__(self):
    method prep_gather_result (line 635) | def prep_gather_result(self):
    method prep_result (line 640) | def prep_result(self):
    method gatherresultdict (line 645) | def gatherresultdict(self):
    method prefetchresultdict (line 651) | def prefetchresultdict(self):
  function format_bp (line 667) | def format_bp(bp):
  function search_databases_with_flat_query (line 681) | def search_databases_with_flat_query(query, databases, **kwargs):
  function search_databases_with_abund_query (line 724) | def search_databases_with_abund_query(query, databases, **kwargs):
  function _find_best (line 755) | def _find_best(counters, query, threshold_bp):
  class GatherDatabases (line 782) | class GatherDatabases:
    method __init__ (line 785) | def __init__(
    method _update_scaled (line 847) | def _update_scaled(self, scaled):
    method scaled (line 871) | def scaled(self):
    method __iter__ (line 874) | def __iter__(self):
    method __next__ (line 877) | def __next__(self):
  function prefetch_database (line 957) | def prefetch_database(query, database, threshold_bp, *, estimate_ani_ci=...

FILE: src/sourmash/sig/__main__.py
  function _check_abundance_compatibility (line 82) | def _check_abundance_compatibility(sig1, sig2):
  function _extend_signatures_with_from_file (line 89) | def _extend_signatures_with_from_file(args, *, target_attr="signatures"):
  function _set_num_scaled (line 99) | def _set_num_scaled(mh, num, scaled):
  function cat (line 114) | def cat(args):
  function split (line 166) | def split(args):
  function describe (line 250) | def describe(args):
  function manifest (line 347) | def manifest(args):
  function overlap (line 389) | def overlap(args):
  function merge (line 505) | def merge(args):
  function intersect (line 572) | def intersect(args):
  function inflate (line 641) | def inflate(args):
  function subtract (line 689) | def subtract(args):
  function rename (line 761) | def rename(args):
  function extract (line 799) | def extract(args):
  function filter (line 876) | def filter(args):
  function flatten (line 927) | def flatten(args):
  function downsample (line 972) | def downsample(args):
  function ingest (line 1048) | def ingest(args):
  function export (line 1105) | def export(args):
  function kmers (line 1133) | def kmers(args):
  function _summarize_manifest (line 1356) | def _summarize_manifest(manifest):
  function fileinfo (line 1389) | def fileinfo(args):
  function check (line 1458) | def check(args):
  function collect (line 1603) | def collect(args):
  function main (line 1724) | def main(arglist=None):

FILE: src/sourmash/sig/grep.py
  function main (line 14) | def main(args):

FILE: src/sourmash/signature.py
  class SigInput (line 22) | class SigInput(Enum):
  class SourmashSignature (line 29) | class SourmashSignature(RustObject):
    method __init__ (line 34) | def __init__(self, minhash, name="", filename=""):
    method minhash (line 45) | def minhash(self):
    method minhash (line 49) | def minhash(self, value):
    method __hash__ (line 53) | def __hash__(self):
    method __str__ (line 56) | def __str__(self):
    method __repr__ (line 59) | def __repr__(self):
    method md5sum (line 79) | def md5sum(self):
    method __eq__ (line 83) | def __eq__(self, other):
    method _name (line 87) | def _name(self):
    method _name (line 91) | def _name(self, value):
    method name (line 95) | def name(self):
    method name (line 99) | def name(self, value):
    method __ne__ (line 102) | def __ne__(self, other):
    method filename (line 106) | def filename(self):
    method filename (line 110) | def filename(self, value):
    method license (line 114) | def license(self):
    method _display_name (line 117) | def _display_name(self, max_length=0):
    method display (line 133) | def display(self, location=None):
    method similarity (line 151) | def similarity(self, other, ignore_abundance=False, downsample=False):
    method jaccard (line 157) | def jaccard(self, other, downsample=False):
    method jaccard_ani (line 163) | def jaccard_ani(
    method angular_similarity (line 181) | def angular_similarity(self, other, downsample=False):
    method contained_by (line 185) | def contained_by(self, other, downsample=False):
    method contained_by_weighted (line 189) | def contained_by_weighted(self, other):
    method containment_ani (line 193) | def containment_ani(
    method max_containment (line 211) | def max_containment(self, other, downsample=False):
    method max_containment_ani (line 215) | def max_containment_ani(
    method avg_containment (line 233) | def avg_containment(self, other, downsample=False):
    method avg_containment_ani (line 240) | def avg_containment_ani(self, other, *, downsample=False):
    method add_sequence (line 247) | def add_sequence(self, sequence, force=False):
    method add_protein (line 250) | def add_protein(self, sequence):
    method from_params (line 254) | def from_params(params):
    method __len__ (line 258) | def __len__(self):
    method __getstate__ (line 261) | def __getstate__(self):  # enable pickling
    method __setstate__ (line 268) | def __setstate__(self, tup):
    method __reduce__ (line 279) | def __reduce__(self):
    method __copy__ (line 285) | def __copy__(self):
    method to_frozen (line 295) | def to_frozen(self):
    method to_mutable (line 301) | def to_mutable(self):
    method into_frozen (line 305) | def into_frozen(self):
  class FrozenSourmashSignature (line 312) | class FrozenSourmashSignature(SourmashSignature):
    method minhash (line 316) | def minhash(self, value):
    method _name (line 320) | def _name(self, value):
    method name (line 324) | def name(self, value):
    method filename (line 328) | def filename(self, value):
    method add_sequence (line 331) | def add_sequence(self, sequence, force=False):
    method add_protein (line 334) | def add_protein(self, sequence):
    method __copy__ (line 337) | def __copy__(self):
    method to_frozen (line 342) | def to_frozen(self):
    method to_mutable (line 346) | def to_mutable(self):
    method into_frozen (line 353) | def into_frozen(self):
    method update (line 358) | def update(self):
  function _detect_input_type (line 376) | def _detect_input_type(data):
  function load_signatures_from_json (line 409) | def load_signatures_from_json(
  function load_one_signature_from_json (line 499) | def load_one_signature_from_json(
  function save_signatures_to_json (line 519) | def save_signatures_to_json(siglist, fp=None, compression=0):

FILE: src/sourmash/sketchcomparison.py
  class BaseMinHashComparison (line 12) | class BaseMinHashComparison:
    method downsample_and_handle_ignore_abundance (line 20) | def downsample_and_handle_ignore_abundance(self, cmp_num=None, cmp_sca...
    method check_compatibility_and_downsample (line 39) | def check_compatibility_and_downsample(self, cmp_num=None, cmp_scaled=...
    method intersect_mh (line 55) | def intersect_mh(self):
    method jaccard (line 60) | def jaccard(self):
    method estimate_jaccard_ani (line 63) | def estimate_jaccard_ani(self, jaccard=None):
    method angular_similarity (line 72) | def angular_similarity(self):
    method cosine_similarity (line 77) | def cosine_similarity(self):
  class NumMinHashComparison (line 82) | class NumMinHashComparison(BaseMinHashComparison):
    method __post_init__ (line 87) | def __post_init__(self):
    method size_may_be_inaccurate (line 94) | def size_may_be_inaccurate(self):
  class FracMinHashComparison (line 99) | class FracMinHashComparison(BaseMinHashComparison):
    method __post_init__ (line 108) | def __post_init__(self):
    method pass_threshold (line 117) | def pass_threshold(self):
    method size_may_be_inaccurate (line 121) | def size_may_be_inaccurate(self):
    method total_unique_intersect_hashes (line 129) | def total_unique_intersect_hashes(self):
    method mh1_containment_in_mh2 (line 140) | def mh1_containment_in_mh2(self):
    method estimate_ani_from_mh1_containment_in_mh2 (line 143) | def estimate_ani_from_mh1_containment_in_mh2(self, containment=None):
    method mh2_containment_in_mh1 (line 162) | def mh2_containment_in_mh1(self):
    method estimate_ani_from_mh2_containment_in_mh1 (line 165) | def estimate_ani_from_mh2_containment_in_mh1(self, containment=None):
    method max_containment (line 181) | def max_containment(self):
    method estimate_max_containment_ani (line 184) | def estimate_max_containment_ani(self, max_containment=None):
    method avg_containment (line 201) | def avg_containment(self):
    method avg_containment_ani (line 205) | def avg_containment_ani(self):
    method estimate_all_containment_ani (line 222) | def estimate_all_containment_ani(self):
    method weighted_intersection (line 242) | def weighted_intersection(self, from_mh=None, from_abundD={}):

FILE: src/sourmash/sourmash_args.py
  function check_scaled_bounds (line 61) | def check_scaled_bounds(arg):
  function check_num_bounds (line 73) | def check_num_bounds(arg):
  function get_moltype (line 85) | def get_moltype(sig, require=False):
  function calculate_moltype (line 95) | def calculate_moltype(args, default=None):
  function load_picklist (line 127) | def load_picklist(args):
  function report_picklist (line 157) | def report_picklist(args, picklist):
  function load_include_exclude_db_patterns (line 176) | def load_include_exclude_db_patterns(args):
  function apply_picklist_and_pattern (line 207) | def apply_picklist_and_pattern(db, picklist, pattern):
  function load_query_signature (line 225) | def load_query_signature(filename, ksize, select_moltype, select_md5=None):
  function _check_suffix (line 276) | def _check_suffix(filename, endings):
  function traverse_find_sigs (line 283) | def traverse_find_sigs(filenames, yield_all_files=False):
  function load_dbs_and_sigs (line 306) | def load_dbs_and_sigs(
  function load_pathlist_from_file (line 388) | def load_pathlist_from_file(filename):
  class FileOutput (line 410) | class FileOutput:
    method __init__ (line 432) | def __init__(self, filename, mode="wt", *, newline=None, encoding="utf...
    method open (line 439) | def open(self):
    method close (line 447) | def close(self):
    method __enter__ (line 451) | def __enter__(self):
    method __exit__ (line 454) | def __exit__(self, type, value, traceback):
  class FileOutputCSV (line 462) | class FileOutputCSV(FileOutput):
    method __init__ (line 484) | def __init__(self, filename):
    method open (line 488) | def open(self):
  class _DictReader_with_version (line 498) | class _DictReader_with_version:
    method __init__ (line 507) | def __init__(self, textfp, *, delimiter=","):
    method __iter__ (line 531) | def __iter__(self):
  function FileInputCSV (line 536) | def FileInputCSV(
  class SignatureLoadingProgress (line 609) | class SignatureLoadingProgress:
    method __init__ (line 621) | def __init__(self, reporting_interval=10):
    method __len__ (line 626) | def __len__(self):
    method short_notify (line 629) | def short_notify(self, msg_template, *args, **kwargs):
    method notify (line 645) | def notify(self, location):
    method start_file (line 650) | def start_file(self, location, loader):
  function load_many_signatures (line 678) | def load_many_signatures(
  function get_manifest (line 735) | def get_manifest(idx, *, require=True, rebuild=False):
  function load_file_as_signatures (line 773) | def load_file_as_signatures(
  function load_one_signature (line 825) | def load_one_signature(

FILE: src/sourmash/sqlite_utils.py
  function open_sqlite_db (line 10) | def open_sqlite_db(filename):
  function add_sourmash_internal (line 49) | def add_sourmash_internal(cursor, use_type, version):
  function get_sourmash_internal (line 80) | def get_sourmash_internal(cursor):

FILE: src/sourmash/tax/__main__.py
  function make_outfile (line 57) | def make_outfile(base, output_type, *, output_dir=""):
  function metagenome (line 73) | def metagenome(args):
  function genome (line 323) | def genome(args):
  function annotate (line 486) | def annotate(args):
  function prepare (line 600) | def prepare(args):
  function grep (line 628) | def grep(args):
  function summarize (line 684) | def summarize(args):
  function main (line 752) | def main(arglist=None):

FILE: src/sourmash/tax/tax_utils.py
  class LineagePair (line 84) | class LineagePair(NamedTuple):
  class BaseLineageInfo (line 91) | class BaseLineageInfo:
    method __post_init__ (line 117) | def __post_init__(self):
    method __eq__ (line 129) | def __eq__(self, other):
    method taxlist (line 137) | def taxlist(self):
    method ascending_taxlist (line 141) | def ascending_taxlist(self):
    method lowest_rank (line 145) | def lowest_rank(self):
    method rank_index (line 150) | def rank_index(self, rank):
    method name_at_rank (line 154) | def name_at_rank(self, rank):
    method filled_lineage (line 163) | def filled_lineage(self):
    method lowest_lineage_name (line 172) | def lowest_lineage_name(self):
    method lowest_lineage_taxid (line 179) | def lowest_lineage_taxid(self):
    method _init_empty (line 185) | def _init_empty(self):
    method _init_from_lineage_tuples (line 194) | def _init_from_lineage_tuples(self):
    method _init_from_lineage_str (line 220) | def _init_from_lineage_str(self):
    method zip_lineage (line 236) | def zip_lineage(self, truncate_empty=False):
    method zip_taxid (line 250) | def zip_taxid(self, truncate_empty=False):
    method display_lineage (line 263) | def display_lineage(self, truncate_empty=True, null_as_unclassified=Fa...
    method display_taxid (line 271) | def display_taxid(self, truncate_empty=True, sep=";"):
    method check_rank_availability (line 275) | def check_rank_availability(self, rank):
    method rank_is_filled (line 280) | def rank_is_filled(self, rank, other=None):
    method is_compatible (line 289) | def is_compatible(self, other):
    method is_lineage_match (line 294) | def is_lineage_match(self, other, rank):
    method pop_to_rank (line 312) | def pop_to_rank(self, rank):
    method lineage_at_rank (line 325) | def lineage_at_rank(self, rank):
    method find_lca (line 335) | def find_lca(self, other):
  class RankLineageInfo (line 347) | class RankLineageInfo(BaseLineageInfo):
    method __post_init__ (line 370) | def __post_init__(self):
    method _init_from_lineage_dict (line 384) | def _init_from_lineage_dict(self):
  class ICTVRankLineageInfo (line 435) | class ICTVRankLineageInfo(RankLineageInfo):
    method __post_init__ (line 461) | def __post_init__(self):
    method _init_from_lineage_dict (line 473) | def _init_from_lineage_dict(self):
  class LINLineageInfo (line 508) | class LINLineageInfo(BaseLineageInfo):
    method __post_init__ (line 534) | def __post_init__(self):
    method __eq__ (line 544) | def __eq__(self, other):
    method _init_ranks_from_n_lin_positions (line 556) | def _init_ranks_from_n_lin_positions(self):
    method _init_empty (line 560) | def _init_empty(self):
    method _init_from_lineage_str (line 575) | def _init_from_lineage_str(self):
    method _init_from_lineage_tuples (line 605) | def _init_from_lineage_tuples(self):
    method is_compatible (line 625) | def is_compatible(self, other):
  class LineageTree (line 642) | class LineageTree:
    method __post_init__ (line 651) | def __post_init__(self):
    method add_lineage (line 655) | def add_lineage(self, lineage):
    method add_lineages (line 669) | def add_lineages(self, lineages):
    method find_lca (line 679) | def find_lca(self):
    method ordered_paths (line 698) | def ordered_paths(self, include_internal=False):
  function get_ident (line 726) | def get_ident(ident, *, keep_full_identifiers=False, keep_identifier_ver...
  function ascending_taxlist (line 737) | def ascending_taxlist(include_strain=True):
  function collect_gather_csvs (line 755) | def collect_gather_csvs(cmdline_gather_input, *, from_file=None):
  function read_lingroups (line 777) | def read_lingroups(lingroup_csv):
  function parse_lingroups (line 801) | def parse_lingroups(lingroupD):
  function load_gather_results (line 815) | def load_gather_results(
  function check_and_load_gather_csvs (line 891) | def check_and_load_gather_csvs(
  function report_missing_and_skipped_identities (line 960) | def report_missing_and_skipped_identities(gather_results):
  function aggregate_by_lineage_at_rank (line 988) | def aggregate_by_lineage_at_rank(
  function format_for_krona (line 1027) | def format_for_krona(
  function write_krona (line 1088) | def write_krona(header, krona_results, out_fp, *, sep="\t"):
  function write_output (line 1101) | def write_output(header, results, out_fp, *, sep=",", write_header=True):
  function write_bioboxes (line 1113) | def write_bioboxes(header_lines, results, out_fp, *, sep="\t"):
  function write_summary (line 1129) | def write_summary(
  function write_human_summary (line 1157) | def write_human_summary(
  function write_lineage_sample_frac (line 1203) | def write_lineage_sample_frac(sample_names, lineage_dict, out_fp, *, sep...
  class LineageDB (line 1242) | class LineageDB(abc.Mapping):
    method __init__ (line 1245) | def __init__(self, assign_d, avail_ranks):
    method __getitem__ (line 1249) | def __getitem__(self, ident):
    method __iter__ (line 1253) | def __iter__(self):
    method __len__ (line 1257) | def __len__(self):
    method __bool__ (line 1261) | def __bool__(self):
    method load (line 1266) | def load(
    method load_from_gather_with_lineages (line 1412) | def load_from_gather_with_lineages(
  class LineageDB_Sqlite (line 1487) | class LineageDB_Sqlite(abc.Mapping):
    method __init__ (line 1505) | def __init__(self, conn, *, table_name=None):
    method load (line 1536) | def load(cls, location):
    method _make_tup (line 1567) | def _make_tup(self, row):
    method __getitem__ (line 1572) | def __getitem__(self, ident):
    method __bool__ (line 1592) | def __bool__(self):
    method __len__ (line 1596) | def __len__(self):
    method __iter__ (line 1603) | def __iter__(self):
    method items (line 1612) | def items(self):
  class MultiLineageDB (line 1624) | class MultiLineageDB(abc.Mapping):
    method __init__ (line 1630) | def __init__(self):
    method available_ranks (line 1634) | def available_ranks(self):
    method add (line 1642) | def add(self, db):
    method __iter__ (line 1646) | def __iter__(self):
    method items (line 1655) | def items(self):
    method shadowed_identifiers (line 1664) | def shadowed_identifiers(self):
    method __getitem__ (line 1675) | def __getitem__(self, ident):
    method __len__ (line 1684) | def __len__(self):
    method __bool__ (line 1690) | def __bool__(self):
    method save (line 1694) | def save(self, filename_or_fp, file_format):
    method _save_sqlite (line 1725) | def _save_sqlite(self, filename, *, conn=None):
    method _save_csv (line 1781) | def _save_csv(self, fp):
    method load (line 1801) | def load(cls, locations, **kwargs):
  function filter_row (line 1842) | def filter_row(row, dataclass_type):
  class GatherRow (line 1857) | class GatherRow:
  class QueryInfo (line 1895) | class QueryInfo:
    method __post_init__ (line 1907) | def __post_init__(self):
    method total_weighted_bp (line 1918) | def total_weighted_bp(self):
  class BaseTaxResult (line 1923) | class BaseTaxResult:
    method get_ident (line 1938) | def get_ident(self, id_col=None):
    method get_match_lineage (line 1954) | def get_match_lineage(
  class AnnotateTaxResult (line 1978) | class AnnotateTaxResult(BaseTaxResult):
    method __post_init__ (line 1985) | def __post_init__(self):
    method row_with_lineages (line 1994) | def row_with_lineages(self):
  class TaxResult (line 2002) | class TaxResult(BaseTaxResult):
    method __post_init__ (line 2032) | def __post_init__(self):
  class SummarizedGatherResult (line 2058) | class SummarizedGatherResult:
    method __post_init__ (line 2073) | def __post_init__(self):
    method check_values (line 2076) | def check_values(self):
    method set_query_ani (line 2089) | def set_query_ani(self, query_info):
    method as_lineage_dict (line 2098) | def as_lineage_dict(self, query_info, ranks):
    method as_summary_dict (line 2111) | def as_summary_dict(self, query_info, limit_float=False, lingroups=None):
    method as_human_friendly_dict (line 2139) | def as_human_friendly_dict(self, query_info):
    method as_kreport_dict (line 2149) | def as_kreport_dict(self, query_info, *, use_abund=True):
    method as_lingroup_dict (line 2188) | def as_lingroup_dict(self, query_info, lg_name):
    method as_cami_bioboxes (line 2202) | def as_cami_bioboxes(self):
  class ClassificationResult (line 2227) | class ClassificationResult(SummarizedGatherResult):
    method __post_init__ (line 2241) | def __post_init__(self):
    method set_status (line 2246) | def set_status(self, query_info, containment_threshold=None, ani_thres...
    method build_krona_result (line 2263) | def build_krona_result(self, rank=None):
  class QueryTaxResult (line 2283) | class QueryTaxResult:
    method __post_init__ (line 2298) | def __post_init__(self):
    method _init_taxresult_vars (line 2304) | def _init_taxresult_vars(self):
    method _init_summarization_vars (line 2313) | def _init_summarization_vars(self):
    method _init_summarization_results (line 2320) | def _init_summarization_results(self):
    method _init_classification_results (line 2326) | def _init_classification_results(self):
    method is_compatible (line 2334) | def is_compatible(self, taxresult):
    method ascending_ranks (line 2342) | def ascending_ranks(self):
    method add_taxresult (line 2348) | def add_taxresult(self, taxresult):
    method summarize_up_ranks (line 2369) | def summarize_up_ranks(self, single_rank=None, force_resummarize=False):
    method build_summarized_result (line 2421) | def build_summarized_result(self, single_rank=None, force_resummarize=...
    method build_classification_result (line 2490) | def build_classification_result(
    method make_krona_header (line 2577) | def make_krona_header(self, min_rank):
    method check_classification (line 2587) | def check_classification(self):
    method check_summarization (line 2591) | def check_summarization(self):
    method make_human_summary (line 2595) | def make_human_summary(self, display_rank, classification=False):
    method make_full_summary (line 2609) | def make_full_summary(
    method make_kreport_results (line 2687) | def make_kreport_results(self, *, use_abund=True):
    method make_lingroup_results (line 2773) | def make_lingroup_results(
    method make_cami_bioboxes (line 2819) | def make_cami_bioboxes(self):

FILE: src/sourmash/utils.py
  class RustObject (line 9) | class RustObject:
    method __init__ (line 14) | def __init__(self):
    method _from_objptr (line 18) | def _from_objptr(cls, ptr, shared=False):
    method _methodcall (line 24) | def _methodcall(self, func, *args):
    method _get_objptr (line 27) | def _get_objptr(self):
    method __del__ (line 32) | def __del__(self):
  function decode_str (line 41) | def decode_str(s):
  function encode_str (line 52) | def encode_str(s):
  function rustcall (line 65) | def rustcall(func, *args):

FILE: tests/conftest.py
  function cli_v4_and_v5 (line 18) | def cli_v4_and_v5(request):
  function cli_v4_only (line 24) | def cli_v4_only(request):
  function cli_v5_only (line 30) | def cli_v5_only(request):
  function runtmp (line 35) | def runtmp():
  function runtmp_session (line 41) | def runtmp_session():
  function run (line 47) | def run():
  function track_abundance (line 52) | def track_abundance(request):
  function dayhoff (line 57) | def dayhoff(request):
  function hp (line 62) | def hp(request):
  function keep_identifiers (line 67) | def keep_identifiers(request):
  function keep_versions (line 72) | def keep_versions(request):
  function n_children (line 77) | def n_children(request):
  function linear_gather (line 82) | def linear_gather(request):
  function prefetch_gather (line 87) | def prefetch_gather(request):
  function disk_index_type (line 92) | def disk_index_type(request):
  function use_manifest (line 97) | def use_manifest(request):
  function lca_db_format (line 102) | def lca_db_format(request):
  function manifest_db_format (line 107) | def manifest_db_format(request):
  function sig_save_extension (line 112) | def sig_save_extension(request):
  function sig_save_extension_abund (line 117) | def sig_save_extension_abund(request):
  function abspath_or_relpath (line 124) | def abspath_or_relpath(request):
  function abspath_relpath_v4 (line 132) | def abspath_relpath_v4(request):
  function pytest_collection_modifyitems (line 138) | def pytest_collection_modifyitems(items, config):
  function pytest_addoption (line 156) | def pytest_addoption(parser):
  function pytest_runtest_setup (line 169) | def pytest_runtest_setup(item):

FILE: tests/sourmash_tst_utils.py
  function scriptpath (line 32) | def scriptpath(scriptname="sourmash"):
  function _runscript (line 50) | def _runscript(scriptname):
  function runscript (line 78) | def runscript(scriptname, args, **kwargs):
  function get_test_data (line 141) | def get_test_data(filename):
  class TempDirectory (line 148) | class TempDirectory:
    method __init__ (line 149) | def __init__(self):
    method __enter__ (line 152) | def __enter__(self):
    method __exit__ (line 155) | def __exit__(self, exc_type, exc_value, traceback):
  class SourmashCommandFailed (line 165) | class SourmashCommandFailed(Exception):
    method __init__ (line 166) | def __init__(self, msg):
  class RunnerContext (line 171) | class RunnerContext:
    method __init__ (line 182) | def __init__(self, location):
    method run_sourmash (line 187) | def run_sourmash(self, *args, **kwargs):
    method run (line 220) | def run(self, scriptname, *args, **kwargs):
    method output (line 228) | def output(self, path):
    method __str__ (line 231) | def __str__(self):
  function in_tempdir (line 250) | def in_tempdir(fn):
  function in_thisdir (line 260) | def in_thisdir(fn):

FILE: tests/test__minhash_hypothesis.py
  function test_set_abundance_num_hypothesis (line 16) | def test_set_abundance_num_hypothesis(hashes, abundances, sketch_size):
  function test_set_abundance_scaled_hypothesis (line 36) | def test_set_abundance_scaled_hypothesis(hashes, abundances, scaled):

FILE: tests/test_api.py
  function test_sourmash_signature_api (line 9) | def test_sourmash_signature_api(c):
  function test_load_index_0_no_file (line 24) | def test_load_index_0_no_file(c):
  function test_load_index_1 (line 30) | def test_load_index_1():
  function test_load_index_2 (line 38) | def test_load_index_2():
  function test_load_index_3 (line 46) | def test_load_index_3():
  function test_load_index_4 (line 54) | def test_load_index_4():
  function test_load_index_4_b (line 62) | def test_load_index_4_b():
  function test_load_fasta_as_signature (line 70) | def test_load_fasta_as_signature():
  function test_load_and_search_sbt_api (line 85) | def test_load_and_search_sbt_api():

FILE: tests/test_bugs.py
  function test_bug_803 (line 5) | def test_bug_803(c):

FILE: tests/test_cmd_index.py
  function _index_filename (line 16) | def _index_filename(prefix, index_type):
  function test_index_signatures (line 27) | def test_index_signatures(runtmp, disk_index_type):
  function test_search_metagenome (line 53) | def test_search_metagenome(runtmp, disk_index_type):
  function test_search_metagenome_index_downsample_fail (line 82) | def test_search_metagenome_index_downsample_fail(runtmp, disk_index_type):
  function test_search_metagenome_downsample_containment (line 116) | def test_search_metagenome_downsample_containment(runtmp, disk_index_type):
  function test_search_metagenome_downsample_index (line 152) | def test_search_metagenome_downsample_index(runtmp, disk_index_type):
  function test_gather (line 201) | def test_gather(runtmp, linear_gather, prefetch_gather, disk_index_type):
  function test_gather_metagenome (line 240) | def test_gather_metagenome(runtmp, disk_index_type):
  function test_gather_metagenome_num_results (line 274) | def test_gather_metagenome_num_results(runtmp, disk_index_type):
  function test_gather_metagenome_threshold_bp (line 309) | def test_gather_metagenome_threshold_bp(
  function test_gather_metagenome_threshold_bp_low (line 350) | def test_gather_metagenome_threshold_bp_low(
  function test_gather_metagenome_threshold_bp_too_high (line 385) | def test_gather_metagenome_threshold_bp_too_high(
  function test_gather_metagenome_abund (line 420) | def test_gather_metagenome_abund(runtmp, disk_index_type):
  function test_gather_metagenome_downsample (line 444) | def test_gather_metagenome_downsample(
  function test_gather_save_matches (line 492) | def test_gather_save_matches(runtmp, linear_gather, prefetch_gather, dis...
  function test_gather_save_matches_and_save_prefetch (line 528) | def test_gather_save_matches_and_save_prefetch(runtmp, linear_gather, di...
  function test_gather_metagenome_picklist (line 572) | def test_gather_metagenome_picklist(runtmp, disk_index_type):
  function test_index_best_containment_threshold_1 (line 612) | def test_index_best_containment_threshold_1(runtmp, disk_index_type):
  function test_index_best_containment_threshold_5 (line 668) | def test_index_best_containment_threshold_5(runtmp, disk_index_type):
  function test_gather_single_return (line 709) | def test_gather_single_return(runtmp, disk_index_type):
  function test_sbt_jaccard_ordering (line 739) | def test_sbt_jaccard_ordering(runtmp, disk_index_type):
  function test_index_protein (line 793) | def test_index_protein(runtmp, disk_index_type):
  function test_index_protein_search_no_threshold (line 846) | def test_index_protein_search_no_threshold(runtmp, disk_index_type):
  function test_index_protein_command_search (line 881) | def test_index_protein_command_search(runtmp, disk_index_type):
  function test_index_hp_command_index (line 900) | def test_index_hp_command_index(runtmp, disk_index_type):
  function test_index_hp_command_search (line 952) | def test_index_hp_command_search(runtmp, disk_index_type):
  function test_index_dayhoff_command_index (line 970) | def test_index_dayhoff_command_index(runtmp, disk_index_type):
  function test_index_dayhoff_command_search (line 1022) | def test_index_dayhoff_command_search(runtmp, disk_index_type):
  function test_index_skipm1n3_command_search (line 1040) | def test_index_skipm1n3_command_search(runtmp, disk_index_type):
  function test_index_skipm2n3_command_search (line 1088) | def test_index_skipm2n3_command_search(runtmp, disk_index_type):

FILE: tests/test_cmd_signature.py
  function _write_file (line 29) | def _write_file(runtmp, basename, lines, *, gz=False):
  function test_run_sourmash_signature_cmd (line 41) | def test_run_sourmash_signature_cmd():
  function test_run_sourmash_sig_cmd (line 48) | def test_run_sourmash_sig_cmd():
  function test_run_cat_via_parse_args (line 55) | def test_run_cat_via_parse_args():
  function test_sig_merge_1_use_full_signature_in_cmd (line 66) | def test_sig_merge_1_use_full_signature_in_cmd(runtmp):
  function test_sig_merge_1_fromfile_picklist (line 88) | def test_sig_merge_1_fromfile_picklist(runtmp):
  function test_sig_merge_1_fromfile_picklist_gz (line 121) | def test_sig_merge_1_fromfile_picklist_gz(runtmp):
  function test_sig_merge_1 (line 158) | def test_sig_merge_1(c):
  function test_sig_merge_1_multisig (line 179) | def test_sig_merge_1_multisig(c):
  function test_sig_merge_1_name (line 199) | def test_sig_merge_1_name(c):
  function test_sig_merge_1_ksize_moltype (line 230) | def test_sig_merge_1_ksize_moltype(c):
  function test_sig_merge_1_ksize_moltype_fail (line 251) | def test_sig_merge_1_ksize_moltype_fail(c):
  function test_sig_merge_2 (line 264) | def test_sig_merge_2(c):
  function test_sig_merge_3_abund_ab_ok (line 281) | def test_sig_merge_3_abund_ab_ok(c):
  function test_sig_merge_3_abund_ab (line 292) | def test_sig_merge_3_abund_ab(c):
  function test_sig_merge_3_abund_ba (line 308) | def test_sig_merge_3_abund_ba(c):
  function test_sig_filter_1 (line 324) | def test_sig_filter_1(c):
  function test_sig_filter_2 (line 348) | def test_sig_filter_2(c):
  function test_sig_filter_3 (line 367) | def test_sig_filter_3(c):
  function test_sig_filter_3_ksize_select (line 386) | def test_sig_filter_3_ksize_select(c):
  function test_sig_merge_flatten (line 405) | def test_sig_merge_flatten(c):
  function test_sig_merge_flatten_2 (line 427) | def test_sig_merge_flatten_2(c):
  function test_sig_intersect_0 (line 448) | def test_sig_intersect_0(runtmp):
  function test_sig_intersect_1 (line 459) | def test_sig_intersect_1(runtmp):
  function test_sig_intersect_1_rename (line 481) | def test_sig_intersect_1_rename(runtmp):
  function test_sig_intersect_1_fromfile_picklist (line 502) | def test_sig_intersect_1_fromfile_picklist(runtmp):
  function test_sig_intersect_2 (line 536) | def test_sig_intersect_2(c):
  function test_sig_intersect_3 (line 558) | def test_sig_intersect_3(c):
  function test_sig_intersect_4 (line 590) | def test_sig_intersect_4(c):
  function test_sig_intersect_5 (line 622) | def test_sig_intersect_5(c):
  function test_sig_intersect_6_ksize_fail (line 633) | def test_sig_intersect_6_ksize_fail(c):
  function test_sig_intersect_6_ksize_succeed (line 644) | def test_sig_intersect_6_ksize_succeed(c):
  function test_sig_intersect_7 (line 656) | def test_sig_intersect_7(c):
  function test_sig_intersect_8_multisig (line 675) | def test_sig_intersect_8_multisig(c):
  function test_sig_inflate_1 (line 688) | def test_sig_inflate_1(runtmp):
  function test_sig_inflate_2 (line 708) | def test_sig_inflate_2(runtmp):
  function test_sig_inflate_3 (line 739) | def test_sig_inflate_3(runtmp):
  function test_sig_inflate_4_picklist (line 750) | def test_sig_inflate_4_picklist(runtmp):
  function test_sig_inflate_5_bad_moltype (line 791) | def test_sig_inflate_5_bad_moltype(runtmp):
  function test_sig_subtract_1 (line 802) | def test_sig_subtract_1(runtmp):
  function test_sig_subtract_1_name (line 822) | def test_sig_subtract_1_name(runtmp):
  function test_sig_subtract_1_sigzip (line 842) | def test_sig_subtract_1_sigzip(runtmp):
  function test_sig_subtract_1_sigzip (line 864) | def test_sig_subtract_1_sigzip(runtmp):
  function test_sig_subtract_1_abund (line 886) | def test_sig_subtract_1_abund(runtmp):
  function test_sig_subtract_1_abund_is_flat (line 919) | def test_sig_subtract_1_abund_is_flat(runtmp):
  function test_sig_subtract_1_flatten (line 931) | def test_sig_subtract_1_flatten(runtmp):
  function test_sig_subtract_1_multisig (line 953) | def test_sig_subtract_1_multisig(runtmp):
  function test_sig_subtract_2 (line 968) | def test_sig_subtract_2(runtmp):
  function test_sig_subtract_3 (line 978) | def test_sig_subtract_3(runtmp):
  function test_sig_subtract_4_ksize_fail (line 988) | def test_sig_subtract_4_ksize_fail(runtmp):
  function test_sig_subtract_4_ksize_succeed (line 998) | def test_sig_subtract_4_ksize_succeed(runtmp):
  function test_sig_subtract_5_bad_moltype (line 1008) | def test_sig_subtract_5_bad_moltype(runtmp):
  function test_sig_rename_1 (line 1019) | def test_sig_rename_1(runtmp):
  function test_sig_rename_1_fromfile_picklist (line 1040) | def test_sig_rename_1_fromfile_picklist(runtmp):
  function test_sig_rename_1_multisig (line 1074) | def test_sig_rename_1_multisig(c):
  function test_sig_rename_1_multisig_ksize (line 1092) | def test_sig_rename_1_multisig_ksize(c):
  function test_sig_rename_2_output_to_same (line 1110) | def test_sig_rename_2_output_to_same(c):
  function test_sig_rename_3_file_dne (line 1125) | def test_sig_rename_3_file_dne(c):
  function test_sig_rename_3_file_dne_force (line 1134) | def test_sig_rename_3_file_dne_force(c):
  function test_sig_rename_4_pattern_include (line 1142) | def test_sig_rename_4_pattern_include(runtmp):
  function test_sig_rename_4_pattern_exclude (line 1156) | def test_sig_rename_4_pattern_exclude(runtmp):
  function test_sig_cat_1 (line 1171) | def test_sig_cat_1(c):
  function test_sig_cat_1_no_unique (line 1186) | def test_sig_cat_1_no_unique(c):
  function test_sig_cat_1_unique (line 1205) | def test_sig_cat_1_unique(c):
  function test_sig_cat_2 (line 1226) | def test_sig_cat_2(c):
  function test_sig_cat_2_out (line 1246) | def test_sig_cat_2_out(c):
  function test_sig_cat_2_out_inplace (line 1266) | def test_sig_cat_2_out_inplace(c):
  function test_sig_cat_3_filelist (line 1291) | def test_sig_cat_3_filelist(c):
  function test_sig_cat_4_filelist_with_dbs (line 1330) | def test_sig_cat_4_filelist_with_dbs(c):
  function test_sig_cat_5_from_file (line 1369) | def test_sig_cat_5_from_file(c):
  function test_sig_cat_5_from_file_picklist (line 1407) | def test_sig_cat_5_from_file_picklist(runtmp):
  function test_sig_cat_6_pattern_include (line 1455) | def test_sig_cat_6_pattern_include(runtmp):
  function test_sig_cat_6_pattern_exclude (line 1468) | def test_sig_cat_6_pattern_exclude(runtmp):
  function test_sig_cat_6_pattern_exclude_no_manifest (line 1481) | def test_sig_cat_6_pattern_exclude_no_manifest(runtmp):
  function test_sig_split_1 (line 1491) | def test_sig_split_1(runtmp):
  function test_sig_split_1_fromfile_picklist (line 1507) | def test_sig_split_1_fromfile_picklist(runtmp):
  function test_sig_split_1_overwrite (line 1535) | def test_sig_split_1_overwrite(c):
  function test_sig_split_2 (line 1551) | def test_sig_split_2(c):
  function test_sig_split_2_outdir (line 1572) | def test_sig_split_2_outdir(c):
  function test_sig_split_2_output_dir (line 1594) | def test_sig_split_2_output_dir(c):
  function test_sig_split_3_multisig (line 1616) | def test_sig_split_3_multisig(c):
  function test_sig_split_3_multisig_sig_gz (line 1634) | def test_sig_split_3_multisig_sig_gz(runtmp):
  function test_sig_split_3_multisig_zip (line 1654) | def test_sig_split_3_multisig_zip(runtmp):
  function test_sig_split_4_sbt_prot (line 1675) | def test_sig_split_4_sbt_prot(c):
  function test_sig_split_4_lca_prot (line 1695) | def test_sig_split_4_lca_prot(c):
  function test_sig_split_5_no_exist (line 1718) | def test_sig_split_5_no_exist(c):
  function test_sig_split_6_numsigs (line 1724) | def test_sig_split_6_numsigs(runtmp):
  function test_sig_extract_1 (line 1744) | def test_sig_extract_1(runtmp):
  function test_sig_extract_1_from_file (line 1760) | def test_sig_extract_1_from_file(runtmp):
  function test_sig_extract_2 (line 1778) | def test_sig_extract_2(runtmp):
  function test_sig_extract_2_zipfile (line 1798) | def test_sig_extract_2_zipfile(runtmp):
  function test_sig_extract_3 (line 1819) | def test_sig_extract_3(runtmp):
  function test_sig_extract_4 (line 1828) | def test_sig_extract_4(runtmp):
  function test_sig_extract_5 (line 1848) | def test_sig_extract_5(runtmp):
  function test_sig_extract_5_to_zip (line 1857) | def test_sig_extract_5_to_zip(runtmp):
  function test_sig_extract_6 (line 1871) | def test_sig_extract_6(runtmp):
  function test_sig_extract_7 (line 1888) | def test_sig_extract_7(runtmp):
  function test_sig_extract_7_no_ksize (line 1904) | def test_sig_extract_7_no_ksize(runtmp):
  function test_sig_extract_8_empty_picklist_fail (line 1920) | def test_sig_extract_8_empty_picklist_fail(runtmp):
  function test_sig_extract_8_nofile_picklist_fail (line 1941) | def test_sig_extract_8_nofile_picklist_fail(runtmp):
  function test_sig_extract_8_picklist_md5 (line 1959) | def test_sig_extract_8_picklist_md5(runtmp):
  function test_sig_extract_8_picklist_md5_zipfile (line 2000) | def test_sig_extract_8_picklist_md5_zipfile(runtmp):
  function test_sig_extract_8_picklist_md5_lca_fail (line 2042) | def test_sig_extract_8_picklist_md5_lca_fail(runtmp):
  function test_sig_extract_8_picklist_md5_include (line 2084) | def test_sig_extract_8_picklist_md5_include(runtmp):
  function test_sig_extract_8_picklist_md5_exclude (line 2125) | def test_sig_extract_8_picklist_md5_exclude(runtmp):
  function test_sig_extract_8_picklist_md5_require_all (line 2166) | def test_sig_extract_8_picklist_md5_require_all(runtmp):
  function test_sig_extract_8_picklist_name (line 2228) | def test_sig_extract_8_picklist_name(runtmp):
  function test_sig_extract_8_picklist_name_exclude (line 2261) | def test_sig_extract_8_picklist_name_exclude(runtmp):
  function test_sig_extract_8_picklist_ident (line 2294) | def test_sig_extract_8_picklist_ident(runtmp):
  function test_sig_extract_8_picklist_ident_exclude (line 2327) | def test_sig_extract_8_picklist_ident_exclude(runtmp):
  function test_sig_extract_8_picklist_ident_dot (line 2360) | def test_sig_extract_8_picklist_ident_dot(runtmp):
  function test_sig_extract_8_picklist_ident_dot_exclude (line 2393) | def test_sig_extract_8_picklist_ident_dot_exclude(runtmp):
  function test_sig_extract_8_picklist_md5_short (line 2426) | def test_sig_extract_8_picklist_md5_short(runtmp):
  function test_sig_extract_8_picklist_md5_short_exclude (line 2459) | def test_sig_extract_8_picklist_md5_short_exclude(runtmp):
  function test_sig_extract_8_picklist_md5_short_alias (line 2492) | def test_sig_extract_8_picklist_md5_short_alias(runtmp):
  function test_sig_extract_8_picklist_md5_short_alias_exclude (line 2525) | def test_sig_extract_8_picklist_md5_short_alias_exclude(runtmp):
  function test_sig_extract_8_picklist_md5_short_alias_with_md5_selector_nomatch (line 2558) | def test_sig_extract_8_picklist_md5_short_alias_with_md5_selector_nomatc...
  function test_sig_extract_8_picklist_md5_short_alias_with_md5_selector_nomatch_exclude (line 2589) | def test_sig_extract_8_picklist_md5_short_alias_with_md5_selector_nomatc...
  function test_sig_extract_8_picklist_md5_short_alias_with_md5_selector (line 2622) | def test_sig_extract_8_picklist_md5_short_alias_with_md5_selector(runtmp):
  function test_sig_extract_8_picklist_md5_short_alias_with_md5_selector_exclude (line 2664) | def test_sig_extract_8_picklist_md5_short_alias_with_md5_selector_exclud...
  function test_sig_extract_8_picklist_md5_nomatch (line 2706) | def test_sig_extract_8_picklist_md5_nomatch(runtmp):
  function test_sig_extract_8_picklist_md5_nomatch_exclude (line 2731) | def test_sig_extract_8_picklist_md5_nomatch_exclude(runtmp):
  function test_sig_extract_9_picklist_md5_ksize_hp_select (line 2765) | def test_sig_extract_9_picklist_md5_ksize_hp_select(runtmp):
  function test_sig_extract_9_picklist_md5_ksize_hp_select_exclude (line 2793) | def test_sig_extract_9_picklist_md5_ksize_hp_select_exclude(runtmp):
  function test_sig_extract_10_picklist_md5_dups_and_empty (line 2821) | def test_sig_extract_10_picklist_md5_dups_and_empty(runtmp):
  function test_sig_extract_10_picklist_md5_dups_and_empty_exclude (line 2855) | def test_sig_extract_10_picklist_md5_dups_and_empty_exclude(runtmp):
  function test_sig_extract_11_picklist_bad_coltype (line 2889) | def test_sig_extract_11_picklist_bad_coltype(runtmp):
  function test_sig_extract_11_picklist_bad_coltype_exclude (line 2912) | def test_sig_extract_11_picklist_bad_coltype_exclude(runtmp):
  function test_sig_extract_12_picklist_bad_argstr (line 2935) | def test_sig_extract_12_picklist_bad_argstr(runtmp):
  function test_sig_extract_12_picklist_bad_pickstyle (line 2958) | def test_sig_extract_12_picklist_bad_pickstyle(runtmp):
  function test_sig_extract_12_picklist_bad_colname (line 2984) | def test_sig_extract_12_picklist_bad_colname(runtmp):
  function test_sig_extract_12_picklist_bad_colname_exclude (line 3007) | def test_sig_extract_12_picklist_bad_colname_exclude(runtmp):
  function test_sig_extract_11_pattern_include (line 3030) | def test_sig_extract_11_pattern_include(runtmp):
  function test_sig_extract_11_pattern_exclude (line 3045) | def test_sig_extract_11_pattern_exclude(runtmp):
  function test_sig_extract_identical_md5s (line 3060) | def test_sig_extract_identical_md5s(runtmp):
  function test_sig_flatten_1 (line 3085) | def test_sig_flatten_1(runtmp):
  function test_sig_flatten_1_from_file (line 3106) | def test_sig_flatten_1_from_file(runtmp):
  function test_sig_flatten_1_select_name (line 3138) | def test_sig_flatten_1_select_name(c):
  function test_sig_flatten_1_select_md5 (line 3157) | def test_sig_flatten_1_select_md5(runtmp):
  function test_sig_flatten_2_ksize (line 3178) | def test_sig_flatten_2_ksize(runtmp):
  function test_sig_downsample_1_scaled (line 3194) | def test_sig_downsample_1_scaled(c):
  function test_sig_downsample_1_scaled_downsample_multisig (line 3212) | def test_sig_downsample_1_scaled_downsample_multisig(c):
  function test_sig_downsample_1_scaled_to_num (line 3225) | def test_sig_downsample_1_scaled_to_num(c):
  function test_sig_downsample_check_num_bounds_negative (line 3247) | def test_sig_downsample_check_num_bounds_negative(runtmp):
  function test_sig_downsample_check_num_bounds_less_than_minimum (line 3257) | def test_sig_downsample_check_num_bounds_less_than_minimum(runtmp):
  function test_sig_downsample_check_num_bounds_more_than_maximum (line 3266) | def test_sig_downsample_check_num_bounds_more_than_maximum(runtmp):
  function test_sig_downsample_1_scaled_to_num_fail (line 3279) | def test_sig_downsample_1_scaled_to_num_fail(c):
  function test_sig_downsample_1_scaled_empty (line 3288) | def test_sig_downsample_1_scaled_empty(c):
  function test_sig_downsample_2_num (line 3297) | def test_sig_downsample_2_num(c):
  function test_sig_downsample_2_num_to_scaled (line 3315) | def test_sig_downsample_2_num_to_scaled(c):
  function test_sig_downsample_2_num_to_scaled_fail (line 3340) | def test_sig_downsample_2_num_to_scaled_fail(c):
  function test_sig_downsample_2_num_and_scaled_both_fail (line 3352) | def test_sig_downsample_2_num_and_scaled_both_fail(c):
  function test_sig_downsample_2_num_empty (line 3372) | def test_sig_downsample_2_num_empty(c):
  function test_sig_describe_1 (line 3380) | def test_sig_describe_1(runtmp):
  function test_sig_describe_1_fromfile_picklist (line 3402) | def test_sig_describe_1_fromfile_picklist(runtmp):
  function test_sig_describe_protein (line 3435) | def test_sig_describe_protein(c):
  function test_sig_describe_hp (line 3449) | def test_sig_describe_hp(c):
  function test_sig_describe_dayhoff (line 3463) | def test_sig_describe_dayhoff(c):
  function test_sig_describe_1_hp (line 3476) | def test_sig_describe_1_hp(runtmp):
  function test_sig_describe_1_multisig (line 3599) | def test_sig_describe_1_multisig(c):
  function test_sig_describe_1_sbt (line 3619) | def test_sig_describe_1_sbt(c):
  function test_sig_describe_1_lca (line 3636) | def test_sig_describe_1_lca(c):
  function test_sig_describe_1_dir (line 3653) | def test_sig_describe_1_dir(c):
  function test_sig_describe_1_zipfile (line 3674) | def test_sig_describe_1_zipfile(c):
  function test_sig_describe_1_sig_abund (line 3694) | def test_sig_describe_1_sig_abund(runtmp):
  function test_sig_describe_stdin (line 3718) | def test_sig_describe_stdin(c):
  function test_sig_describe_empty (line 3731) | def test_sig_describe_empty(c):
  function test_sig_describe_sqldb (line 3762) | def test_sig_describe_sqldb(runtmp):
  function test_sig_describe_2_csv (line 3781) | def test_sig_describe_2_csv(runtmp):
  function test_sig_describe_2_csv_gz (line 3806) | def test_sig_describe_2_csv_gz(runtmp):
  function test_sig_describe_2_csv_abund (line 3831) | def test_sig_describe_2_csv_abund(runtmp):
  function test_sig_describe_2_csv_as_picklist (line 3860) | def test_sig_describe_2_csv_as_picklist(runtmp):
  function test_sig_describe_2_include_db_pattern (line 3887) | def test_sig_describe_2_include_db_pattern(runtmp):
  function test_sig_describe_2_exclude_db_pattern (line 3910) | def test_sig_describe_2_exclude_db_pattern(runtmp):
  function test_sig_describe_3_manifest_works (line 3935) | def test_sig_describe_3_manifest_works(runtmp):
  function test_sig_describe_3_manifest_fails_when_moved (line 3949) | def test_sig_describe_3_manifest_fails_when_moved(runtmp):
  function test_sig_overlap (line 3960) | def test_sig_overlap(runtmp):
  function test_sig_overlap_2 (line 3978) | def test_sig_overlap_2(runtmp):
  function test_sig_overlap_inaccurate_size_estimate (line 3999) | def test_sig_overlap_inaccurate_size_estimate(runtmp):
  function test_sig_overlap_abund (line 4027) | def test_sig_overlap_abund(runtmp):
  function test_sig_overlap_num (line 4053) | def test_sig_overlap_num(runtmp):
  function test_import_export_1 (line 4072) | def test_import_export_1(c):
  function test_import_export_1_by_md5 (line 4087) | def test_import_export_1_by_md5(c):
  function test_import_export_2 (line 4102) | def test_import_export_2(c):
  function test_import_mash_csv_to_sig (line 4118) | def test_import_mash_csv_to_sig(runtmp):
  function test_sig_manifest_1_zipfile (line 4135) | def test_sig_manifest_1_zipfile(runtmp):
  function test_sig_manifest_1_zipfile_csv_gz (line 4150) | def test_sig_manifest_1_zipfile_csv_gz(runtmp):
  function test_sig_manifest_1_zipfile_already_exists (line 4165) | def test_sig_manifest_1_zipfile_already_exists(runtmp):
  function test_sig_manifest_1_zipfile_already_exists_force (line 4177) | def test_sig_manifest_1_zipfile_already_exists_force(runtmp):
  function test_sig_manifest_1_zipfile_already_exists_sql (line 4196) | def test_sig_manifest_1_zipfile_already_exists_sql(runtmp):
  function test_sig_manifest_2_sigfile (line 4212) | def test_sig_manifest_2_sigfile(runtmp):
  function test_sig_manifest_3_sbt (line 4229) | def test_sig_manifest_3_sbt(runtmp):
  function test_sig_manifest_4_lca (line 4244) | def test_sig_manifest_4_lca(runtmp):
  function test_sig_manifest_5_dir (line 4259) | def test_sig_manifest_5_dir(runtmp):
  function test_sig_manifest_6_pathlist (line 4274) | def test_sig_manifest_6_pathlist(runtmp):
  function test_sig_manifest_does_not_exist (line 4302) | def test_sig_manifest_does_not_exist(runtmp):
  function test_sig_manifest_7_allzip_1 (line 4312) | def test_sig_manifest_7_allzip_1(runtmp, cli_v4_only):
  function test_sig_manifest_7_allzip_2 (line 4332) | def test_sig_manifest_7_allzip_2(runtmp):
  function test_sig_manifest_7_allzip_3_no_rebuild (line 4346) | def test_sig_manifest_7_allzip_3_no_rebuild(runtmp, cli_v4_only):
  function test_sig_manifest_7_allzip_3_no_rebuild_is_default_v5 (line 4363) | def test_sig_manifest_7_allzip_3_no_rebuild_is_default_v5(runtmp, cli_v5...
  function test_sig_manifest_8_sqldb (line 4378) | def test_sig_manifest_8_sqldb(runtmp):
  function test_sig_manifest_8_sqldb_out (line 4409) | def test_sig_manifest_8_sqldb_out(runtmp):
  function test_sig_kmers_1_dna (line 4432) | def test_sig_kmers_1_dna(runtmp):
  function test_sig_kmers_1_dna_more_in_query (line 4490) | def test_sig_kmers_1_dna_more_in_query(runtmp):
  function test_sig_kmers_1_dna_empty_seq (line 4518) | def test_sig_kmers_1_dna_empty_seq(runtmp):
  function test_sig_kmers_1_dna_empty_sig (line 4543) | def test_sig_kmers_1_dna_empty_sig(runtmp):
  function test_sig_kmers_1_dna_single_sig (line 4563) | def test_sig_kmers_1_dna_single_sig(runtmp):
  function test_sig_kmers_1_dna_lowscaled (line 4584) | def test_sig_kmers_1_dna_lowscaled(runtmp):
  function test_sig_kmers_1_dna_num (line 4642) | def test_sig_kmers_1_dna_num(runtmp):
  function test_sig_kmers_1_dna_translate_protein (line 4700) | def test_sig_kmers_1_dna_translate_protein(runtmp):
  function test_sig_kmers_1_dna_translate_dayhoff (line 4759) | def test_sig_kmers_1_dna_translate_dayhoff(runtmp):
  function test_sig_kmers_1_dna_translate_hp (line 4818) | def test_sig_kmers_1_dna_translate_hp(runtmp):
  function test_sig_kmers_2_protein (line 4877) | def test_sig_kmers_2_protein(runtmp):
  function test_sig_kmers_2_dayhoff (line 4936) | def test_sig_kmers_2_dayhoff(runtmp):
  function test_sig_kmers_2_hp (line 4995) | def test_sig_kmers_2_hp(runtmp):
  function test_sig_check_1 (line 5054) | def test_sig_check_1(runtmp, abspath_relpath_v4):
  function test_sig_check_1_fail_abspath_relpath (line 5088) | def test_sig_check_1_fail_abspath_relpath(runtmp):
  function test_sig_check_1_warn_abspath_relpath (line 5110) | def test_sig_check_1_warn_abspath_relpath(runtmp, abspath_or_relpath):
  function test_sig_check_1_mf_csv_gz (line 5131) | def test_sig_check_1_mf_csv_gz(runtmp, abspath_relpath_v4):
  function test_sig_check_1_gz (line 5165) | def test_sig_check_1_gz(runtmp, abspath_relpath_v4):
  function test_sig_check_1_nofail (line 5204) | def test_sig_check_1_nofail(runtmp, abspath_relpath_v4):
  function test_sig_check_1_no_picklist (line 5239) | def test_sig_check_1_no_picklist(runtmp):
  function test_sig_check_1_column (line 5260) | def test_sig_check_1_column(runtmp, column, coltype, abspath_relpath_v4):
  function test_sig_check_1_diff_col_name (line 5296) | def test_sig_check_1_diff_col_name(runtmp, abspath_relpath_v4):
  function test_sig_check_1_diff_col_name_zip (line 5346) | def test_sig_check_1_diff_col_name_zip(runtmp, abspath_relpath_v4):
  function test_sig_check_1_diff_col_name_exclude (line 5400) | def test_sig_check_1_diff_col_name_exclude(runtmp, abspath_relpath_v4):
  function test_sig_check_1_ksize (line 5434) | def test_sig_check_1_ksize(runtmp, abspath_relpath_v4):
  function test_sig_check_1_ksize_output_sql (line 5468) | def test_sig_check_1_ksize_output_sql(runtmp, abspath_relpath_v4):
  function test_sig_check_2_output_missing (line 5504) | def test_sig_check_2_output_missing(runtmp, abspath_relpath_v4):
  function test_sig_check_2_output_missing_error_exit (line 5537) | def test_sig_check_2_output_missing_error_exit(runtmp):
  function test_sig_check_2_output_missing_column (line 5580) | def test_sig_check_2_output_missing_column(runtmp, column, coltype, absp...
  function test_sig_check_2_output_missing_exclude (line 5607) | def test_sig_check_2_output_missing_exclude(runtmp):
  function test_sig_check_3_no_manifest (line 5629) | def test_sig_check_3_no_manifest(runtmp):
  function test_sig_check_3_no_manifest_ok (line 5644) | def test_sig_check_3_no_manifest_ok(runtmp, abspath_relpath_v4):
  function test_sig_check_4_manifest_cwd_cwd (line 5667) | def test_sig_check_4_manifest_cwd_cwd(runtmp, abspath_relpath_v4):
  function test_sig_check_4_manifest_subdir_cwd (line 5693) | def test_sig_check_4_manifest_subdir_cwd(runtmp, abspath_or_relpath):
  function test_sig_check_4_manifest_cwd_subdir (line 5724) | def test_sig_check_4_manifest_cwd_subdir(runtmp, abspath_relpath_v4):
  function test_sig_check_4_manifest_subdir_subdir (line 5754) | def test_sig_check_4_manifest_subdir_subdir(runtmp, abspath_or_relpath):
  function test_sig_check_5_relpath (line 5786) | def test_sig_check_5_relpath(runtmp):
  function test_sig_check_5_relpath_subdir (line 5827) | def test_sig_check_5_relpath_subdir(runtmp, cli_v4_and_v5):
  function test_sig_check_5_relpath_subdir_default_v5 (line 5869) | def test_sig_check_5_relpath_subdir_default_v5(runtmp, cli_v5_only):
  function test_sig_check_5_abspath (line 5910) | def test_sig_check_5_abspath(runtmp, cli_v4_and_v5):
  function test_sig_check_5_no_abspath (line 5947) | def test_sig_check_5_no_abspath(runtmp, cli_v4_only):

FILE: tests/test_cmd_signature_collect.py
  function test_sig_collect_0_nothing (line 17) | def test_sig_collect_0_nothing(runtmp, manifest_db_format, abspath_relpa...
  function test_sig_collect_0_fail_abspath_relpath (line 39) | def test_sig_collect_0_fail_abspath_relpath(runtmp, manifest_db_format):
  function test_sig_collect_1_zipfile (line 61) | def test_sig_collect_1_zipfile(runtmp, manifest_db_format, abspath_relpa...
  function test_sig_collect_1_zipfile_csv_gz (line 87) | def test_sig_collect_1_zipfile_csv_gz(runtmp, abspath_relpath_v4):
  function test_sig_collect_1_zipfile_csv_gz_roundtrip (line 110) | def test_sig_collect_1_zipfile_csv_gz_roundtrip(runtmp, abspath_relpath_...
  function test_sig_collect_2_exists_fail (line 144) | def test_sig_collect_2_exists_fail(runtmp, manifest_db_format):
  function test_sig_collect_2_exists_merge (line 170) | def test_sig_collect_2_exists_merge(runtmp, manifest_db_format, abspath_...
  function test_sig_collect_2_exists_sql_merge_csv (line 205) | def test_sig_collect_2_exists_sql_merge_csv(runtmp, manifest_db_format):
  function test_sig_collect_2_exists_csv_merge_sql (line 231) | def test_sig_collect_2_exists_csv_merge_sql(runtmp):
  function test_sig_collect_2_no_exists_merge (line 257) | def test_sig_collect_2_no_exists_merge(runtmp, manifest_db_format, abspa...
  function test_sig_collect_3_multiple (line 286) | def test_sig_collect_3_multiple(runtmp, manifest_db_format):
  function test_sig_collect_3_multiple_use_fromfile (line 325) | def test_sig_collect_3_multiple_use_fromfile(runtmp, manifest_db_format):
  function test_sig_collect_4_multiple_from_sig (line 369) | def test_sig_collect_4_multiple_from_sig(runtmp, manifest_db_format):
  function test_sig_collect_4_multiple_from_sig_abspath (line 394) | def test_sig_collect_4_multiple_from_sig_abspath(runtmp, manifest_db_for...
  function test_sig_collect_4_multiple_no_abspath (line 435) | def test_sig_collect_4_multiple_no_abspath(runtmp, manifest_db_format):
  function test_sig_collect_4_multiple_subdir_subdir_relpath (line 474) | def test_sig_collect_4_multiple_subdir_subdir_relpath(runtmp, manifest_d...
  function test_sig_collect_4_multiple_subdir_subdir_default_is_relpath (line 519) | def test_sig_collect_4_multiple_subdir_subdir_default_is_relpath(
  function test_sig_collect_4_multiple_cwd_subdir_no_abspath (line 566) | def test_sig_collect_4_multiple_cwd_subdir_no_abspath(runtmp, manifest_d...
  function test_sig_collect_5_no_manifest_sbt_fail (line 607) | def test_sig_collect_5_no_manifest_sbt_fail(runtmp, manifest_db_format):
  function test_sig_collect_5_no_manifest_sbt_succeed (line 619) | def test_sig_collect_5_no_manifest_sbt_succeed(
  function test_sig_collect_6_path_cwd_cwd (line 648) | def test_sig_collect_6_path_cwd_cwd(runtmp, manifest_db_format, abspath_...
  function test_sig_collect_6_path_cwd_subdir (line 673) | def test_sig_collect_6_path_cwd_subdir(runtmp, manifest_db_format, abspa...
  function test_sig_collect_6_path_subdir_cwd (line 699) | def test_sig_collect_6_path_subdir_cwd(runtmp, manifest_db_format, abspa...
  function test_sig_collect_6_path_subdir_subdir (line 726) | def test_sig_collect_6_path_subdir_subdir(

FILE: tests/test_cmd_signature_fileinfo.py
  function test_fileinfo_1_sig (line 18) | def test_fileinfo_1_sig(runtmp):
  function test_fileinfo_1_sig_summarize (line 42) | def test_fileinfo_1_sig_summarize(runtmp):
  function test_fileinfo_1_sig_abund (line 66) | def test_fileinfo_1_sig_abund(runtmp):
  function test_fileinfo_2_lca (line 90) | def test_fileinfo_2_lca(runtmp):
  function test_fileinfo_3_sbt_zip (line 114) | def test_fileinfo_3_sbt_zip(runtmp):
  function test_fileinfo_4_zip (line 138) | def test_fileinfo_4_zip(runtmp):
  function test_fileinfo_4_zip_json_out (line 165) | def test_fileinfo_4_zip_json_out(runtmp):
  function test_fileinfo_4_zip_rebuild (line 228) | def test_fileinfo_4_zip_rebuild(runtmp):
  function test_fileinfo_5_dir (line 258) | def test_fileinfo_5_dir(runtmp):
  function test_fileinfo_6_pathlist (line 284) | def test_fileinfo_6_pathlist(runtmp):
  function test_fileinfo_7_sbt_json (line 322) | def test_fileinfo_7_sbt_json(runtmp, db):
  function test_sig_fileinfo_stdin (line 345) | def test_sig_fileinfo_stdin(runtmp):
  function test_sig_fileinfo_does_not_exist (line 372) | def test_sig_fileinfo_does_not_exist(runtmp):
  function test_sig_fileinfo_8_manifest_works (line 383) | def test_sig_fileinfo_8_manifest_works(runtmp):
  function test_sig_fileinfo_8_manifest_works_when_moved (line 398) | def test_sig_fileinfo_8_manifest_works_when_moved(runtmp):
  function test_sig_fileinfo_9_sqldb_make (line 417) | def test_sig_fileinfo_9_sqldb_make(runtmp):
  function test_sig_fileinfo_9_sqldb_exists (line 435) | def test_sig_fileinfo_9_sqldb_exists(runtmp):
  function test_sig_fileinfo_9_sql_manifest (line 452) | def test_sig_fileinfo_9_sql_manifest(runtmp):
  function test_sig_fileinfo_9_sql_lca_db (line 471) | def test_sig_fileinfo_9_sql_lca_db(runtmp):

FILE: tests/test_cmd_signature_grep.py
  function test_grep_1_sig_name (line 20) | def test_grep_1_sig_name(runtmp):
  function test_grep_1_sig_name_case_sensitive (line 35) | def test_grep_1_sig_name_case_sensitive(runtmp):
  function test_grep_1_sig_name_case_insensitive (line 43) | def test_grep_1_sig_name_case_insensitive(runtmp):
  function test_grep_1_sig_name_exclude (line 58) | def test_grep_1_sig_name_exclude(runtmp):
  function test_grep_2_sig_md5 (line 67) | def test_grep_2_sig_md5(runtmp):
  function test_grep_2_sig_md5_case_sensitive (line 81) | def test_grep_2_sig_md5_case_sensitive(runtmp):
  function test_grep_2_sig_md5_case_insensitive (line 89) | def test_grep_2_sig_md5_case_insensitive(runtmp):
  function test_grep_3_filename (line 103) | def test_grep_3_filename(runtmp):
  function test_grep_3_filename_regexp (line 118) | def test_grep_3_filename_regexp(runtmp):
  function test_grep_4_no_manifest (line 133) | def test_grep_4_no_manifest(runtmp):
  function test_grep_4_no_manifest_ok (line 148) | def test_grep_4_no_manifest_ok(runtmp):
  function test_grep_5_zip_include (line 161) | def test_grep_5_zip_include(runtmp):
  function test_grep_5_zip_include_picklist (line 176) | def test_grep_5_zip_include_picklist(runtmp):
  function test_grep_5_zip_include_case_insensitive (line 205) | def test_grep_5_zip_include_case_insensitive(runtmp):
  function test_grep_5_zip_exclude (line 220) | def test_grep_5_zip_exclude(runtmp):
  function test_grep_5_zip_exclude_case_insensitive (line 235) | def test_grep_5_zip_exclude_case_insensitive(runtmp):
  function test_grep_6_zip_manifest_csv (line 250) | def test_grep_6_zip_manifest_csv(runtmp):
  function test_grep_6_zip_manifest_csv_gz (line 276) | def test_grep_6_zip_manifest_csv_gz(runtmp):
  function test_sig_grep_7_lca (line 308) | def test_sig_grep_7_lca(runtmp):
  function test_sig_grep_7_picklist_md5_lca_fail (line 335) | def test_sig_grep_7_picklist_md5_lca_fail(runtmp):
  function test_sig_grep_8_count (line 376) | def test_sig_grep_8_count(runtmp):
  function test_sig_grep_9_name (line 415) | def test_sig_grep_9_name(runtmp):
  function test_sig_grep_identical_md5s (line 451) | def test_sig_grep_identical_md5s(runtmp):

FILE: tests/test_compare.py
  function siglist (line 20) | def siglist():
  function scaled_siglist (line 30) | def scaled_siglist():
  function ignore_abundance (line 44) | def ignore_abundance(track_abundance):
  function test_compare_serial (line 48) | def test_compare_serial(siglist, ignore_abundance):
  function test_compare_parallel (line 66) | def test_compare_parallel(siglist, ignore_abundance):
  function test_compare_all_pairs (line 86) | def test_compare_all_pairs(siglist, ignore_abundance):
  function test_compare_serial_jaccardANI (line 94) | def test_compare_serial_jaccardANI(scaled_siglist, ignore_abundance):
  function test_compare_parallel_jaccardANI (line 112) | def test_compare_parallel_jaccardANI(scaled_siglist, ignore_abundance):
  function test_compare_all_pairs_jaccardANI (line 129) | def test_compare_all_pairs_jaccardANI(scaled_siglist, ignore_abundance):
  function test_compare_serial_containmentANI (line 139) | def test_compare_serial_containmentANI(scaled_siglist):
  function test_compare_serial_maxcontainmentANI (line 157) | def test_compare_serial_maxcontainmentANI(scaled_siglist):
  function test_compare_serial_avg_containmentANI (line 178) | def test_compare_serial_avg_containmentANI(scaled_siglist):

FILE: tests/test_deprecated.py
  function test_load_textmode (line 5) | def test_load_textmode(track_abundance):

FILE: tests/test_distance_utils.py
  function test_aniresult (line 21) | def test_aniresult():
  function test_aniresult_bad_distance (line 35) | def test_aniresult_bad_distance():
  function test_jaccard_aniresult (line 49) | def test_jaccard_aniresult():
  function test_jaccard_aniresult_nojaccarderror (line 62) | def test_jaccard_aniresult_nojaccarderror():
  function test_ci_aniresult (line 70) | def test_ci_aniresult():
  function test_containment_to_distance_zero (line 84) | def test_containment_to_distance_zero():
  function test_containment_to_distance_one (line 116) | def test_containment_to_distance_one():
  function test_containment_to_distance_scaled1 (line 144) | def test_containment_to_distance_scaled1():
  function test_containment_to_distance_scaled100 (line 175) | def test_containment_to_distance_scaled100():
  function test_containment_to_distance_scaled100_2 (line 192) | def test_containment_to_distance_scaled100_2():
  function test_containment_to_distance_k10 (line 208) | def test_containment_to_distance_k10():
  function test_containment_to_distance_confidence (line 224) | def test_containment_to_distance_confidence():
  function test_nkmers_to_bp_containment (line 261) | def test_nkmers_to_bp_containment():
  function test_jaccard_to_distance_zero (line 294) | def test_jaccard_to_distance_zero():
  function test_jaccard_to_distance_one (line 308) | def test_jaccard_to_distance_one():
  function test_jaccard_to_distance_scaled (line 322) | def test_jaccard_to_distance_scaled():
  function test_jaccard_to_distance_k31 (line 345) | def test_jaccard_to_distance_k31():
  function test_jaccard_to_distance_k31_2 (line 363) | def test_jaccard_to_distance_k31_2():
  function test_nkmers_to_bp_jaccard (line 376) | def test_nkmers_to_bp_jaccard():
  function test_exp_prob_nothing_common (line 394) | def test_exp_prob_nothing_common():
  function test_containment_to_distance_tinytestdata_var0 (line 412) | def test_containment_to_distance_tinytestdata_var0():
  function test_var_n_mutated (line 435) | def test_var_n_mutated():
  function test_handle_seqlen_nkmers (line 459) | def test_handle_seqlen_nkmers():
  function test_set_size_chernoff (line 476) | def test_set_size_chernoff():
  function test_set_size_exact_prob (line 515) | def test_set_size_exact_prob():

FILE: tests/test_hll.py
  function test_hll_add_python (line 17) | def test_hll_add_python():
  function test_hll_consume_string (line 46) | def test_hll_consume_string():
  function test_hll_similarity_containment (line 60) | def test_hll_similarity_containment():
  function test_hll_save_load (line 116) | def test_hll_save_load():

FILE: tests/test_index.py
  function test_simple_index (line 34) | def test_simple_index(n_children):
  function test_linear_index_prefetch_empty (line 98) | def test_linear_index_prefetch_empty():
  function test_linear_index_prefetch_lazy (line 114) | def test_linear_index_prefetch_lazy():
  function test_linear_index_search_subj_has_abundance (line 150) | def test_linear_index_search_subj_has_abundance():
  function test_linear_index_gather_subj_has_abundance (line 167) | def test_linear_index_gather_subj_has_abundance():
  function test_index_search_subj_scaled_is_lower (line 185) | def test_index_search_subj_scaled_is_lower():
  function test_index_search_subj_num_is_lower (line 210) | def test_index_search_subj_num_is_lower():
  function test_index_search_query_num_is_lower (line 233) | def test_index_search_query_num_is_lower():
  function test_linear_index_search_abund (line 254) | def test_linear_index_search_abund():
  function test_linear_index_search_abund_downsample_query (line 272) | def test_linear_index_search_abund_downsample_query():
  function test_linear_index_search_abund_downsample_subj (line 295) | def test_linear_index_search_abund_downsample_subj():
  function test_linear_index_search_abund_requires_threshold (line 318) | def test_linear_index_search_abund_requires_threshold():
  function test_linear_index_search_abund_query_flat (line 336) | def test_linear_index_search_abund_query_flat():
  function test_linear_index_search_abund_subj_flat (line 356) | def test_linear_index_search_abund_subj_flat():
  function test_linear_index_save (line 377) | def test_linear_index_save(runtmp):
  function test_linear_index_load (line 408) | def test_linear_index_load(runtmp):
  function test_linear_index_save_load (line 429) | def test_linear_index_save_load(runtmp):
  function test_linear_gather_threshold_1 (line 455) | def test_linear_gather_threshold_1():
  function test_linear_gather_threshold_5 (line 513) | def test_linear_gather_threshold_5():
  function test_linear_index_multik_select (line 556) | def test_linear_index_multik_select():
  function test_linear_index_moltype_select (line 574) | def test_linear_index_moltype_select():
  function test_linear_index_picklist_select (line 604) | def test_linear_index_picklist_select():
  function test_linear_index_picklist_select_exclude (line 627) | def test_linear_index_picklist_select_exclude():
  function test_index_same_md5sum_fsstorage (line 656) | def test_index_same_md5sum_fsstorage(runtmp):
  function test_index_same_md5sum_sbt_zipstorage (line 671) | def test_index_same_md5sum_sbt_zipstorage(runtmp):
  function test_zipfile_does_not_exist (line 688) | def test_zipfile_does_not_exist(runtmp):
  function test_zipfile_protein_command_search (line 700) | def test_zipfile_protein_command_search(runtmp):
  function test_zipfile_hp_command_search (line 717) | def test_zipfile_hp_command_search(runtmp):
  function test_zipfile_dayhoff_command_search (line 734) | def test_zipfile_dayhoff_command_search(runtmp):
  function test_zipfile_protein_command_search_combined (line 751) | def test_zipfile_protein_command_search_combined(runtmp):
  function test_zipfile_hp_command_search_combined (line 768) | def test_zipfile_hp_command_search_combined(runtmp):
  function test_zipfile_dayhoff_command_search_combined (line 785) | def test_zipfile_dayhoff_command_search_combined(runtmp):
  function test_zipfile_dayhoff_command_search_protein (line 802) | def test_zipfile_dayhoff_command_search_protein(runtmp):
  function test_zipfile_API_signatures (line 821) | def test_zipfile_API_signatures(use_manifest):
  function test_zipfile_bool (line 836) | def test_zipfile_bool():
  function test_zipfile_API_signatures_traverse_yield_all (line 862) | def test_zipfile_API_signatures_traverse_yield_all(use_manifest):
  function test_zipfile_API_signatures_traverse_yield_all_select (line 879) | def test_zipfile_API_signatures_traverse_yield_all_select(use_manifest):
  function test_zipfile_API_signatures_traverse_yield_all_manifest (line 892) | def test_zipfile_API_signatures_traverse_yield_all_manifest():
  function test_zipfile_API_signatures_select (line 909) | def test_zipfile_API_signatures_select(use_manifest):
  function test_zipfile_API_signatures_select_abund_false (line 930) | def test_zipfile_API_signatures_select_abund_false(use_manifest):
  function test_zipfile_API_signatures_select_abund_true (line 946) | def test_zipfile_API_signatures_select_abund_true(use_manifest):
  function test_zipfile_API_signatures_select_abund_none (line 962) | def test_zipfile_API_signatures_select_abund_none(use_manifest):
  function test_zipfile_API_signatures_select_twice (line 978) | def test_zipfile_API_signatures_select_twice(use_manifest):
  function test_zipfile_API_save (line 1001) | def test_zipfile_API_save():
  function test_zipfile_API_insert (line 1011) | def test_zipfile_API_insert():
  function test_zipfile_API_location (line 1022) | def test_zipfile_API_location(use_manifest):
  function test_zipfile_load_file_as_signatures (line 1031) | def test_zipfile_load_file_as_signatures(use_manifest):
  function test_zipfile_load_file_as_signatures_traverse_yield_all (line 1049) | def test_zipfile_load_file_as_signatures_traverse_yield_all(use_manifest):
  function test_zipfile_load_database_fail_if_not_zip (line 1066) | def test_zipfile_load_database_fail_if_not_zip(runtmp):
  function test_multi_index_search (line 1080) | def test_multi_index_search():
  function test_multi_index_gather (line 1134) | def test_multi_index_gather():
  function test_multi_index_signatures (line 1164) | def test_multi_index_signatures():
  function test_multi_index_create (line 1189) | def test_multi_index_create():
  function test_multi_index_create_prepend (line 1195) | def test_multi_index_create_prepend():
  function test_multi_index_load_from_directory (line 1202) | def test_multi_index_load_from_directory():
  function test_multi_index_load_from_directory_2 (line 1235) | def test_multi_index_load_from_directory_2():
  function test_multi_index_load_from_directory_3_simple_bad_file (line 1244) | def test_multi_index_load_from_directory_3_simple_bad_file(runtmp):
  function test_multi_index_load_from_directory_3 (line 1255) | def test_multi_index_load_from_directory_3(runtmp):
  function test_multi_index_load_from_directory_3_yield_all_true (line 1275) | def test_multi_index_load_from_directory_3_yield_all_true(runtmp):
  function test_multi_index_load_from_directory_3_yield_all_true_subdir (line 1297) | def test_multi_index_load_from_directory_3_yield_all_true_subdir(runtmp):
  function test_multi_index_load_from_directory_3_sig_gz (line 1324) | def test_multi_index_load_from_directory_3_sig_gz(runtmp):
  function test_multi_index_load_from_directory_3_check_traverse_fn (line 1349) | def test_multi_index_load_from_directory_3_check_traverse_fn(runtmp):
  function test_multi_index_load_from_directory_no_exist (line 1362) | def test_multi_index_load_from_directory_no_exist():
  function test_multi_index_load_from_file_path (line 1369) | def test_multi_index_load_from_file_path():
  function test_multi_index_load_from_file_path_no_exist (line 1378) | def test_multi_index_load_from_file_path_no_exist():
  function test_multi_index_load_from_pathlist_no_exist (line 1385) | def test_multi_index_load_from_pathlist_no_exist():
  function test_multi_index_load_from_pathlist_1 (line 1392) | def test_multi_index_load_from_pathlist_1(runtmp):
  function test_multi_index_load_from_pathlist_2 (line 1412) | def test_multi_index_load_from_pathlist_2(runtmp):
  function test_multi_index_load_from_pathlist_3_zipfile (line 1435) | def test_multi_index_load_from_pathlist_3_zipfile(runtmp):
  class JaccardSearchBestOnly_ButIgnore (line 1456) | class JaccardSearchBestOnly_ButIgnore(JaccardSearch):
    method __init__ (line 1459) | def __init__(self, ignore_list):
    method collect (line 1464) | def collect(self, score, match):
  function test_linear_index_gather_ignore (line 1477) | def test_linear_index_gather_ignore():
  function test_lca_index_gather_ignore (line 1508) | def test_lca_index_gather_ignore():
  function test_sbt_index_gather_ignore (line 1544) | def test_sbt_index_gather_ignore():
  function test_counter_gather_test_consume (line 1581) | def test_counter_gather_test_consume():
  function test_counter_gather_identical_md5sum (line 1682) | def test_counter_gather_identical_md5sum():
  function test_lazy_index_1 (line 1714) | def test_lazy_index_1():
  function test_lazy_index_2 (line 1738) | def test_lazy_index_2():
  function test_lazy_index_3 (line 1760) | def test_lazy_index_3():
  function test_lazy_index_4_bool (line 1778) | def test_lazy_index_4_bool():
  function test_lazy_index_wraps_multi_index_location (line 1792) | def test_lazy_index_wraps_multi_index_location():
  function test_standalone_manifest_signatures (line 1815) | def test_standalone_manifest_signatures(runtmp):
  function test_standalone_manifest_signatures_prefix (line 1839) | def test_standalone_manifest_signatures_prefix(runtmp):
  function test_standalone_manifest_signatures_prefix_fail (line 1863) | def test_standalone_manifest_signatures_prefix_fail(runtmp):
  function test_standalone_manifest_load_from_dir (line 1894) | def test_standalone_manifest_load_from_dir(runtmp):
  function test_standalone_manifest_lazy_load (line 1914) | def test_standalone_manifest_lazy_load(runtmp):
  function test_standalone_manifest_lazy_load_2_prefix (line 1947) | def test_standalone_manifest_lazy_load_2_prefix(runtmp):
  function test_standalone_manifest_search (line 1982) | def test_standalone_manifest_search(runtmp):
  function test_standalone_manifest_prefetch_lazy (line 1994) | def test_standalone_manifest_prefetch_lazy(runtmp):

FILE: tests/test_index_protocol.py
  function _load_three_sigs (line 31) | def _load_three_sigs():
  function build_linear_index (line 44) | def build_linear_index(runtmp):
  function build_lazy_linear_index (line 55) | def build_lazy_linear_index(runtmp):
  function build_sbt_index (line 60) | def build_sbt_index(runtmp):
  function build_sbt_index_save_load (line 73) | def build_sbt_index_save_load(runtmp):
  function build_zipfile_index (line 81) | def build_zipfile_index(runtmp):
  function build_multi_index (line 93) | def build_multi_index(runtmp):
  function build_standalone_manifest_index (line 101) | def build_standalone_manifest_index(runtmp):
  function build_lca_index (line 123) | def build_lca_index(runtmp):
  function build_lca_index_save_load (line 132) | def build_lca_index_save_load(runtmp):
  function build_sqlite_index (line 140) | def build_sqlite_index(runtmp):
  function build_revindex (line 151) | def build_revindex(runtmp):
  function build_disk_revindex (line 162) | def build_disk_revindex(runtmp):
  function build_lca_index_save_load_sql (line 168) | def build_lca_index_save_load_sql(runtmp):
  function index_obj (line 202) | def index_obj(request, runtmp):
  function test_index_search_exact_match (line 214) | def test_index_search_exact_match(index_obj):
  function test_index_search_lower_threshold (line 225) | def test_index_search_lower_threshold(index_obj):
  function test_index_search_lower_threshold_2 (line 239) | def test_index_search_lower_threshold_2(index_obj):
  function test_index_search_higher_threshold_2 (line 253) | def test_index_search_higher_threshold_2(index_obj):
  function test_index_search_containment (line 266) | def test_index_search_containment(index_obj):
  function test_index_signatures (line 280) | def test_index_signatures(index_obj):
  function test_index_signatures_with_location (line 294) | def test_index_signatures_with_location(index_obj):
  function test_index_len (line 308) | def test_index_len(index_obj):
  function test_index_bool (line 313) | def test_index_bool(index_obj):
  function test_index_location (line 318) | def test_index_location(index_obj):
  function test_index_manifest (line 323) | def test_index_manifest(index_obj):
  function test_index_select_basic (line 330) | def test_index_select_basic(index_obj):
  function test_index_select_fail (line 354) | def test_index_select_fail(index_obj):
  function test_index_select_nada (line 388) | def test_index_select_nada(index_obj):
  function test_index_prefetch (line 404) | def test_index_prefetch(index_obj):
  function test_index_best_containment (line 426) | def test_index_best_containment(index_obj):
  function test_index_best_containment_threshold_1 (line 441) | def test_index_best_containment_threshold_1(index_obj):
  function test_best_containment_threshold_5 (line 487) | def test_best_containment_threshold_5(index_obj):
  function create_basic_counter_gather (line 525) | def create_basic_counter_gather(runtmp):
  class CounterGather_LinearIndex (line 530) | class CounterGather_LinearIndex:
    method __init__ (line 536) | def __init__(self, orig_query):
    method add (line 549) | def add(self, ss, *, location=None, require_overlap=True):
    method signatures (line 573) | def signatures(self):
    method downsample (line 577) | def downsample(self, scaled):
    method peek (line 583) | def peek(self, cur_query_mh, *, threshold_bp=0):
    method consume (line 612) | def consume(self, *args, **kwargs):
  class CounterGather_LCA (line 617) | class CounterGather_LCA:
    method __init__ (line 624) | def __init__(self, query):
    method add (line 638) | def add(self, ss, *, location=None, require_overlap=True):
    method signatures (line 655) | def signatures(self):
    method downsample (line 659) | def downsample(self, scaled):
    method peek (line 665) | def peek(self, query_mh, *, threshold_bp=0):
    method consume (line 701) | def consume(self, intersect_mh):
  function build_RevIndex_CounterGather (line 705) | def build_RevIndex_CounterGather(query):
  function counter_gather_constructor (line 721) | def counter_gather_constructor(request):
  function test_counter_get_signatures (line 728) | def test_counter_get_signatures(counter_gather_constructor):
  function _consume_all (line 759) | def _consume_all(query_mh, counter, threshold_bp=0):
  function test_counter_gather_1 (line 784) | def test_counter_gather_1(counter_gather_constructor):
  function test_counter_gather_1_b (line 825) | def test_counter_gather_1_b(counter_gather_constructor):
  function test_counter_gather_1_c_with_threshold (line 869) | def test_counter_gather_1_c_with_threshold(counter_gather_constructor):
  function test_counter_gather_1_d_diff_scaled (line 911) | def test_counter_gather_1_d_diff_scaled(counter_gather_constructor):
  function test_counter_gather_1_d_diff_scaled_query (line 951) | def test_counter_gather_1_d_diff_scaled_query(counter_gather_constructor):
  function test_counter_gather_1_e_abund_query (line 993) | def test_counter_gather_1_e_abund_query(counter_gather_constructor):
  function test_counter_gather_1_f_abund_match (line 1034) | def test_counter_gather_1_f_abund_match(counter_gather_constructor):
  function test_counter_gather_2 (line 1075) | def test_counter_gather_2(counter_gather_constructor):
  function test_counter_gather_exact_match (line 1116) | def test_counter_gather_exact_match(counter_gather_constructor):
  function test_counter_gather_multiple_identical_matches (line 1135) | def test_counter_gather_multiple_identical_matches(counter_gather_constr...
  function test_counter_gather_add_after_peek (line 1164) | def test_counter_gather_add_after_peek(counter_gather_constructor):
  function test_counter_gather_add_after_consume (line 1180) | def test_counter_gather_add_after_consume(counter_gather_constructor):
  function test_counter_gather_consume_empty_intersect (line 1198) | def test_counter_gather_consume_empty_intersect(counter_gather_construct...
  function test_counter_gather_empty_initial_query (line 1212) | def test_counter_gather_empty_initial_query(counter_gather_constructor):
  function test_counter_gather_num_query (line 1228) | def test_counter_gather_num_query(counter_gather_constructor):
  function test_counter_gather_empty_cur_query (line 1238) | def test_counter_gather_empty_cur_query(counter_gather_constructor):
  function test_counter_gather_add_num_matchy (line 1253) | def test_counter_gather_add_num_matchy(counter_gather_constructor):
  function test_counter_gather_bad_cur_query (line 1269) | def test_counter_gather_bad_cur_query(counter_gather_constructor):
  function test_counter_gather_add_no_overlap (line 1285) | def test_counter_gather_add_no_overlap(counter_gather_constructor):
  function test_counter_gather_big_threshold (line 1303) | def test_counter_gather_big_threshold(counter_gather_constructor):
  function test_counter_gather_empty_counter (line 1323) | def test_counter_gather_empty_counter(counter_gather_constructor):

FILE: tests/test_jaccard.py
  function test_jaccard_1 (line 16) | def test_jaccard_1(track_abundance):
  function test_jaccard_2_difflen (line 32) | def test_jaccard_2_difflen(track_abundance):
  function test_common_1 (line 46) | def test_common_1(track_abundance):
  function test_diff_seed (line 59) | def test_diff_seed(track_abundance):
  function test_dna_mh (line 72) | def test_dna_mh(track_abundance):
  function test_protein_mh (line 87) | def test_protein_mh(track_abundance):
  function test_pickle (line 105) | def test_pickle(track_abundance):
  function test_bad_construct_1 (line 130) | def test_bad_construct_1(track_abundance):
  function test_bad_construct_2 (line 138) | def test_bad_construct_2(track_abundance):
  function test_abund_similarity (line 146) | def test_abund_similarity():
  function test_abund_similarity_zero (line 162) | def test_abund_similarity_zero():
  function test_jaccard_on_real_data (line 175) | def test_jaccard_on_real_data():
  function test_scaled_on_real_data (line 205) | def test_scaled_on_real_data():
  function test_scaled_on_real_data_2 (line 236) | def test_scaled_on_real_data_2():
  function test_downsample_scaled_with_num (line 267) | def test_downsample_scaled_with_num():

FILE: tests/test_lca.py
  function test_api_create_search (line 24) | def test_api_create_search():
  function test_api_find_picklist_select (line 45) | def test_api_find_picklist_select():
  function test_api_find_picklist_select_exclude (line 77) | def test_api_find_picklist_select_exclude():
  function test_api_create_insert (line 109) | def test_api_create_insert():
  function test_api_create_insert_bad_ksize (line 136) | def test_api_create_insert_bad_ksize():
  function test_api_create_insert_bad_ident (line 145) | def test_api_create_insert_bad_ident():
  function test_api_create_insert_bad_scaled (line 164) | def test_api_create_insert_bad_scaled():
  function test_api_create_insert_bad_moltype (line 175) | def test_api_create_insert_bad_moltype():
  function test_api_create_insert_ident (line 186) | def test_api_create_insert_ident():
  function test_api_create_insert_two (line 216) | def test_api_create_insert_two():
  function test_api_create_insert_w_lineage (line 257) | def test_api_create_insert_w_lineage():
  function test_api_create_insert_w_bad_lineage (line 295) | def test_api_create_insert_w_bad_lineage():
  function test_api_create_insert_w_bad_lineage_2 (line 306) | def test_api_create_insert_w_bad_lineage_2():
  function test_api_create_gather (line 317) | def test_api_create_gather():
  function test_api_add_genome_lineage (line 331) | def test_api_add_genome_lineage():
  function test_api_insert_update (line 346) | def test_api_insert_update():
  function test_api_insert_retrieve_check_name (line 371) | def test_api_insert_retrieve_check_name():
  function test_api_create_insert_two_then_scale (line 386) | def test_api_create_insert_two_then_scale():
  function test_api_create_insert_two_then_scale_then_add (line 407) | def test_api_create_insert_two_then_scale_then_add():
  function test_api_create_insert_scale_two (line 434) | def test_api_create_insert_scale_two():
  function test_load_single_db (line 456) | def test_load_single_db():
  function test_load_single_db_empty (line 466) | def test_load_single_db_empty(runtmp):
  function test_databases (line 479) | def test_databases():
  function test_databases_load_fail_on_no_JSON (line 491) | def test_databases_load_fail_on_no_JSON():
  function test_databases_load_fail_on_dir (line 501) | def test_databases_load_fail_on_dir():
  function test_databases_load_fail_on_not_exist (line 512) | def test_databases_load_fail_on_not_exist():
  function test_db_repr (line 523) | def test_db_repr():
  function test_db_repr_no_filename (line 530) | def test_db_repr_no_filename():
  function test_lca_index_signatures_method (line 537) | def test_lca_index_signatures_method():
  function test_lca_index_select (line 546) | def test_lca_index_select():
  function test_lca_index_select_picklist (line 571) | def test_lca_index_select_picklist():
  function test_lca_index_find_picklist_check_overlap (line 591) | def test_lca_index_find_picklist_check_overlap():
  function test_lca_index_select_picklist_exclude (line 611) | def test_lca_index_select_picklist_exclude():
  function test_lca_index_select_picklist_twice (line 631) | def test_lca_index_select_picklist_twice():
  function test_search_db_scaled_gt_sig_scaled (line 650) | def test_search_db_scaled_gt_sig_scaled():
  function test_search_db_scaled_lt_sig_scaled (line 662) | def test_search_db_scaled_lt_sig_scaled():
  function test_gather_db_scaled_gt_sig_scaled (line 679) | def test_gather_db_scaled_gt_sig_scaled():
  function test_gather_db_scaled_lt_sig_scaled (line 691) | def test_gather_db_scaled_lt_sig_scaled():
  function test_db_lineage_to_lid (line 704) | def test_db_lineage_to_lid():
  function test_db_lid_to_idx (line 723) | def test_db_lid_to_idx():
  function test_db_idx_to_ident (line 736) | def test_db_idx_to_ident():
  function test_run_sourmash_lca (line 752) | def test_run_sourmash_lca():
  function test_basic_index (line 757) | def test_basic_index(runtmp, lca_db_format):
  function test_basic_index_twice (line 789) | def test_basic_index_twice(runtmp, lca_db_format):
  function test_basic_index_bad_spreadsheet (line 809) | def test_basic_index_bad_spreadsheet(runtmp, lca_db_format):
  function test_basic_index_broken_spreadsheet (line 837) | def test_basic_index_broken_spreadsheet(runtmp, lca_db_format):
  function test_basic_index_too_many_strains_too_few_species (line 853) | def test_basic_index_too_many_strains_too_few_species(runtmp, lca_db_for...
  function test_basic_index_too_few_species (line 878) | def test_basic_index_too_few_species(runtmp, lca_db_format):
  function test_basic_index_require_taxonomy (line 897) | def test_basic_index_require_taxonomy(runtmp, lca_db_format):
  function test_basic_index_column_start (line 923) | def test_basic_index_column_start(runtmp, lca_db_format):
  function test_index_empty_sketch_name (line 951) | def test_index_empty_sketch_name(runtmp, lca_db_format):
  function test_basic_index_and_classify_with_tsv_and_gz (line 982) | def test_basic_index_and_classify_with_tsv_and_gz(runtmp, lca_db_format):
  function test_basic_index_and_classify (line 1034) | def test_basic_index_and_classify(runtmp, lca_db_format):
  function test_basic_index_and_classify_dup_lineage (line 1080) | def test_basic_index_and_classify_dup_lineage(runtmp, lca_db_format):
  function test_index_traverse (line 1130) | def test_index_traverse(runtmp, lca_db_format):
  function test_index_traverse_force (line 1163) | def test_index_traverse_force(runtmp, lca_db_format):
  function test_index_from_file_cmdline_sig (line 1192) | def test_index_from_file_cmdline_sig(runtmp, lca_db_format):
  function test_index_from_file (line 1228) | def test_index_from_file(runtmp, lca_db_format):
  function test_index_fail_on_num (line 1263) | def test_index_fail_on_num(runtmp, lca_db_format):
  function test_index_traverse_real_spreadsheet_no_report (line 1289) | def test_index_traverse_real_spreadsheet_no_report(runtmp, lca_db_format):
  function test_index_traverse_real_spreadsheet_report (line 1323) | def test_index_traverse_real_spreadsheet_report(runtmp, lca_db_format):
  function test_single_classify (line 1370) | def test_single_classify(runtmp):
  function test_single_classify_zip_query (line 1390) | def test_single_classify_zip_query(runtmp):
  function test_single_classify_to_output (line 1415) | def test_single_classify_to_output(runtmp):
  function test_single_classify_to_output_no_name (line 1445) | def test_single_classify_to_output_no_name(runtmp):
  function test_single_classify_empty (line 1482) | def test_single_classify_empty(runtmp):
  function test_single_classify_traverse (line 1498) | def test_single_classify_traverse(runtmp):
  function test_multi_query_classify_traverse (line 1520) | def test_multi_query_classify_traverse(runtmp):
  function test_multi_query_classify_query_from_file (line 1546) | def test_multi_query_classify_query_from_file(c):
  function test_multi_query_classify_query_from_file_and_query (line 1576) | def test_multi_query_classify_query_from_file_and_query(c):
  function test_multi_db_multi_query_classify_traverse (line 1614) | def test_multi_db_multi_query_classify_traverse(runtmp):
  function test_unassigned_internal_index_and_classify (line 1640) | def test_unassigned_internal_index_and_classify(runtmp, lca_db_format):
  function test_unassigned_last_index_and_classify (line 1686) | def test_unassigned_last_index_and_classify(runtmp, lca_db_format):
  function test_index_and_classify_internal_unassigned_multi (line 1732) | def test_index_and_classify_internal_unassigned_multi(runtmp, lca_db_for...
  function test_classify_majority_vote_1 (line 1799) | def test_classify_majority_vote_1(runtmp, lca_db_format):
  function test_classify_majority_vote_2 (line 1861) | def test_classify_majority_vote_2(runtmp, lca_db_format):
  function test_classify_majority_vote_3 (line 1928) | def test_classify_majority_vote_3(runtmp, lca_db_format):
  function test_multi_db_classify (line 1981) | def test_multi_db_classify(runtmp):
  function test_classify_unknown_hashes (line 2005) | def test_classify_unknown_hashes(runtmp, lca_db_format):
  function test_single_summarize (line 2039) | def test_single_summarize(runtmp):
  function test_single_summarize_singleton (line 2057) | def test_single_summarize_singleton(runtmp):
  function test_single_summarize_traverse (line 2087) | def test_single_summarize_traverse(c):
  function test_single_summarize_singleton_traverse (line 2110) | def test_single_summarize_singleton_traverse(c):
  function test_single_summarize_to_output (line 2133) | def test_single_summarize_to_output(runtmp):
  function test_single_summarize_to_output_check_filename (line 2162) | def test_single_summarize_to_output_check_filename(runtmp):
  function test_summarize_unknown_hashes_to_output_check_total_counts (line 2201) | def test_summarize_unknown_hashes_to_output_check_total_counts(runtmp, l...
  function test_single_summarize_scaled (line 2244) | def test_single_summarize_scaled(runtmp):
  function test_single_summarize_scaled_zip_query (line 2262) | def test_single_summarize_scaled_zip_query(runtmp):
  function test_multi_summarize_with_unassigned_singleton (line 2292) | def test_multi_summarize_with_unassigned_singleton(runtmp, lca_db_format):
  function test_multi_summarize_with_zip_unassigned_singleton (line 2379) | def test_multi_summarize_with_zip_unassigned_singleton(runtmp, lca_db_fo...
  function test_summarize_to_root (line 2472) | def test_summarize_to_root(runtmp, lca_db_format):
  function test_summarize_unknown_hashes (line 2511) | def test_summarize_unknown_hashes(runtmp, lca_db_format):
  function test_summarize_to_root_abund (line 2545) | def test_summarize_to_root_abund(runtmp, lca_db_format):
  function test_summarize_unknown_hashes_abund (line 2576) | def test_summarize_unknown_hashes_abund(runtmp, lca_db_format):
  function test_summarize_abund_hmp (line 2611) | def test_summarize_abund_hmp(c):
  function test_summarize_abund_fake_no_abund (line 2624) | def test_summarize_abund_fake_no_abund(c):
  function test_summarize_abund_fake_yes_abund (line 2642) | def test_summarize_abund_fake_yes_abund(c):
  function test_rankinfo_on_multi (line 2653) | def test_rankinfo_on_multi(runtmp):
  function test_rankinfo_on_single (line 2677) | def test_rankinfo_on_single(runtmp):
  function test_rankinfo_no_tax (line 2700) | def test_rankinfo_no_tax(runtmp, lca_db_format):
  function test_rankinfo_with_min (line 2732) | def test_rankinfo_with_min(runtmp):
  function test_rankinfo_with_min_2 (line 2756) | def test_rankinfo_with_min_2(runtmp):
  function test_compare_csv (line 2770) | def test_compare_csv(runtmp):
  function test_compare_csv_real (line 2788) | def test_compare_csv_real(runtmp):
  function test_incompat_lca_db_ksize_2_fail (line 2824) | def test_incompat_lca_db_ksize_2_fail(runtmp, lca_db_format):
  function test_incompat_lca_db_ksize_2_nofail (line 2872) | def test_incompat_lca_db_ksize_2_nofail(runtmp, lca_db_format):
  function test_lca_index_empty (line 2919) | def test_lca_index_empty(runtmp, lca_db_format):
  function test_lca_gather_threshold_1 (line 2961) | def test_lca_gather_threshold_1():
  function test_lca_gather_threshold_5 (line 3021) | def test_lca_gather_threshold_5():
  function test_gather_multiple_return (line 3068) | def test_gather_multiple_return():
  function test_lca_db_protein_build (line 3091) | def test_lca_db_protein_build():
  function test_lca_db_protein_save_load (line 3122) | def test_lca_db_protein_save_load(c):
  function test_lca_db_protein_command_index (line 3161) | def test_lca_db_protein_command_index(runtmp, lca_db_format):
  function test_lca_db_protein_command_search (line 3217) | def test_lca_db_protein_command_search(c):
  function test_lca_db_hp_build (line 3233) | def test_lca_db_hp_build():
  function test_lca_db_hp_save_load (line 3264) | def test_lca_db_hp_save_load(c):
  function test_lca_db_hp_command_index (line 3301) | def test_lca_db_hp_command_index(runtmp, lca_db_format):
  function test_lca_db_hp_command_search (line 3357) | def test_lca_db_hp_command_search(c):
  function test_lca_db_dayhoff_build (line 3373) | def test_lca_db_dayhoff_build():
  function test_lca_db_dayhoff_save_load (line 3404) | def test_lca_db_dayhoff_save_load(c):
  function test_lca_db_dayhoff_command_index (line 3441) | def test_lca_db_dayhoff_command_index(runtmp, lca_db_format):
  function test_lca_db_dayhoff_command_search (line 3497) | def test_lca_db_dayhoff_command_search(c):
  function test_lca_index_with_picklist (line 3513) | def test_lca_index_with_picklist(runtmp, lca_db_format):
  function test_lca_index_with_picklist_exclude (line 3554) | def test_lca_index_with_picklist_exclude(runtmp, lca_db_format):
  function test_lca_index_select_with_picklist (line 3591) | def test_lca_index_select_with_picklist(runtmp, lca_db_format):
  function test_lca_index_select_with_picklist_exclude (line 3625) | def test_lca_index_select_with_picklist_exclude(runtmp, lca_db_format):
  function test_lca_jaccard_ordering (line 3658) | def test_lca_jaccard_ordering():
  function test_lca_db_protein_save_twice (line 3704) | def test_lca_db_protein_save_twice(runtmp, lca_db_format):

FILE: tests/test_lca_db_protocol.py
  function build_inmem_lca_db (line 15) | def build_inmem_lca_db(runtmp):
  function build_json_lca_db (line 42) | def build_json_lca_db(runtmp):
  function build_sql_lca_db (line 55) | def build_sql_lca_db(runtmp):
  function lca_db_obj (line 69) | def lca_db_obj(request, runtmp):
  function test_get_lineage_assignments (line 75) | def test_get_lineage_assignments(lca_db_obj):
  function test_hashvals (line 98) | def test_hashvals(lca_db_obj):
  function test_get_identifiers_for_hashval (line 104) | def test_get_identifiers_for_hashval(lca_db_obj):
  function test_get_identifiers_for_hashval_2 (line 114) | def test_get_identifiers_for_hashval_2(lca_db_obj):
  function test_downsample_scaled (line 131) | def test_downsample_scaled(lca_db_obj):
  function test_downsample_scaled_fail (line 138) | def test_downsample_scaled_fail(lca_db_obj):

FILE: tests/test_lca_functions.py
  class FakeLCA_Database (line 22) | class FakeLCA_Database:
    method __init__ (line 23) | def __init__(self):
    method _set_lineage_assignment (line 26) | def _set_lineage_assignment(self, hashval, assignment):
    method get_lineage_assignments (line 29) | def get_lineage_assignments(self, hashval):
  function test_taxlist_1 (line 36) | def test_taxlist_1():
  function test_taxlist_2 (line 49) | def test_taxlist_2():
  function test_zip_lineage_1 (line 61) | def test_zip_lineage_1():
  function test_zip_lineage_2 (line 66) | def test_zip_lineage_2():
  function test_zip_lineage_3 (line 71) | def test_zip_lineage_3():
  function test_zip_lineage_3_truncate (line 80) | def test_zip_lineage_3_truncate():
  function test_zip_lineage_4 (line 89) | def test_zip_lineage_4():
  function test_display_lineage_1 (line 97) | def test_display_lineage_1():
  function test_display_lineage_2 (line 102) | def test_display_lineage_2():
  function test_build_tree (line 111) | def test_build_tree():
  function test_build_tree_2 (line 116) | def test_build_tree_2():
  function test_build_tree_3 (line 132) | def test_build_tree_3():  # empty 'rank2' name
  function test_build_tree_4 (line 137) | def test_build_tree_4():
  function test_build_tree_5 (line 159) | def test_build_tree_5():
  function test_find_lca (line 164) | def test_find_lca():
  function test_find_lca_2 (line 177) | def test_find_lca_2():
  function test_find_lca_3 (line 189) | def test_find_lca_3():
  function test_gather_assignments_1 (line 198) | def test_gather_assignments_1():
  function test_gather_assignments_2 (line 212) | def test_gather_assignments_2():
  function test_gather_assignments_3 (line 227) | def test_gather_assignments_3():
  function test_count_lca_for_assignments_1 (line 246) | def test_count_lca_for_assignments_1():
  function test_count_lca_for_assignments_2 (line 262) | def test_count_lca_for_assignments_2():
  function test_count_lca_for_assignments_3 (line 283) | def test_count_lca_for_assignments_3():
  function test_count_lca_for_assignments_abund_1 (line 307) | def test_count_lca_for_assignments_abund_1():
  function test_count_lca_for_assignments_abund_2 (line 326) | def test_count_lca_for_assignments_abund_2():
  function test_count_lca_for_assignments_abund_3 (line 350) | def test_count_lca_for_assignments_abund_3():
  function test_count_lca_for_assignments_abund_4 (line 378) | def test_count_lca_for_assignments_abund_4():
  function test_count_lca_for_assignments_abund_5 (line 411) | def test_count_lca_for_assignments_abund_5():
  function test_is_lineage_match_1 (line 436) | def test_is_lineage_match_1():
  function test_is_lineage_match_2 (line 450) | def test_is_lineage_match_2():
  function test_is_lineage_match_3 (line 464) | def test_is_lineage_match_3():
  function test_pop_to_rank_1 (line 478) | def test_pop_to_rank_1():
  function test_pop_to_rank_2 (line 488) | def test_pop_to_rank_2():

FILE: tests/test_manifest.py
  function test_generate_manifest (line 14) | def test_generate_manifest():
  function test_manifest_operations (line 40) | def test_manifest_operations():
  function test_manifest_operations_fail (line 65) | def test_manifest_operations_fail():
  function test_manifest_to_picklist (line 84) | def test_manifest_to_picklist():
  function test_manifest_compare (line 105) | def test_manifest_compare():
  function test_save_load_manifest (line 134) | def test_save_load_manifest():
  function test_manifest_to_picklist_bug (line 189) | def test_manifest_to_picklist_bug(runtmp):
  function test_generate_manifest_iterate_once (line 220) | def test_generate_manifest_iterate_once():

FILE: tests/test_manifest_protocol.py
  function build_simple_manifest (line 15) | def build_simple_manifest(runtmp):
  function build_sqlite_manifest (line 24) | def build_sqlite_manifest(runtmp):
  function save_load_manifest (line 35) | def save_load_manifest(runtmp):
  function manifest_obj (line 49) | def manifest_obj(request, runtmp):
  function test_manifest_len (line 60) | def test_manifest_len(manifest_obj):
  function test_manifest_rows (line 65) | def test_manifest_rows(manifest_obj):
  function test_manifest_bool (line 76) | def test_manifest_bool(manifest_obj):
  function test_make_manifest_row (line 81) | def test_make_manifest_row(manifest_obj):
  function test_manifest_create_manifest (line 102) | def test_manifest_create_manifest(manifest_obj):
  function test_manifest_select_to_manifest (line 121) | def test_manifest_select_to_manifest(manifest_obj):
  function test_manifest_locations (line 127) | def test_manifest_locations(manifest_obj):
  function test_manifest___contains__ (line 144) | def test_manifest___contains__(manifest_obj):
  function test_manifest_to_picklist (line 158) | def test_manifest_to_picklist(manifest_obj):
  function test_manifest_filter_rows (line 166) | def test_manifest_filter_rows(manifest_obj):
  function test_manifest_filter_cols (line 178) | def test_manifest_filter_cols(manifest_obj):
  function test_manifest_iadd (line 190) | def test_manifest_iadd(manifest_obj):
  function test_manifest_add (line 205) | def test_manifest_add(manifest_obj):

FILE: tests/test_minhash.py
  function _kmers_from_all_coding_frames (line 75) | def _kmers_from_all_coding_frames(sequence, ksize):
  function _hash_fwd_only (line 95) | def _hash_fwd_only(mh_translate, seq):
  function test_basic_dna (line 102) | def test_basic_dna(track_abundance):
  function test_div_zero (line 119) | def test_div_zero(track_abundance):
  function test_div_zero_contained (line 129) | def test_div_zero_contained(track_abundance):
  function test_contained_requires_scaled (line 139) | def test_contained_requires_scaled(track_abundance):
  function test_contained_requires_scaled_2 (line 154) | def test_contained_requires_scaled_2(track_abundance):
  function test_contained_requires_scaled_3 (line 169) | def test_contained_requires_scaled_3(track_abundance):
  function test_bytes_dna (line 184) | def test_bytes_dna(track_abundance):
  function test_add_long_seqs_force (line 201) | def test_add_long_seqs_force():
  function test_seq_to_hashes (line 210) | def test_seq_to_hashes(track_abundance):
  function test_seq_to_hashes_protein_1 (line 225) | def test_seq_to_hashes_protein_1(track_abundance, dayhoff):
  function test_seq_to_hashes_protein_2 (line 246) | def test_seq_to_hashes_protein_2(track_abundance):
  function test_seq_to_hashes_translated (line 256) | def test_seq_to_hashes_translated(track_abundance):
  function test_seq_to_hashes_bad_kmers_as_zeroes_1 (line 269) | def test_seq_to_hashes_bad_kmers_as_zeroes_1():
  function test_seq_to_hashes_bad_kmers_as_zeroes_2 (line 279) | def test_seq_to_hashes_bad_kmers_as_zeroes_2():
  function test_seq_to_hashes_translated_short (line 287) | def test_seq_to_hashes_translated_short():
  function test_bytes_protein_dayhoff (line 294) | def test_bytes_protein_dayhoff(track_abundance, dayhoff):
  function test_protein_dayhoff (line 317) | def test_protein_dayhoff(track_abundance, dayhoff):
  function test_bytes_protein_hp (line 332) | def test_bytes_protein_hp(track_abundance, hp):
  function test_protein_hp (line 352) | def test_protein_hp(track_abundance, hp):
  function test_module_translate_codon (line 365) | def test_module_translate_codon(track_abundance):
  function test_dayhoff (line 376) | def test_dayhoff(track_abundance):
  function test_dayhoff_2 (line 394) | def test_dayhoff_2(track_abundance):
  function test_hp (line 419) | def test_hp(track_abundance):
  function test_hp_2 (line 437) | def test_hp_2(track_abundance):
  function test_protein_short (line 460) | def test_protein_short(track_abundance):
  function test_size_limit (line 468) | def test_size_limit(track_abundance):
  function test_scaled (line 479) | def test_scaled(track_abundance):
  function test_no_scaled (line 497) | def test_no_scaled(track_abundance):
  function test_max_hash_conversion (line 503) | def test_max_hash_conversion():
  function test_max_hash_and_scaled_zero (line 510) | def test_max_hash_and_scaled_zero():
  function test_max_hash_and_scaled_error (line 517) | def test_max_hash_and_scaled_error(track_abundance):
  function test_max_hash_cannot_limit (line 523) | def test_max_hash_cannot_limit(track_abundance):
  function test_no_downsample_scaled_if_n (line 531) | def test_no_downsample_scaled_if_n(track_abundance):
  function test_scaled_num_both (line 540) | def test_scaled_num_both(track_abundance):
  function test_mh_jaccard_similarity (line 546) | def test_mh_jaccard_similarity():
  function test_mh_similarity_downsample_jaccard_value (line 556) | def test_mh_similarity_downsample_jaccard_value():
  function test_mh_angular_similarity (line 571) | def test_mh_angular_similarity():
  function test_mh_angular_similarity_2 (line 588) | def test_mh_angular_similarity_2():
  function test_mh_similarity_downsample_angular_value (line 601) | def test_mh_similarity_downsample_angular_value():
  function test_mh_angular_similarity_fail (line 621) | def test_mh_angular_similarity_fail():
  function test_mh_similarity_downsample_true (line 652) | def test_mh_similarity_downsample_true(track_abundance):
  function test_mh_similarity_downsample_errors (line 680) | def test_mh_similarity_downsample_errors(track_abundance):
  function test_basic_dna_bad (line 715) | def test_basic_dna_bad(track_abundance):
  function test_basic_dna_bad_2 (line 726) | def test_basic_dna_bad_2(track_abundance):
  function test_basic_dna_bad_force (line 734) | def test_basic_dna_bad_force(track_abundance):
  function test_basic_dna_bad_force_2 (line 746) | def test_basic_dna_bad_force_2(track_abundance):
  function test_consume_lowercase (line 759) | def test_consume_lowercase(track_abundance):
  function test_similarity_1 (line 772) | def test_similarity_1(track_abundance):
  function test_copy (line 801) | def test_copy(track_abundance):
  function test_frozen_copy (line 810) | def test_frozen_copy(track_abundance):
  function test_mh_copy (line 819) | def test_mh_copy(track_abundance):
  function test_mh_len (line 827) | def test_mh_len(track_abundance):
  function test_mh_len_2 (line 835) | def test_mh_len_2(track_abundance):
  function test_mh_unsigned_long_long (line 843) | def test_mh_unsigned_long_long(track_abundance):
  function test_mh_count_common (line 849) | def test_mh_count_common(track_abundance):
  function test_mh_count_common_diff_protein (line 862) | def test_mh_count_common_diff_protein(track_abundance):
  function test_mh_count_common_diff_maxhash (line 870) | def test_mh_count_common_diff_maxhash(track_abundance):
  function test_mh_count_common_diff_seed (line 890) | def test_mh_count_common_diff_seed(track_abundance):
  function test_mh_count_common_diff_ksize (line 898) | def test_mh_count_common_diff_ksize(track_abundance):
  function test_mh_count_common_notmh (line 906) | def test_mh_count_common_notmh(track_abundance):
  function test_mh_downsample_num_error (line 914) | def test_mh_downsample_num_error(track_abundance):
  function test_mh_jaccard_asymmetric_num (line 920) | def test_mh_jaccard_asymmetric_num(track_abundance):
  function test_mh_merge_typeerror (line 943) | def test_mh_merge_typeerror(track_abundance):
  function test_mh_merge (line 949) | def test_mh_merge(track_abundance):
  function test_mh_merge_empty_num (line 972) | def test_mh_merge_empty_num(track_abundance):
  function test_mh_merge_empty_scaled (line 994) | def test_mh_merge_empty_scaled(track_abundance):
  function test_mh_merge_check_length (line 1016) | def test_mh_merge_check_length(track_abundance):
  function test_mh_merge_check_length2 (line 1030) | def test_mh_merge_check_length2(track_abundance):
  function test_mh_asymmetric_merge (line 1047) | def test_mh_asymmetric_merge(track_abundance):
  function test_mh_inplace_concat_asymmetric (line 1086) | def test_mh_inplace_concat_asymmetric(track_abundance):
  function test_mh_inplace_concat (line 1126) | def test_mh_inplace_concat(track_abundance):
  function test_mh_merge_diff_protein (line 1147) | def test_mh_merge_diff_protein(track_abundance):
  function test_mh_merge_diff_ksize (line 1155) | def test_mh_merge_diff_ksize(track_abundance):
  function test_mh_similarity_diff_protein (line 1163) | def test_mh_similarity_diff_protein(track_abundance):
  function test_mh_similarity_diff_ksize (line 1171) | def test_mh_similarity_diff_ksize(track_abundance):
  function test_mh_similarity_diff_seed (line 1179) | def test_mh_similarity_diff_seed(track_abundance):
  function test_mh_compare_diff_max_hash (line 1187) | def test_mh_compare_diff_max_hash(track_abundance):
  function test_mh_concat_diff_protein (line 1196) | def test_mh_concat_diff_protein(track_abundance):
  function test_mh_concat_diff_ksize (line 1204) | def test_mh_concat_diff_ksize(track_abundance):
  function test_mh_concat_diff_max_hash (line 1212) | def test_mh_concat_diff_max_hash(track_abundance):
  function test_mh_concat_diff_seed (line 1220) | def test_mh_concat_diff_seed(track_abundance):
  function test_short_sequence (line 1228) | def test_short_sequence(track_abundance):
  function test_bytes_murmur (line 1235) | def test_bytes_murmur():
  function test_murmur (line 1246) | def test_murmur():
  function test_abundance_simple (line 1263) | def test_abundance_simple():
  function test_add_hash_with_abundance (line 1275) | def test_add_hash_with_abundance():
  function test_add_hash_with_abundance_2 (line 1288) | def test_add_hash_with_abundance_2():
  function test_clear (line 1297) | def test_clear():
  function test_clear_2 (line 1307) | def test_clear_2():
  function test_abundance_simple_2 (line 1317) | def test_abundance_simple_2():
  function test_abundance_count_common (line 1333) | def test_abundance_count_common():
  function test_abundance_similarity (line 1350) | def test_abundance_similarity():
  function test_set_abundance (line 1379) | def test_set_abundance():
  function test_set_abundance_2 (line 1388) | def test_set_abundance_2():
  function test_set_abundance_clear (line 1400) | def test_set_abundance_clear():
  function test_set_abundance_clear_2 (line 1411) | def test_set_abundance_clear_2():
  function test_set_abundance_clear_3 (line 1422) | def test_set_abundance_clear_3():
  function test_set_abundance_clear_4 (line 1432) | def test_set_abundance_clear_4():
  function test_clear_abundance_on_zero (line 1444) | def test_clear_abundance_on_zero():
  function test_reset_abundance_initialized (line 1462) | def test_reset_abundance_initialized():
  function test_set_abundance_initialized (line 1473) | def test_set_abundance_initialized():
  function test_set_abundance_num (line 1485) | def test_set_abundance_num():
  function test_mh_copy_and_clear (line 1493) | def test_mh_copy_and_clear(track_abundance):
  function test_mh_copy_and_clear_with_max_hash (line 1511) | def test_mh_copy_and_clear_with_max_hash(track_abundance):
  function test_scaled_property (line 1529) | def test_scaled_property(track_abundance):
  function test_pickle_protein (line 1535) | def test_pickle_protein(track_abundance):
  function test_pickle_dayhoff (line 1561) | def test_pickle_dayhoff(track_abundance):
  function test_pickle_hp (line 1587) | def test_pickle_hp(track_abundance):
  function test_pickle_max_hash (line 1613) | def test_pickle_max_hash(track_abundance):
  function test_pickle_scaled (line 1632) | def test_pickle_scaled(track_abundance):
  function test_minhash_abund_add (line 1651) | def test_minhash_abund_add():
  function test_minhash_abund_capacity_increase (line 1666) | def test_minhash_abund_capacity_increase():
  function test_minhash_abund_merge_flat (line 1679) | def test_minhash_abund_merge_flat():
  function test_minhash_abund_merge_flat_2 (line 1698) | def test_minhash_abund_merge_flat_2():
  function test_distance_matrix (line 1714) | def test_distance_matrix(track_abundance):
  function test_remove_many (line 1740) | def test_remove_many(track_abundance):
  function test_remove_minhash (line 1760) | def test_remove_minhash(track_abundance):
  function test_add_many (line 1783) | def test_add_many(track_abundance):
  function test_set_abundances_huge (line 1801) | def test_set_abundances_huge():
  function test_try_change_hashes (line 1811) | def test_try_change_hashes(track_abundance):
  function test_flatten (line 1822) | def test_flatten():
  function test_inflate (line 1849) | def test_inflate():
  function test_inflate_error (line 1884) | def test_inflate_error():
  function test_inflate_not_a_subset (line 1921) | def test_inflate_not_a_subset():
  function test_add_kmer (line 1954) | def test_add_kmer(track_abundance):
  function test_add_kmer_too_long (line 1972) | def test_add_kmer_too_long(track_abundance):
  function test_get_mins_deprecated (line 1980) | def test_get_mins_deprecated(track_abundance):
  function test_get_hashes_deprecated (line 1998) | def test_get_hashes_deprecated(track_abundance):
  function test_downsample_num (line 2011) | def test_downsample_num(track_abundance):
  function test_downsample_scaled (line 2029) | def test_downsample_scaled(track_abundance):
  function test_is_molecule_type_1 (line 2053) | def test_is_molecule_type_1(track_abundance):
  function test_is_molecule_type_2 (line 2062) | def test_is_molecule_type_2(track_abundance):
  function test_is_molecule_type_3 (line 2071) | def test_is_molecule_type_3(track_abundance):
  function test_is_molecule_type_4 (line 2080) | def test_is_molecule_type_4(track_abundance):
  function test_addition_num_incompatible (line 2089) | def test_addition_num_incompatible():
  function test_addition_abund (line 2102) | def test_addition_abund():
  function test_addition_noabund (line 2116) | def test_addition_noabund():
  function test_iaddition_abund (line 2129) | def test_iaddition_abund():
  function test_iaddition_noabund (line 2146) | def test_iaddition_noabund():
  function test_intersection_1_num (line 2159) | def test_intersection_1_num():
  function test_and_operator (line 2174) | def test_and_operator():
  function test_intersection_2_scaled (line 2195) | def test_intersection_2_scaled():
  function test_intersection_3_abundance_error (line 2210) | def test_intersection_3_abundance_error():
  function test_intersection_4_incompatible_ksize (line 2221) | def test_intersection_4_incompatible_ksize():
  function test_intersection_5_incompatible (line 2232) | def test_intersection_5_incompatible():
  function test_intersection_6_full_num (line 2242) | def test_intersection_6_full_num():
  function test_intersection_7_full_scaled (line 2270) | def test_intersection_7_full_scaled():
  function test_intersection_and_union_8_incompatible_ksize (line 2298) | def test_intersection_and_union_8_incompatible_ksize():
  function test_merge_abund (line 2308) | def test_merge_abund():
  function test_merge_noabund (line 2329) | def test_merge_noabund():
  function test_merge_full_num (line 2344) | def test_merge_full_num():
  function test_merge_scaled (line 2372) | def test_merge_scaled():
  function test_add_is_symmetric (line 2397) | def test_add_is_symmetric():
  function test_or_equals_add (line 2411) | def test_or_equals_add():
  function test_max_containment (line 2424) | def test_max_containment():
  function test_max_containment_empty (line 2437) | def test_max_containment_empty():
  function test_max_containment_equal (line 2449) | def test_max_containment_equal():
  function test_avg_containment (line 2462) | def test_avg_containment():
  function test_avg_containment_empty (line 2475) | def test_avg_containment_empty():
  function test_avg_containment_equal (line 2487) | def test_avg_containment_equal():
  function test_frozen_and_mutable_1 (line 2500) | def test_frozen_and_mutable_1(track_abundance):
  function test_frozen_and_mutable_2 (line 2509) | def test_frozen_and_mutable_2(track_abundance):
  function test_frozen_and_mutable_3 (line 2520) | def test_frozen_and_mutable_3(track_abundance):
  function test_dna_kmers (line 2536) | def test_dna_kmers():
  function test_dna_kmers_2 (line 2570) | def test_dna_kmers_2():
  function test_dna_kmers_3_bad_dna (line 2586) | def test_dna_kmers_3_bad_dna():
  function test_dna_kmers_4_bad_dna (line 2597) | def test_dna_kmers_4_bad_dna():
  function test_protein_kmers (line 2622) | def test_protein_kmers():
  function test_protein_kmers_2 (line 2656) | def test_protein_kmers_2():
  function test_dayhoff_kmers (line 2672) | def test_dayhoff_kmers():
  function test_dayhoff_kmers_2 (line 2706) | def test_dayhoff_kmers_2():
  function test_hp_kmers (line 2722) | def test_hp_kmers():
  function test_hp_kmers_2 (line 2756) | def test_hp_kmers_2():
  function test_translate_protein_hashes (line 2772) | def test_translate_protein_hashes():
  function test_translate_protein_hashes_2 (line 2787) | def test_translate_protein_hashes_2():
  function test_translate_hp_hashes (line 2802) | def test_translate_hp_hashes():
  function test_translate_hp_hashes_2 (line 2817) | def test_translate_hp_hashes_2():
  function test_translate_dayhoff_hashes (line 2832) | def test_translate_dayhoff_hashes():
  function test_translate_dayhoff_hashes_2 (line 2847) | def test_translate_dayhoff_hashes_2():
  function test_containment (line 2862) | def test_containment(track_abundance):
  function test_sum_abundances (line 2877) | def test_sum_abundances(track_abundance):
  function test_mean_abundance (line 2896) | def test_mean_abundance(track_abundance):
  function test_median_abundance (line 2915) | def test_median_abundance(track_abundance):
  function test_std_abundance (line 2934) | def test_std_abundance(track_abundance):
  function test_unique_dataset_hashes (line 2953) | def test_unique_dataset_hashes(track_abundance):
  function test_containment_ANI (line 2968) | def test_containment_ANI():
  function test_containment_ANI_precalc_containment (line 3004) | def test_containment_ANI_precalc_containment():
  function test_avg_containment_ani (line 3027) | def test_avg_containment_ani():
  function test_containment_ANI_downsample (line 3042) | def test_containment_ANI_downsample():
  function test_jaccard_ANI (line 3078) | def test_jaccard_ANI():
  function test_jaccard_ANI_untrustworthy (line 3097) | def test_jaccard_ANI_untrustworthy():
  function test_jaccard_ANI_precalc_jaccard (line 3115) | def test_jaccard_ANI_precalc_jaccard():
  function test_jaccard_ANI_downsample (line 3133) | def test_jaccard_ANI_downsample():
  function test_containment_ani_ci_tiny_testdata (line 3155) | def test_containment_ani_ci_tiny_testdata():
  function test_containment_num_fail (line 3176) | def test_containment_num_fail():
  function test_ANI_num_fail (line 3194) | def test_ANI_num_fail():
  function test_minhash_set_size_estimate_is_accurate (line 3218) | def test_minhash_set_size_estimate_is_accurate():
  function test_minhash_ani_inaccurate_size_est (line 3260) | def test_minhash_ani_inaccurate_size_est():
  function test_size_num_fail (line 3287) | def test_size_num_fail():

FILE: tests/test_moltypes.py
  function moltype (line 21) | def moltype(request):
  function moltype2 (line 28) | def moltype2(request):
  function moltype_sketches (line 35) | def moltype_sketches(runtmp_session, moltype):
  function test_factory_moltype (line 100) | def test_factory_moltype(moltype):
  function test_factory_moltype_equal (line 109) | def test_factory_moltype_equal(moltype):
  function test_factory_moltype_ne (line 127) | def test_factory_moltype_ne(moltype, moltype2):
  function test_manifest_row_to_compute_parameters (line 147) | def test_manifest_row_to_compute_parameters(moltype, moltype2):
  function test_api_load (line 168) | def test_api_load(moltype_sketches):
  function test_api_overlap (line 179) | def test_api_overlap(moltype_sketches):
  function test_sig_cat (line 195) | def test_sig_cat(moltype_sketches):
  function test_sig_describe (line 208) | def test_sig_describe(moltype_sketches):
  function test_search (line 216) | def test_search(moltype_sketches):
  function test_compare (line 233) | def test_compare(moltype_sketches):
  function test_index (line 250) | def test_index(moltype_sketches, disk_index_type):
  function test_gather (line 264) | def test_gather(moltype_sketches):
  function test_prefetch (line 281) | def test_prefetch(moltype_sketches):
  function test_sig_manifest (line 298) | def test_sig_manifest(moltype_sketches):

FILE: tests/test_nodegraph.py
  function test_nodegraph_to_khmer_basic (line 14) | def test_nodegraph_to_khmer_basic():
  function test_nodegraph_khmer_compare (line 25) | def test_nodegraph_khmer_compare():
  function test_nodegraph_same_file (line 49) | def test_nodegraph_same_file():
  function test_nodegraph_expected_collisions (line 95) | def test_nodegraph_expected_collisions():
  function test_nodegraph_expected_collisions_error (line 103) | def test_nodegraph_expected_collisions_error():

FILE: tests/test_np_utils.py
  function test_memmap (line 7) | def test_memmap():

FILE: tests/test_picklist.py
  function test_load_empty_picklist_fail (line 17) | def test_load_empty_picklist_fail():
  function test_load_empty_picklist_allow (line 25) | def test_load_empty_picklist_allow():
  function test_dup_md5_picked (line 32) | def test_dup_md5_picked(runtmp):
  function test_dup_md5_picked_mf_to_picklist (line 69) | def test_dup_md5_picked_mf_to_picklist(runtmp):
  function test_dup_md5_picked_mf_to_picklist_sqlite (line 101) | def test_dup_md5_picked_mf_to_picklist_sqlite(runtmp):

FILE: tests/test_plugin_framework.py
  class FakeEntryPoint (line 23) | class FakeEntryPoint:
    method __init__ (line 33) | def __init__(self, name, load_obj, *, error_on_import=None):
    method load (line 38) | def load(self):
  class Test_EntryPointBasics_LoadFrom (line 49) | class Test_EntryPointBasics_LoadFrom:
    method get_some_sigs (line 50) | def get_some_sigs(self, location, *args, **kwargs):
    method setup_method (line 65) | def setup_method(self):
    method teardown_method (line 74) | def teardown_method(self):
    method test_load_1 (line 77) | def test_load_1(self):
    method test_load_2 (line 81) | def test_load_2(self, runtmp):
  class Test_EntryPoint_LoadFrom_Priority (line 90) | class Test_EntryPoint_LoadFrom_Priority:
    method get_some_sigs (line 91) | def get_some_sigs(self, location, *args, **kwargs):
    method set_called_flag_1 (line 106) | def set_called_flag_1(self, location, *args, **kwargs):
    method set_called_flag_2 (line 114) | def set_called_flag_2(self, location, *args, **kwargs):
    method set_called_flag_3 (line 123) | def set_called_flag_3(self, location, *args, **kwargs):
    method setup_method (line 132) | def setup_method(self):
    method teardown_method (line 144) | def teardown_method(self):
    method test_load_1 (line 147) | def test_load_1(self):
    method test_load_2 (line 155) | def test_load_2(self, runtmp):
  class FakeSaveClass (line 173) | class FakeSaveClass(Base_SaveSignaturesToLocation):
    method __init__ (line 180) | def __init__(self, location):
    method matches (line 185) | def matches(cls, location):
    method add (line 189) | def add(self, ss):
  class FakeSaveClass_HighPriority (line 194) | class FakeSaveClass_HighPriority(FakeSaveClass):
  class Test_EntryPointBasics_SaveTo (line 198) | class Test_EntryPointBasics_SaveTo:
    method setup_method (line 200) | def setup_method(self):
    method teardown_method (line 209) | def teardown_method(self):
    method test_save_1 (line 212) | def test_save_1(self):
    method test_save_2 (line 217) | def test_save_2(self, runtmp):
  class Test_EntryPointPriority_SaveTo (line 246) | class Test_EntryPointPriority_SaveTo:
    method setup_method (line 249) | def setup_method(self):
    method teardown_method (line 256) | def teardown_method(self):
    method test_save_1 (line 259) | def test_save_1(self):
    method test_save_2 (line 264) | def test_save_2(self, runtmp):
  class FakeCommandClass (line 299) | class FakeCommandClass(plugins.CommandLinePlugin):
    method __init__ (line 307) | def __init__(self, parser):
    method main (line 313) | def main(self, args):
  class Test_EntryPointBasics_Command (line 323) | class Test_EntryPointBasics_Command:
    method setup_method (line 325) | def setup_method(self):
    method teardown_method (line 331) | def teardown_method(self):
    method test_empty (line 334) | def test_empty(self, runtmp):
    method test_cmd_0 (line 346) | def test_cmd_0(self, runtmp):
    method test_cmd_1 (line 358) | def test_cmd_1(self):
    method test_cmd_2 (line 368) | def test_cmd_2(self):
    method test_cmd_3 (line 374) | def test_cmd_3(self, runtmp):
    method test_cmd_4 (line 387) | def test_cmd_4(self, runtmp):
    method test_cmd_5 (line 399) | def test_cmd_5(self, runtmp):
  class FakeCommandClass_Second (line 415) | class FakeCommandClass_Second(plugins.CommandLinePlugin):
    method __init__ (line 423) | def __init__(self, parser):
    method main (line 429) | def main(self, args):
  class FakeCommandClass_Broken_1 (line 439) | class FakeCommandClass_Broken_1:
    method __init__ (line 446) | def __init__(self, parser):
    method main (line 449) | def main(self, args):
  class FakeCommandClass_Broken_2 (line 453) | class FakeCommandClass_Broken_2:
    method __init__ (line 461) | def __init__(self, parser):
    method main (line 464) | def main(self, args):
  class Test_EntryPointBasics_TwoCommands (line 468) | class Test_EntryPointBasics_TwoCommands:
    method setup_method (line 470) | def setup_method(self):
    method teardown_method (line 484) | def teardown_method(self):
    method test_cmd_0 (line 487) | def test_cmd_0(self, runtmp):
    method test_cmd_1 (line 502) | def test_cmd_1(self, runtmp):
    method test_cmd_2 (line 516) | def test_cmd_2(self, runtmp):
    method test_sourmash_info (line 530) | def test_sourmash_info(self, runtmp):
  function test_cli_scripts_getattr_fail (line 549) | def test_cli_scripts_getattr_fail():
  function test_cli_scripts_getattr_succ (line 557) | def test_cli_scripts_getattr_succ():

FILE: tests/test_prefetch.py
  function approx_eq (line 24) | def approx_eq(val1, val2):
  function test_prefetch_basic (line 30) | def test_prefetch_basic(runtmp, linear_gather):
  function test_prefetch_select_query_ksize (line 71) | def test_prefetch_select_query_ksize(runtmp, linear_gather):
  function test_prefetch_subject_scaled_is_larger (line 89) | def test_prefetch_subject_scaled_is_larger(runtmp, linear_gather):
  function test_prefetch_subject_scaled_is_larger_outsigs (line 129) | def test_prefetch_subject_scaled_is_larger_outsigs(runtmp, linear_gather):
  function test_prefetch_query_abund (line 178) | def test_prefetch_query_abund(runtmp, linear_gather):
  function test_prefetch_subj_abund (line 215) | def test_prefetch_subj_abund(runtmp, linear_gather):
  function test_prefetch_csv_out (line 252) | def test_prefetch_csv_out(runtmp, linear_gather):
  function test_prefetch_csv_gz_out (line 280) | def test_prefetch_csv_gz_out(runtmp, linear_gather):
  function test_prefetch_matches (line 308) | def test_prefetch_matches(runtmp, linear_gather):
  function test_prefetch_matches_to_dir (line 345) | def test_prefetch_matches_to_dir(runtmp, linear_gather):
  function test_prefetch_matches_to_sig_gz (line 385) | def test_prefetch_matches_to_sig_gz(runtmp, linear_gather):
  function test_prefetch_matches_to_zip (line 431) | def test_prefetch_matches_to_zip(runtmp, linear_gather):
  function test_prefetch_matching_hashes (line 478) | def test_prefetch_matching_hashes(runtmp, linear_gather):
  function test_prefetch_nomatch_hashes (line 517) | def test_prefetch_nomatch_hashes(runtmp, linear_gather):
  function test_prefetch_no_num_query (line 556) | def test_prefetch_no_num_query(runtmp, linear_gather):
  function test_prefetch_no_num_subj (line 573) | def test_prefetch_no_num_subj(runtmp, linear_gather):
  function test_prefetch_db_fromfile (line 594) | def test_prefetch_db_fromfile(runtmp, linear_gather):
  function test_prefetch_no_db (line 640) | def test_prefetch_no_db(runtmp, linear_gather):
  function test_prefetch_check_scaled_bounds_negative (line 656) | def test_prefetch_check_scaled_bounds_negative(runtmp, linear_gather):
  function test_prefetch_check_scaled_bounds_less_than_minimum (line 680) | def test_prefetch_check_scaled_bounds_less_than_minimum(runtmp, linear_g...
  function test_prefetch_check_scaled_bounds_more_than_maximum (line 706) | def test_prefetch_check_scaled_bounds_more_than_maximum(runtmp, linear_g...
  function test_prefetch_downsample_scaled (line 732) | def test_prefetch_downsample_scaled(runtmp, linear_gather):
  function test_prefetch_downsample_multiple (line 760) | def test_prefetch_downsample_multiple(runtmp, linear_gather):
  function test_prefetch_empty (line 802) | def test_prefetch_empty(runtmp, linear_gather):
  function test_prefetch_basic_many_sigs (line 831) | def test_prefetch_basic_many_sigs(runtmp, linear_gather):
  function test_prefetch_with_picklist (line 856) | def test_prefetch_with_picklist(runtmp):
  function test_prefetch_with_picklist_exclude (line 883) | def test_prefetch_with_picklist_exclude(runtmp):
  function test_prefetch_with_pattern_include (line 909) | def test_prefetch_with_pattern_include(runtmp):
  function test_prefetch_with_pattern_exclude (line 930) | def test_prefetch_with_pattern_exclude(runtmp):
  function test_prefetch_output_with_abundance (line 951) | def test_prefetch_output_with_abundance(runtmp, prefetch_gather, linear_...
  function test_prefetch_ani_csv_out (line 978) | def test_prefetch_ani_csv_out(runtmp, linear_gather):
  function test_prefetch_ani_csv_out_estimate_ci (line 1026) | def test_prefetch_ani_csv_out_estimate_ci(runtmp, linear_gather):
  function test_prefetch_ani_containment_asymmetry (line 1097) | def test_prefetch_ani_containment_asymmetry(runtmp):

FILE: tests/test_revindex.py
  class JaccardSearchBestOnly_ButIgnore (line 22) | class JaccardSearchBestOnly_ButIgnore(JaccardSearch):
    method __init__ (line 25) | def __init__(self, ignore_list):
    method collect (line 30) | def collect(self, score, match):
  function test_mem_revindex_empty (line 43) | def test_mem_revindex_empty():
  function test_mem_revindex_num (line 52) | def test_mem_revindex_num():
  function test_mem_revindex_basic (line 59) | def test_mem_revindex_basic():
  function test_mem_revindex_manifest (line 71) | def test_mem_revindex_manifest():
  function test_mem_revindex_index_search (line 84) | def test_mem_revindex_index_search():
  function test_mem_revindex_index_search_picklist (line 132) | def test_mem_revindex_index_search_picklist(runtmp):
  function test_mem_revindex_index_search_retrieve_orig (line 170) | def test_mem_revindex_index_search_retrieve_orig():
  function test_mem_revindex_best_containment (line 217) | def test_mem_revindex_best_containment():
  function test_mem_revindex_gather_ignore (line 243) | def test_mem_revindex_gather_ignore():
  function test_mem_revindex_insert_after_init (line 277) | def test_mem_revindex_insert_after_init():
  function test_mem_revindex_union_found (line 295) | def test_mem_revindex_union_found():
  function test_mem_revindex_index_check_errors (line 323) | def test_mem_revindex_index_check_errors():
  function test_mem_revindex_index_check_nomatches (line 357) | def test_mem_revindex_index_check_nomatches():
  function test_disk_revindex_basic (line 385) | def test_disk_revindex_basic():
  function test_disk_revindex_manifest (line 394) | def test_disk_revindex_manifest():
  function test_disk_revindex_prefetch_to_revindex (line 408) | def test_disk_revindex_prefetch_to_revindex():
  function test_disk_revindex_ksize_wrong (line 419) | def test_disk_revindex_ksize_wrong():
  function test_disk_revindex_load (line 426) | def test_disk_revindex_load(runtmp):
  function test_disk_revindex_len (line 438) | def test_disk_revindex_len():
  function test_disk_revindex_signatures (line 445) | def test_disk_revindex_signatures():
  function test_disk_revindex_signatures_with_internal (line 458) | def test_disk_revindex_signatures_with_internal():
  function test_disk_revindex_signatures_with_picklist (line 477) | def test_disk_revindex_signatures_with_picklist():
  function test_disk_revindex_signatures_with_internal_with_picklist (line 494) | def test_disk_revindex_signatures_with_internal_with_picklist():
  function test_disk_revindex_best_containment (line 516) | def test_disk_revindex_best_containment():
  function test_disk_revindex_prefetch (line 531) | def test_disk_revindex_prefetch():
  function test_disk_revindex_ksize_wrong (line 553) | def test_disk_revindex_ksize_wrong():
  function test_disk_revindex_ksize (line 560) | def test_disk_revindex_ksize():
  function test_create_dataset_picklist_1 (line 567) | def test_create_dataset_picklist_1():
  function test_create_dataset_picklist_2 (line 591) | def test_create_dataset_picklist_2():
  function test_create_dataset_picklist_3 (line 615) | def test_create_dataset_picklist_3():
  function test_create_dataset_picklist_4 (line 639) | def test_create_dataset_picklist_4():
  function test_create_dataset_picklist_5 (line 663) | def test_create_dataset_picklist_5():
  function test_disk_revindex_against_bad_abund_rocksdb (line 678) | def test_disk_revindex_against_bad_abund_rocksdb(runtmp):
  function test_disk_revindex_prefetch_to_cg_colors_1 (line 688) | def test_disk_revindex_prefetch_to_cg_colors_1():
  function test_disk_revindex_prefetch_to_cg_colors_2 (line 700) | def test_disk_revindex_prefetch_to_cg_colors_2():
  function test_disk_revindex_prefetch_to_cg_colors_3 (line 715) | def test_disk_revindex_prefetch_to_cg_colors_3():
  function test_disk_revindex_prefetch_to_cg_colors_4 (line 730) | def test_disk_revindex_prefetch_to_cg_colors_4():
  function test_disk_revindex_prefetch_to_cg_colors_5 (line 757) | def test_disk_revindex_prefetch_to_cg_colors_5():
  function test_disk_revindex_prefetch_to_cg_colors_6 (line 803) | def test_disk_revindex_prefetch_to_cg_colors_6():
  function test_disk_revindex_prefetch_to_cg_colors_7 (line 817) | def test_disk_revindex_prefetch_to_cg_colors_7():
  function test_disk_revindex_prefetch_to_cg_colors_8 (line 831) | def test_disk_revindex_prefetch_to_cg_colors_8():
  function test_disk_revindex_union_found (line 845) | def test_disk_revindex_union_found():
  function test_disk_revindex_index_search_picklist (line 865) | def test_disk_revindex_index_search_picklist(runtmp):

FILE: tests/test_rustobj.py
  function test_rustobj_init (line 7) | def test_rustobj_init():
  function test_to_bytes (line 12) | def test_to_bytes():

FILE: tests/test_sbt.py
  function test_simple (line 22) | def test_simple(runtmp, n_children):
  function test_longer_search (line 96) | def test_longer_search(n_children):
  function test_tree_old_load (line 154) | def test_tree_old_load(old_version):
  function test_load_future (line 179) | def test_load_future(tmpdir):
  function test_tree_save_load (line 189) | def test_tree_save_load(runtmp, n_children):
  function test_search_minhashes (line 217) | def test_search_minhashes():
  function test_binary_nary_tree (line 239) | def test_binary_nary_tree():
  function test_sbt_combine (line 269) | def test_sbt_combine(n_children):
  function test_sbt_fsstorage (line 316) | def test_sbt_fsstorage(runtmp):
  function test_sbt_zipstorage (line 350) | def test_sbt_zipstorage(tmpdir):
  function test_sbt_ipfsstorage (line 385) | def test_sbt_ipfsstorage(runtmp):
  function test_sbt_redisstorage (line 424) | def test_sbt_redisstorage(runtmp):
  function test_save_zip (line 462) | def test_save_zip(tmpdir):
  function test_load_zip (line 491) | def test_load_zip(tmpdir):
  function test_load_zip_uncompressed (line 510) | def test_load_zip_uncompressed(tmpdir):
  function test_tree_repair (line 532) | def test_tree_repair():
  function test_tree_repair_insert (line 550) | def test_tree_repair_insert():
  function test_save_sparseness (line 571) | def test_save_sparseness(runtmp, n_children):
  function test_sbt_as_index_select (line 612) | def test_sbt_as_index_select():
  function test_sbt_as_index_select_picklist (line 642) | def test_sbt_as_index_select_picklist():
  function test_sbt_as_index_select_picklist_exclude (line 668) | def test_sbt_as_index_select_picklist_exclude():
  function test_sbt_as_index_find_picklist (line 694) | def test_sbt_as_index_find_picklist():
  function test_sbt_as_index_find_picklist_exclude (line 728) | def test_sbt_as_index_find_picklist_exclude():
  function test_sbt_as_index_find_picklist_twice (line 762) | def test_sbt_as_index_find_picklist_twice():
  function test_sbt_as_index_signatures (line 794) | def test_sbt_as_index_signatures():
  function test_sbt_gather_threshold_1 (line 812) | def test_sbt_gather_threshold_1():
  function test_sbt_gather_threshold_5 (line 870) | def test_sbt_gather_threshold_5():
  function test_gather_single_return (line 915) | def test_gather_single_return(c):
  function test_sbt_jaccard_ordering (line 941) | def test_sbt_jaccard_ordering(runtmp):
  function test_sbt_protein_command_index (line 988) | def test_sbt_protein_command_index(runtmp):
  function test_sbt_protein_search_no_threshold (line 1036) | def test_sbt_protein_search_no_threshold(c):
  function test_sbt_protein_command_search (line 1062) | def test_sbt_protein_command_search(c):
  function test_sbt_hp_command_index (line 1078) | def test_sbt_hp_command_index(c):
  function test_sbt_hp_command_search (line 1121) | def test_sbt_hp_command_search(c):
  function test_sbt_dayhoff_command_index (line 1137) | def test_sbt_dayhoff_command_index(c):
  function test_sbt_dayhoff_command_search (line 1180) | def test_sbt_dayhoff_command_search(c):
  function test_sbt_node_cache (line 1195) | def test_sbt_node_cache():
  function test_sbt_no_containment_on_num (line 1216) | def test_sbt_no_containment_on_num():
  function test_build_sbt_zip_with_dups (line 1231) | def test_build_sbt_zip_with_dups(runtmp):
  function test_build_sbt_zip_with_dups_exists (line 1246) | def test_build_sbt_zip_with_dups_exists(runtmp):
  function test_build_sbt_json_with_dups (line 1265) | def test_build_sbt_json_with_dups(runtmp):
  function test_build_sbt_json_with_dups_exists (line 1280) | def test_build_sbt_json_with_dups_exists(runtmp):
  function test_load_fail_on_file_not_dir (line 1299) | def test_load_fail_on_file_not_dir(runtmp):

FILE: tests/test_search.py
  function test_make_jaccard_search_query (line 19) | def test_make_jaccard_search_query():
  function test_make_jaccard_search_query_cont (line 27) | def test_make_jaccard_search_query_cont():
  function test_make_jaccard_search_query_max_cont (line 35) | def test_make_jaccard_search_query_max_cont():
  function test_make_jaccard_search_query_best_only (line 43) | def test_make_jaccard_search_query_best_only():
  function test_make_jaccard_search_query_no_threshold_none (line 51) | def test_make_jaccard_search_query_no_threshold_none():
  function test_make_jaccard_search_query_cont_and_max_cont (line 59) | def test_make_jaccard_search_query_cont_and_max_cont():
  function test_cont_requires_scaled (line 69) | def test_cont_requires_scaled():
  function test_search_requires_flat (line 79) | def test_search_requires_flat():
  function test_score_jaccard_similarity (line 88) | def test_score_jaccard_similarity():
  function test_score_jaccard_containment (line 94) | def test_score_jaccard_containment():
  function test_score_jaccard_containment_zero_query_size (line 100) | def test_score_jaccard_containment_zero_query_size():
  function test_score_jaccard_max_containment_1 (line 106) | def test_score_jaccard_max_containment_1():
  function test_score_jaccard_max_containment_2 (line 112) | def test_score_jaccard_max_containment_2():
  function test_score_jaccard_max_containment_zero_query_size (line 118) | def test_score_jaccard_max_containment_zero_query_size():
  function test_collect (line 124) | def test_collect():
  function test_collect_best_only (line 130) | def test_collect_best_only():
  function test_make_containment_query (line 136) | def test_make_containment_query():
  function test_make_containment_query_no_threshold (line 150) | def test_make_containment_query_no_threshold():
  function test_make_containment_query_num_minhash (line 164) | def test_make_containment_query_num_minhash():
  function test_make_containment_query_empty_minhash (line 177) | def test_make_containment_query_empty_minhash():
  function test_make_containment_query_high_threshold (line 190) | def test_make_containment_query_high_threshold():
  class FakeIndex (line 202) | class FakeIndex(LinearIndex):
    method __init__ (line 206) | def __init__(self, validator_fn):
    method find (line 209) | def find(self, search_fn, query, *args, **kwargs):
  function test_index_search_passthru (line 217) | def test_index_search_passthru():
  function test_index_containment_passthru (line 230) | def test_index_containment_passthru():
  function test_search_with_abund_query (line 243) | def test_search_with_abund_query():
  function test_scaledSearchResult (line 258) | def test_scaledSearchResult():
  function test_numSearchResult (line 300) | def test_numSearchResult():
  function test_SearchResult_incompatible_sigs (line 343) | def test_SearchResult_incompatible_sigs():
  function test_SearchResult_notsigs (line 355) | def test_SearchResult_notsigs():
  function test_SearchResult_no_similarity (line 365) | def test_SearchResult_no_similarity():
  function test_PrefetchResult (line 378) | def test_PrefetchResult():
  function test_PrefetchResult_incompatible_sigs (line 436) | def test_PrefetchResult_incompatible_sigs():
  function test_GatherResult (line 451) | def test_GatherResult():
  function test_GatherResult_ci (line 532) | def test_GatherResult_ci():
  function test_GatherResult_incompatible_sigs (line 589) | def test_GatherResult_incompatible_sigs():
  function test_GatherResult_incomplete_input_cmpscaled (line 614) | def test_GatherResult_incomplete_input_cmpscaled():
  function test_GatherResult_incomplete_input_gathermh (line 639) | def test_GatherResult_incomplete_input_gathermh():
  function test_GatherResult_incomplete_input_gather_result_rank (line 664) | def test_GatherResult_incomplete_input_gather_result_rank():
  function test_GatherResult_incomplete_input_total_weighted_hashes (line 686) | def test_GatherResult_incomplete_input_total_weighted_hashes():
  function test_GatherResult_incomplete_input_orig_query_abunds (line 728) | def test_GatherResult_incomplete_input_orig_query_abunds():

FILE: tests/test_signature.py
  function test_minhash_copy (line 20) | def test_minhash_copy(track_abundance):
  function test_sig_copy (line 28) | def test_sig_copy(track_abundance):
  function test_sig_copy_frozen (line 36) | def test_sig_copy_frozen(track_abundance):
  function test_sig_copy_frozen_mutable (line 47) | def test_sig_copy_frozen_mutable(track_abundance):
  function test_compare (line 59) | def test_compare(track_abundance):
  function test_compare_ne (line 72) | def test_compare_ne(track_abundance):
  function test_compare_ne2 (line 85) | def test_compare_ne2(track_abundance):
  function test_compare_ne2_reverse (line 99) | def test_compare_ne2_reverse(track_abundance):
  function test_hashable (line 113) | def test_hashable(track_abundance):
  function test_str (line 124) | def test_str(track_abundance):
  function test_roundtrip (line 138) | def test_roundtrip(track_abundance):
  function test_roundtrip_mutable_frozen (line 157) | def test_roundtrip_mutable_frozen(track_abundance):
  function test_load_signature_ksize_nonint (line 168) | def test_load_signature_ksize_nonint(track_abundance):
  function test_roundtrip_empty (line 180) | def test_roundtrip_empty(track_abundance):
  function test_roundtrip_scaled (line 193) | def test_roundtrip_scaled(track_abundance):
  function test_roundtrip_seed (line 208) | def test_roundtrip_seed(track_abundance):
  function test_similarity_downsample (line 223) | def test_similarity_downsample(track_abundance):
  function test_add_sequence_bad_dna (line 247) | def test_add_sequence_bad_dna(track_abundance):
  function test_md5 (line 258) | def test_md5(track_abundance):
  function test_str_1 (line 265) | def test_str_1(track_abundance):
  function test_str_2 (line 271) | def test_str_2(track_abundance):
  function test_str_3 (line 277) | def test_str_3(track_abundance):
  function test_name_4 (line 283) | def test_name_4(track_abundance):
  function test_save_load_multisig (line 289) | def test_save_load_multisig(track_abundance):
  function test_load_one_fail_nosig (line 307) | def test_load_one_fail_nosig(track_abundance):
  function test_load_one_succeed (line 314) | def test_load_one_succeed(track_abundance):
  function test_load_one_fail_multisig (line 324) | def test_load_one_fail_multisig(track_abundance):
  function test_save_minified (line 337) | def test_save_minified(track_abundance):
  function test_load_minified (line 354) | def test_load_minified(track_abundance):
  function test_load_compressed (line 365) | def test_load_compressed(track_abundance):
  function test_binary_fp (line 378) | def test_binary_fp(tmpdir, track_abundance):
  function test_load_signatures_from_json_no_file_do_raise (line 388) | def test_load_signatures_from_json_no_file_do_raise(tmpdir):
  function test_load_signatures_from_json_no_file_do_not_raise (line 395) | def test_load_signatures_from_json_no_file_do_not_raise(tmpdir):
  function test_max_containment (line 402) | def test_max_containment():
  function test_max_containment_empty (line 417) | def test_max_containment_empty():
  function test_max_containment_equal (line 432) | def test_max_containment_equal():
  function test_containment_ANI (line 448) | def test_containment_ANI():
  function test_containment_ANI_precalc_containment (line 484) | def test_containment_ANI_precalc_containment():
  function test_avg_containment (line 507) | def test_avg_containment():
  function test_avg_containment_ani (line 523) | def test_avg_containment_ani():
  function test_containment_ANI_downsample (line 538) | def test_containment_ANI_downsample():
  function test_jaccard_ANI (line 573) | def test_jaccard_ANI():
  function test_jaccard_ANI_untrustworthy (line 592) | def test_jaccard_ANI_untrustworthy():
  function test_jaccard_ANI_precalc_jaccard (line 610) | def test_jaccard_ANI_precalc_jaccard():
  function test_jaccard_ANI_downsample (line 628) | def test_jaccard_ANI_downsample():
  function test_frozen_signature_update_1 (line 652) | def test_frozen_signature_update_1(track_abundance):
  function test_frozen_signature_update_2 (line 662) | def test_frozen_signature_update_2(track_abundance):
  function test_frozen_signature_update_3 (line 673) | def test_frozen_signature_update_3(track_abundance):

FILE: tests/test_sketchcomparison.py
  function test_FracMinHashComparison (line 16) | def test_FracMinHashComparison(track_abundance):
  function test_FracMinHashComparison_downsample (line 90) | def test_FracMinHashComparison_downsample(track_abundance):
  function test_FracMinHashComparison_autodownsample (line 180) | def test_FracMinHashComparison_autodownsample(track_abundance):
  function test_FracMinHashComparison_ignore_abundance (line 270) | def test_FracMinHashComparison_ignore_abundance(track_abundance):
  function test_FracMinHashComparison_fail_threshold (line 331) | def test_FracMinHashComparison_fail_threshold(track_abundance):
  function test_FracMinHashComparison_potential_false_negative (line 371) | def test_FracMinHashComparison_potential_false_negative():
  function test_FracMinHashComparison_incompatible_ksize (line 434) | def test_FracMinHashComparison_incompatible_ksize(track_abundance):
  function test_FracMinHashComparison_incompatible_moltype (line 454) | def test_FracMinHashComparison_incompatible_moltype(track_abundance):
  function test_FracMinHashComparison_incompatible_sketchtype (line 474) | def test_FracMinHashComparison_incompatible_sketchtype(track_abundance):
  function test_FracMinHashComparison_incompatible_cmp_scaled (line 494) | def test_FracMinHashComparison_incompatible_cmp_scaled(track_abundance):
  function test_FracMinHashComparison_redownsample_without_scaled (line 515) | def test_FracMinHashComparison_redownsample_without_scaled(track_abundan...
  function test_NumMinHashComparison (line 539) | def test_NumMinHashComparison(track_abundance):
  function test_NumMinHashComparison_downsample (line 591) | def test_NumMinHashComparison_downsample(track_abundance):
  function test_NumMinHashComparison_autodownsample (line 652) | def test_NumMinHashComparison_autodownsample(track_abundance):
  function test_NumMinHashComparison_incompatible_ksize (line 713) | def test_NumMinHashComparison_incompatible_ksize(track_abundance):
  function test_NumMinHashComparison_incompatible_moltype (line 734) | def test_NumMinHashComparison_incompatible_moltype(track_abundance):
  function test_NumMinHashComparison_incompatible_sketchtype (line 754) | def test_NumMinHashComparison_incompatible_sketchtype(track_abundance):
  function test_NumMinHashComparison_redownsample_without_num (line 774) | def test_NumMinHashComparison_redownsample_without_num(track_abundance):
  function test_NumMinHashComparison_incompatible_cmp_num (line 797) | def test_NumMinHashComparison_incompatible_cmp_num(track_abundance):
  function test_FracMinHashComparison_ANI (line 818) | def test_FracMinHashComparison_ANI(track_abundance):
  function test_FracMinHashComparison_ANI_provide_similarity (line 874) | def test_FracMinHashComparison_ANI_provide_similarity(track_abundance):
  function test_FracMinHashComparison_ANI_estimate_CI (line 929) | def test_FracMinHashComparison_ANI_estimate_CI(track_abundance):
  function test_FracMinHashComparison_ANI_estimate_CI_ci99 (line 981) | def test_FracMinHashComparison_ANI_estimate_CI_ci99(track_abundance):
  function test_FracMinHashComparison_ANI_downsample (line 1021) | def test_FracMinHashComparison_ANI_downsample(track_abundance):

FILE: tests/test_sourmash.py
  function test_citation_file (line 44) | def test_citation_file():
  function test_run_sourmash (line 59) | def test_run_sourmash():
  function test_run_sourmash_badcmd (line 64) | def test_run_sourmash_badcmd():
  function test_run_sourmash_subcmd_help (line 70) | def test_run_sourmash_subcmd_help():
  function test_sourmash_info (line 83) | def test_sourmash_info():
  function test_sourmash_info_verbose (line 93) | def test_sourmash_info_verbose():
  function test_load_pathlist_from_file_does_not_exist (line 103) | def test_load_pathlist_from_file_does_not_exist():
  function test_load_pathlist_from_file_empty (line 112) | def test_load_pathlist_from_file_empty(c):
  function test_load_pathlist_from_file_badly_formatted (line 122) | def test_load_pathlist_from_file_badly_formatted(c):
  function test_load_pathlist_from_file_badly_formatted_2 (line 132) | def test_load_pathlist_from_file_badly_formatted_2(c):
  function test_load_pathlist_from_file_duplicate (line 144) | def test_load_pathlist_from_file_duplicate(c):
  function test_compare_serial (line 155) | def test_compare_serial(runtmp):
  function test_compare_serial_distance (line 184) | def test_compare_serial_distance(runtmp):
  function test_compare_parallel (line 212) | def test_compare_parallel(runtmp):
  function test_compare_do_serial_compare_with_from_file (line 242) | def test_compare_do_serial_compare_with_from_file(runtmp):
  function test_compare_do_basic_compare_using_rna_arg (line 276) | def test_compare_do_basic_compare_using_rna_arg(runtmp):
  function test_compare_do_basic_using_nucleotide_arg (line 301) | def test_compare_do_basic_using_nucleotide_arg(runtmp):
  function test_compare_quiet (line 325) | def test_compare_quiet(runtmp):
  function test_compare_do_traverse_directory_parse_args (line 338) | def test_compare_do_traverse_directory_parse_args(runtmp):
  function test_compare_do_traverse_directory (line 350) | def test_compare_do_traverse_directory(runtmp):
  function test_compare_do_traverse_directory_compare_force (line 359) | def test_compare_do_traverse_directory_compare_force(runtmp):
  function test_compare_output_csv (line 376) | def test_compare_output_csv(runtmp):
  function test_compare_output_csv_gz (line 402) | def test_compare_output_csv_gz(runtmp):
  function test_compare_downsample (line 428) | def test_compare_downsample(runtmp):
  function test_compare_downsample_scaled (line 448) | def test_compare_downsample_scaled(runtmp):
  function test_compare_downsample_scaled_too_low (line 470) | def test_compare_downsample_scaled_too_low(runtmp):
  function test_compare_downsample_scaled_fail_num (line 496) | def test_compare_downsample_scaled_fail_num(runtmp):
  function test_compare_downsample_scaled_fail_all_num (line 520) | def test_compare_downsample_scaled_fail_all_num(runtmp):
  function test_compare_output_multiple_k (line 547) | def test_compare_output_multiple_k(runtmp):
  function test_compare_output_multiple_moltype (line 567) | def test_compare_output_multiple_moltype(runtmp):
  function test_compare_dayhoff (line 586) | def test_compare_dayhoff(runtmp):
  function test_compare_hp (line 609) | def test_compare_hp(runtmp):
  function _load_compare_matrix_and_sigs (line 630) | def _load_compare_matrix_and_sigs(compare_csv, sigfiles, *, ksize=31):
  function test_compare_containment (line 654) | def test_compare_containment(runtmp):
  function test_compare_containment_distance (line 682) | def test_compare_containment_distance(runtmp):
  function test_compare_max_containment (line 717) | def test_compare_max_containment(runtmp):
  function test_compare_avg_containment (line 751) | def test_compare_avg_containment(runtmp):
  function test_compare_max_containment_and_containment (line 785) | def test_compare_max_containment_and_containment(runtmp):
  function test_compare_avg_containment_and_containment (line 810) | def test_compare_avg_containment_and_containment(runtmp):
  function test_compare_avg_containment_and_max_containment (line 835) | def test_compare_avg_containment_and_max_containment(runtmp):
  function test_compare_containment_abund_flatten_warning (line 860) | def test_compare_containment_abund_flatten_warning(runtmp):
  function test_compare_ani_abund_flatten (line 877) | def test_compare_ani_abund_flatten(runtmp):
  function test_compare_containment_require_scaled (line 894) | def test_compare_containment_require_scaled(runtmp):
  function test_do_plot_comparison (line 911) | def test_do_plot_comparison(runtmp):
  function test_do_plot_comparison_2_pdf (line 927) | def test_do_plot_comparison_2_pdf(runtmp):
  function test_do_plot_comparison_3 (line 942) | def test_do_plot_comparison_3(runtmp):
  function test_do_plot_comparison_4_output_dir (line 958) | def test_do_plot_comparison_4_output_dir(runtmp):
  function test_do_plot_comparison_5_force (line 976) | def test_do_plot_comparison_5_force(runtmp):
  function test_do_plot_comparison_4_fail_not_distance (line 993) | def test_do_plot_comparison_4_fail_not_distance(runtmp):
  function test_plot_6_labels_default (line 1012) | def test_plot_6_labels_default(runtmp):
  function test_plot_6_labels (line 1044) | def test_plot_6_labels(runtmp):
  function test_plot_6_indices (line 1076) | def test_plot_6_indices(runtmp):
  function test_plot_6_no_labels (line 1108) | def test_plot_6_no_labels(runtmp):
  function test_plot_6_no_indices (line 1140) | def test_plot_6_no_indices(runtmp):
  function test_plot_6_no_labels_no_indices (line 1172) | def test_plot_6_no_labels_no_indices(runtmp):
  function test_plot_6_indices_labels (line 1204) | def test_plot_6_indices_labels(runtmp):
  function test_plot_override_labeltext (line 1236) | def test_plot_override_labeltext(runtmp):
  function test_plot_override_labeltext_fail (line 1273) | def test_plot_override_labeltext_fail(runtmp):
  function test_plot_reordered_labels_csv (line 1306) | def test_plot_reordered_labels_csv(runtmp):
  function test_plot_reordered_labels_csv_gz (line 1331) | def test_plot_reordered_labels_csv_gz(runtmp):
  function test_plot_subsample_1 (line 1356) | def test_plot_subsample_1(runtmp):
  function test_plot_subsample_2 (line 1387) | def test_plot_subsample_2(runtmp):
  function test_compare_and_plot_labels_from_to (line 1417) | def test_compare_and_plot_labels_from_to(runtmp):
  function test_compare_and_plot_labels_from_changed (line 1455) | def test_compare_and_plot_labels_from_changed(runtmp):
  function test_compare_and_plot_labels_from_error (line 1491) | def test_compare_and_plot_labels_from_error(runtmp):
  function test_search_query_sig_does_not_exist (line 1529) | def test_search_query_sig_does_not_exist(c):
  function test_search_subject_sig_does_not_exist (line 1543) | def test_search_subject_sig_does_not_exist(c):
  function test_search_second_subject_sig_does_not_exist (line 1556) | def test_search_second_subject_sig_does_not_exist(c):
  function test_search (line 1571) | def test_search(c):
  function test_search_ignore_abundance (line 1582) | def test_search_ignore_abundance(runtmp):
  function test_search_abund_subj_flat (line 1606) | def test_search_abund_subj_flat(runtmp):
  function test_search_abund_csv (line 1620) | def test_search_abund_csv(runtmp):
  function test_search_csv (line 1648) | def test_search_csv(c):
  function test_search_lca_db (line 1671) | def test_search_lca_db(c):
  function test_search_query_db_md5 (line 1681) | def test_search_query_db_md5(runtmp):
  function test_gather_query_db_md5 (line 1689) | def test_gather_query_db_md5(runtmp, linear_gather, prefetch_gather):
  function test_gather_query_db_md5_ambiguous (line 1699) | def test_gather_query_db_md5_ambiguous(runtmp, linear_gather, prefetch_g...
  function test_gather_lca_db (line 1711) | def test_gather_lca_db(runtmp, linear_gather, prefetch_gather):
  function test_gather_csv_output_filename_bug (line 1724) | def test_gather_csv_output_filename_bug(runtmp, linear_gather, prefetch_...
  function test_compare_no_such_file (line 1748) | def test_compare_no_such_file(runtmp):
  function test_compare_no_such_file_force (line 1757) | def test_compare_no_such_file_force(runtmp):
  function test_compare_no_matching_sigs (line 1767) | def test_compare_no_matching_sigs(runtmp):
  function test_compare_deduce_molecule (line 1787) | def test_compare_deduce_molecule(runtmp):
  function test_compare_choose_molecule_dna (line 1800) | def test_compare_choose_molecule_dna(runtmp):
  function test_compare_choose_molecule_protein (line 1824) | def test_compare_choose_molecule_protein(runtmp):
  function test_compare_no_choose_molecule_fail (line 1848) | def test_compare_no_choose_molecule_fail(runtmp):
  function test_compare_deduce_ksize (line 1864) | def test_compare_deduce_ksize(runtmp):
  function test_search_deduce_molecule (line 1877) | def test_search_deduce_molecule(runtmp):
  function test_search_deduce_ksize (line 1891) | def test_search_deduce_ksize(runtmp):
  function test_do_sourmash_index_multik_fail (line 1905) | def test_do_sourmash_index_multik_fail(runtmp):
  function test_do_sourmash_index_multimol_fail (line 1920) | def test_do_sourmash_index_multimol_fail(runtmp):
  function test_do_sourmash_index_multinum_fail (line 1935) | def test_do_sourmash_index_multinum_fail(runtmp):
  function test_do_sourmash_index_multiscaled_fail (line 1954) | def test_do_sourmash_index_multiscaled_fail(runtmp):
  function test_do_sourmash_index_multiscaled_rescale (line 1974) | def test_do_sourmash_index_multiscaled_rescale(c):
  function test_do_sourmash_index_multiscaled_rescale_fail (line 1991) | def test_do_sourmash_index_multiscaled_rescale_fail(c):
  function test_do_sourmash_sbt_search_output (line 2010) | def test_do_sourmash_sbt_search_output(runtmp):
  function test_do_sourmash_sbt_search_check_bug (line 2030) | def test_do_sourmash_sbt_search_check_bug(runtmp):
  function test_do_sourmash_sbt_search_empty_sig (line 2049) | def test_do_sourmash_sbt_search_empty_sig(runtmp):
  function test_do_sourmash_sbt_move_and_search_output (line 2068) | def test_do_sourmash_sbt_move_and_search_output(runtmp):
  function test_search_deduce_ksize_and_select_appropriate (line 2105) | def test_search_deduce_ksize_and_select_appropriate(runtmp):
  function test_search_deduce_ksize_not_unique (line 2124) | def test_search_deduce_ksize_not_unique(runtmp):
  function test_search_deduce_ksize_no_match (line 2149) | def test_search_deduce_ksize_no_match(c):
  function test_search_deduce_ksize_vs_user_specified (line 2162) | def test_search_deduce_ksize_vs_user_specified(runtmp):
  function test_search_containment (line 2177) | def test_search_containment(runtmp):
  function test_search_containment_abund (line 2191) | def test_search_containment_abund(runtmp):
  function test_search_containment_abund_ignore (line 2235) | def test_search_containment_abund_ignore(runtmp):
  function test_search_containment_sbt (line 2281) | def test_search_containment_sbt(runtmp):
  function test_search_containment_s10 (line 2299) | def test_search_containment_s10(runtmp):
  function test_search_containment_s10_no_max (line 2311) | def test_search_containment_s10_no_max(run):
  function test_search_max_containment_s10_pairwise (line 2327) | def test_search_max_containment_s10_pairwise(runtmp):
  function test_search_containment_s10_siglist (line 2339) | def test_search_containment_s10_siglist(runtmp):
  function test_search_max_containment_s10_siglist (line 2354) | def test_search_max_containment_s10_siglist(runtmp):
  function test_search_containment_s10_sbt (line 2369) | def test_search_containment_s10_sbt(runtmp):
  function test_search_containment_s10_sbt_best_only (line 2383) | def test_search_containment_s10_sbt_best_only(runtmp):
  function test_search_containment_s10_sbt_empty (line 2400) | def test_search_containment_s10_sbt_empty(runtmp):
  function test_search_max_containment_s10_sbt (line 2411) | def test_search_max_containment_s10_sbt(runtmp):
  function test_search_max_containment_s10_sbt_best_only (line 2425) | def test_search_max_containment_s10_sbt_best_only(runtmp):
  function test_search_max_containment_s10_sbt_empty (line 2438) | def test_search_max_containment_s10_sbt_empty(runtmp):
  function test_search_containment_s10_lca (line 2449) | def test_search_containment_s10_lca(runtmp):
  function test_search_max_containment_s10_lca (line 2463) | def test_search_max_containment_s10_lca(runtmp):
  function test_search_gzip (line 2477) | def test_search_gzip(runtmp):
  function test_search_2 (line 2498) | def test_search_2(runtmp):
  function test_search_3 (line 2515) | def test_search_3(runtmp):
  function test_search_4 (line 2532) | def test_search_4(runtmp):
  function test_search_5_num_results (line 2551) | def test_search_5_num_results(runtmp):
  function test_index_check_scaled_bounds_negative (line 2563) | def test_index_check_scaled_bounds_negative(runtmp):
  function test_index_check_scaled_bounds_less_than_minimum (line 2582) | def test_index_check_scaled_bounds_less_than_minimum(runtmp):
  function test_index_check_scaled_bounds_more_than_maximum (line 2602) | def test_index_check_scaled_bounds_more_than_maximum(runtmp):
  function test_index_metagenome_fromfile (line 2623) | def test_index_metagenome_fromfile(c):
  function test_index_metagenome_fromfile_no_cmdline_sig (line 2663) | def test_index_metagenome_fromfile_no_cmdline_sig(c):
  function test_search_metagenome_traverse (line 2693) | def test_search_metagenome_traverse(runtmp):
  function test_search_metagenome_traverse_check_csv (line 2712) | def test_search_metagenome_traverse_check_csv(runtmp):
  function test_search_incompatible (line 2746) | def test_search_incompatible(c):
  function test_search_traverse_incompatible (line 2760) | def test_search_traverse_incompatible(c):
  function test_search_check_scaled_bounds_negative (line 2778) | def test_search_check_scaled_bounds_negative(runtmp):
  function test_search_check_scaled_bounds_less_than_minimum (line 2790) | def test_search_check_scaled_bounds_less_than_minimum(runtmp):
  function test_search_check_scaled_bounds_more_than_maximum (line 2805) | def test_search_check_scaled_bounds_more_than_maximum(runtmp):
  function test_search_metagenome_sbt_downsample_fail (line 2823) | def test_search_metagenome_sbt_downsample_fail(runtmp):
  function test_search_with_picklist (line 2854) | def test_search_with_picklist(runtmp):
  function test_search_with_picklist_exclude (line 2885) | def test_search_with_picklist_exclude(runtmp):
  function test_search_with_pattern_include (line 2915) | def test_search_with_pattern_include(runtmp):
  function test_search_with_pattern_exclude (line 2942) | def test_search_with_pattern_exclude(runtmp):
  function test_search_empty_db_fail (line 2969) | def test_search_empty_db_fail(runtmp):
  function test_search_empty_db_nofail (line 2982) | def test_search_empty_db_nofail(runtmp):
  function test_mash_csv_to_sig (line 3006) | def test_mash_csv_to_sig(runtmp):
  function test_do_sourmash_index_bad_args (line 3021) | def test_do_sourmash_index_bad_args(runtmp):
  function test_do_sourmash_sbt_search (line 3047) | def test_do_sourmash_sbt_search(runtmp):
  function test_do_sourmash_sbt_search_wrong_ksize (line 3065) | def test_do_sourmash_sbt_search_wrong_ksize(runtmp):
  function test_do_sourmash_sbt_search_multiple (line 3097) | def test_do_sourmash_sbt_search_multiple(runtmp):
  function test_do_sourmash_sbt_search_and_sigs (line 3119) | def test_do_sourmash_sbt_search_and_sigs(runtmp):
  function test_do_sourmash_sbt_search_downsample (line 3138) | def test_do_sourmash_sbt_search_downsample(runtmp):
  function test_do_sourmash_sbt_search_downsample_2 (line 3162) | def test_do_sourmash_sbt_search_downsample_2(runtmp):
  function test_do_sourmash_index_abund (line 3188) | def test_do_sourmash_index_abund(c):
  function test_do_sourmash_index_single (line 3204) | def test_do_sourmash_index_single(runtmp):
  function test_do_sourmash_sbt_search_selectprot (line 3221) | def test_do_sourmash_sbt_search_selectprot(runtmp):
  function test_do_sourmash_search_multimoltype_query (line 3240) | def test_do_sourmash_search_multimoltype_query(runtmp):
  function test_do_sourmash_index_traverse (line 3276) | def test_do_sourmash_index_traverse(runtmp):
  function test_do_sourmash_index_traverse_force (line 3296) | def test_do_sourmash_index_traverse_force(c):
  function test_do_sourmash_index_sparseness (line 3324) | def test_do_sourmash_index_sparseness(runtmp):
  function test_do_sourmash_sbt_combine (line 3346) | def test_do_sourmash_sbt_combine(runtmp):
  function test_do_sourmash_index_append (line 3373) | def test_do_sourmash_index_append(runtmp):
  function test_do_sourmash_sbt_search_otherdir (line 3417) | def test_do_sourmash_sbt_search_otherdir(runtmp):
  function test_do_sourmash_sbt_search_scaled_vs_num_1 (line 3440) | def test_do_sourmash_sbt_search_scaled_vs_num_1(runtmp):
  function test_do_sourmash_sbt_search_scaled_vs_num_2 (line 3471) | def test_do_sourmash_sbt_search_scaled_vs_num_2(runtmp):
  function test_do_sourmash_sbt_search_scaled_vs_num_3 (line 3502) | def test_do_sourmash_sbt_search_scaled_vs_num_3(runtmp):
  function test_do_sourmash_sbt_search_scaled_vs_num_4 (line 3523) | def test_do_sourmash_sbt_search_scaled_vs_num_4(runtmp):
  function test_do_sourmash_check_search_vs_actual_similarity (line 3544) | def test_do_sourmash_check_search_vs_actual_similarity(runtmp):
  function test_do_sourmash_check_sbt_filenames (line 3558) | def test_do_sourmash_check_sbt_filenames(runtmp):
  function test_do_sourmash_sbt_search_bestonly (line 3583) | def test_do_sourmash_sbt_search_bestonly(runtmp):
  function test_do_sourmash_sbt_search_bestonly_scaled (line 3600) | def test_do_sourmash_sbt_search_bestonly_scaled(runtmp):
  function test_sbt_search_order_dependence (line 3621) | def test_sbt_search_order_dependence(runtmp):
  function test_sbt_search_order_dependence_2 (line 3667) | def test_sbt_search_order_dependence_2(runtmp):
  function test_compare_with_abundance_1 (line 3707) | def test_compare_with_abundance_1(runtmp):
  function test_compare_with_abundance_2 (line 3729) | def test_compare_with_abundance_2(runtmp):
  function test_compare_with_abundance_3 (line 3753) | def test_compare_with_abundance_3(runtmp):
  function test_compare_with_picklist (line 3778) | def test_compare_with_picklist(runtmp):
  function test_compare_with_picklist_exclude (line 3800) | def test_compare_with_picklist_exclude(runtmp):
  function test_compare_with_pattern_include (line 3823) | def test_compare_with_pattern_include(runtmp):
  function test_compare_with_pattern_exclude (line 3838) | def test_compare_with_pattern_exclude(runtmp):
  function test_gather_csv (line 3855) | def test_gather_csv(runtmp, linear_gather, prefetch_gather):
  function test_gather_csv_gz (line 3918) | def test_gather_csv_gz(runtmp, linear_gather, prefetch_gather):
  function test_gather_abund_x_abund (line 3978) | def test_gather_abund_x_abund(runtmp, prefetch_gather, linear_gather):
  function test_gather_multiple_sbts (line 3989) | def test_gather_multiple_sbts(runtmp, prefetch_gather, linear_gather):
  function test_gather_multiple_sbts_save_prefetch (line 4023) | def test_gather_multiple_sbts_save_prefetch(runtmp, linear_gather):
  function test_gather_multiple_sbts_save_prefetch_csv (line 4060) | def test_gather_multiple_sbts_save_prefetch_csv(runtmp, linear_gather):
  function test_gather_multiple_sbts_save_prefetch_csv_gz (line 4101) | def test_gather_multiple_sbts_save_prefetch_csv_gz(runtmp, linear_gather):
  function test_gather_multiple_sbts_save_prefetch_and_prefetch_csv (line 4142) | def test_gather_multiple_sbts_save_prefetch_and_prefetch_csv(runtmp, lin...
  function test_gather_sbt_and_sigs (line 4186) | def test_gather_sbt_and_sigs(runtmp, linear_gather, prefetch_gather):
  function test_gather_file_output (line 4216) | def test_gather_file_output(runtmp, linear_gather, prefetch_gather):
  function test_gather_f_match_orig (line 4248) | def test_gather_f_match_orig(runtmp, linear_gather, prefetch_gather):
  function test_gather_nomatch (line 4318) | def test_gather_nomatch(runtmp, linear_gather, prefetch_gather):
  function test_gather_nomatch_create_empty (line 4343) | def test_gather_nomatch_create_empty(runtmp, linear_gather, prefetch_gat...
  function test_gather_abund_nomatch (line 4373) | def test_gather_abund_nomatch(runtmp, linear_gather, prefetch_gather):
  function test_gather_metagenome_3_thermo (line 4389) | def test_gather_metagenome_3_thermo(runtmp):
  function test_multigather_metagenome (line 4460) | def test_multigather_metagenome(runtmp):
  function test_multigather_metagenome_scaled (line 4504) | def test_multigather_metagenome_scaled(runtmp):
  function test_multigather_check_scaled_bounds_negative (line 4537) | def test_multigather_check_scaled_bounds_negative(runtmp):
  function test_multigather_check_scaled_bounds_less_than_minimum (line 4557) | def test_multigather_check_scaled_bounds_less_than_minimum(runtmp):
  function test_multigather_check_scaled_bounds_more_than_maximum (line 4580) | def test_multigather_check_scaled_bounds_more_than_maximum(runtmp):
  function test_multigather_metagenome_query_from_file (line 4603) | def test_multigather_metagenome_query_from_file(runtmp):
  function test_multigather_metagenome_output (line 4648) | def test_multigather_metagenome_output(runtmp):
  function test_multigather_metagenome_output_outdir (line 4677) | def test_multigather_metagenome_output_outdir(runtmp):
  function test_multigather_metagenome_query_with_sbt (line 4707) | def test_multigather_metagenome_query_with_sbt(runtmp):
  function test_multigather_metagenome_query_with_lca (line 4760) | def test_multigather_metagenome_query_with_lca(runtmp):
  function test_multigather_metagenome_query_on_lca_db (line 4791) | def test_multigather_metagenome_query_on_lca_db(runtmp):
  function test_multigather_metagenome_query_with_sbt_addl_query (line 4824) | def test_multigather_metagenome_query_with_sbt_addl_query(runtmp):
  function test_multigather_metagenome_query_with_sbt_addl_query_fail_overwrite (line 4887) | def test_multigather_metagenome_query_with_sbt_addl_query_fail_overwrite...
  function test_multigather_metagenome_query_with_sbt_addl_query_fail_overwrite_force (line 4923) | def test_multigather_metagenome_query_with_sbt_addl_query_fail_overwrite...
  function test_multigather_metagenome_sbt_query_from_file_with_addl_query (line 4959) | def test_multigather_metagenome_sbt_query_from_file_with_addl_query(runt...
  function test_multigather_metagenome_sbt_query_from_file_incorrect (line 5029) | def test_multigather_metagenome_sbt_query_from_file_incorrect(runtmp):
  function test_multigather_metagenome_lca_query_from_file (line 5056) | def test_multigather_metagenome_lca_query_from_file(runtmp):
  function test_multigather_metagenome_query_from_file_with_addl_query (line 5092) | def test_multigather_metagenome_query_from_file_with_addl_query(runtmp):
  function test_multigather_metagenome_output_unique_empty_filename (line 5148) | def test_multigather_metagenome_output_unique_empty_filename(runtmp):
  function test_multigather_metagenome_output_unique (line 5172) | def test_multigather_metagenome_output_unique(runtmp):
  function test_gather_metagenome_traverse (line 5204) | def test_gather_metagenome_traverse(runtmp, linear_gather, prefetch_gath...
  function test_gather_metagenome_traverse_check_csv (line 5246) | def test_gather_metagenome_traverse_check_csv(runtmp, linear_gather, pre...
  function test_gather_traverse_incompatible (line 5304) | def test_gather_traverse_incompatible(c):
  function test_gather_metagenome_output_unassigned (line 5322) | def test_gather_metagenome_output_unassigned(runtmp):
  function test_gather_metagenome_output_unassigned_as_zip (line 5367) | def test_gather_metagenome_output_unassigned_as_zip(runtmp):
  function test_gather_metagenome_output_unassigned_none (line 5414) | def test_gather_metagenome_output_unassigned_none(runtmp):
  function test_gather_metagenome_output_unassigned_nomatches (line 5457) | def test_gather_metagenome_output_unassigned_nomatches(
  function test_gather_metagenome_output_unassigned_nomatches_protein (line 5485) | def test_gather_metagenome_output_unassigned_nomatches_protein(
  function test_gather_check_scaled_bounds_negative (line 5521) | def test_gather_check_scaled_bounds_negative(runtmp, prefetch_gather, li...
  function test_gather_check_scaled_bounds_less_than_minimum (line 5545) | def test_gather_check_scaled_bounds_less_than_minimum(
  function test_gather_check_scaled_bounds_more_than_maximum (line 5574) | def test_gather_check_scaled_bounds_more_than_maximum(
  function test_gather_query_downsample (line 5602) | def test_gather_query_downsample(runtmp, linear_gather, prefetch_gather):
  function test_gather_query_downsample_explicit (line 5635) | def test_gather_query_downsample_explicit(runtmp, linear_gather, prefetc...
  function test_gather_downsample_multiple (line 5670) | def test_gather_downsample_multiple(runtmp, linear_gather, prefetch_gath...
  function test_gather_with_picklist (line 5714) | def test_gather_with_picklist(runtmp, linear_gather, prefetch_gather):
  function test_gather_with_picklist_exclude (line 5747) | def test_gather_with_picklist_exclude(runtmp, linear_gather, prefetch_ga...
  function test_gather_with_pattern_include (line 5785) | def test_gather_with_pattern_include(runtmp, linear_gather, prefetch_gat...
  function test_gather_with_pattern_exclude (line 5814) | def test_gather_with_pattern_exclude(runtmp, linear_gather, prefetch_gat...
  function test_gather_error_no_sigs_traverse (line 5850) | def test_gather_error_no_sigs_traverse(c):
  function test_gather_error_no_cardinality_query (line 5866) | def test_gather_error_no_cardinality_query(runtmp, linear_gather, prefet...
  function test_gather_deduce_ksize (line 5889) | def test_gather_deduce_ksize(runtmp, prefetch_gather, linear_gather):
  function test_gather_deduce_moltype (line 5918) | def test_gather_deduce_moltype(runtmp, linear_gather, prefetch_gather):
  function test_gather_abund_1_1 (line 5948) | def test_gather_abund_1_1(runtmp, linear_gather, prefetch_gather):
  function test_gather_abund_10_1 (line 5994) | def test_gather_abund_10_1(runtmp, prefetch_gather, linear_gather):
  function test_gather_abund_10_1_ignore_abundance (line 6104) | def test_gather_abund_10_1_ignore_abundance(runtmp, linear_gather, prefe...
  function test_gather_output_unassigned_with_abundance (line 6162) | def test_gather_output_unassigned_with_abundance(
  function test_gather_empty_db_fail (line 6200) | def test_gather_empty_db_fail(runtmp, linear_gather, prefetch_gather):
  function test_gather_empty_db_nofail (line 6222) | def test_gather_empty_db_nofail(runtmp, prefetch_gather, linear_gather):
  function test_multigather_output_unassigned_with_abundance (line 6254) | def test_multigather_output_unassigned_with_abundance(runtmp, sig_save_e...
  function test_multigather_empty_db_fail (line 6291) | def test_multigather_empty_db_fail(runtmp):
  function test_multigather_empty_db_nofail (line 6306) | def test_multigather_empty_db_nofail(runtmp):
  function test_multigather_nomatch (line 6339) | def test_multigather_nomatch(runtmp):
  function test_multigather_abund_nomatch (line 6356) | def test_multigather_abund_nomatch(runtmp):
  function test_sbt_categorize (line 6371) | def test_sbt_categorize(runtmp):
  function test_sbt_categorize_ignore_abundance_1 (line 6403) | def test_sbt_categorize_ignore_abundance_1(runtmp):
  function test_sbt_categorize_ignore_abundance_3 (line 6439) | def test_sbt_categorize_ignore_abundance_3(runtmp):
  function test_sbt_categorize_already_done (line 6472) | def test_sbt_categorize_already_done(runtmp):
  function test_sbt_categorize_already_done_traverse (line 6509) | def test_sbt_categorize_already_done_traverse(runtmp):
  function test_sbt_categorize_multiple_ksizes_moltypes (line 6536) | def test_sbt_categorize_multiple_ksizes_moltypes(runtmp):
  function test_watch_check_num_bounds_negative (line 6553) | def test_watch_check_num_bounds_negative(runtmp):
  function test_watch_check_num_bounds_less_than_minimum (line 6568) | def test_watch_check_num_bounds_less_than_minimum(runtmp):
  function test_watch_check_num_bounds_more_than_maximum (line 6582) | def test_watch_check_num_bounds_more_than_maximum(runtmp):
  function test_watch (line 6598) | def test_watch(runtmp):
  function test_watch_deduce_ksize (line 6614) | def test_watch_deduce_ksize(runtmp):
  function test_watch_coverage (line 6630) | def test_watch_coverage(runtmp):
  function test_watch_output_sig (line 6652) | def test_watch_output_sig(runtmp):
  function test_storage_convert (line 6692) | def test_storage_convert(runtmp):
  function test_storage_convert_identity (line 6742) | def test_storage_convert_identity(runtmp):
  function test_storage_convert_fsstorage_newpath (line 6763) | def test_storage_convert_fsstorage_newpath(runtmp):
  function test_migrate (line 6790) | def test_migrate(runtmp):
  function test_license_cc0 (line 6815) | def test_license_cc0(runtmp):
  function test_license_non_cc0 (line 6828) | def test_license_non_cc0(runtmp):
  function test_license_load_non_cc0 (line 6841) | def test_license_load_non_cc0():
  function test_do_sourmash_index_zipfile (line 6851) | def test_do_sourmash_index_zipfile(c):
  function test_do_sourmash_index_zipfile_append (line 6876) | def test_do_sourmash_index_zipfile_append(c):
  function test_index_with_picklist (line 6928) | def test_index_with_picklist(runtmp):
  function test_index_with_picklist_exclude (line 6953) | def test_index_with_picklist_exclude(runtmp):
  function test_index_matches_search_with_picklist (line 6981) | def test_index_matches_search_with_picklist(runtmp):
  function test_index_matches_search_with_picklist_exclude (line 7030) | def test_index_matches_search_with_picklist_exclude(runtmp):
  function test_gather_with_prefetch_picklist (line 7079) | def test_gather_with_prefetch_picklist(runtmp, linear_gather):
  function test_gather_with_prefetch_picklist_2_prefetch (line 7124) | def test_gather_with_prefetch_picklist_2_prefetch(runtmp, linear_gather):
  function test_gather_with_prefetch_picklist_3_gather (line 7170) | def test_gather_with_prefetch_picklist_3_gather(runtmp, linear_gather):
  function test_gather_with_prefetch_picklist_3_gather_badcol (line 7217) | def test_gather_with_prefetch_picklist_3_gather_badcol(runtmp):
  function test_gather_with_prefetch_picklist_4_manifest (line 7262) | def test_gather_with_prefetch_picklist_4_manifest(runtmp, linear_gather):
  function test_gather_with_prefetch_picklist_4_manifest_excl (line 7303) | def test_gather_with_prefetch_picklist_4_manifest_excl(runtmp, linear_ga...
  function test_gather_with_prefetch_picklist_5_search (line 7341) | def test_gather_with_prefetch_picklist_5_search(runtmp):
  function test_gather_scaled_1 (line 7385) | def test_gather_scaled_1(runtmp, linear_gather, prefetch_gather):
  function test_standalone_manifest_search (line 7404) | def test_standalone_manifest_search(runtmp):
  function test_standalone_manifest_search_fail (line 7433) | def test_standalone_manifest_search_fail(runtmp):
  function test_search_ani_jaccard (line 7459) | def test_search_ani_jaccard(runtmp):
  function test_search_ani_jaccard_error_too_high (line 7487) | def test_search_ani_jaccard_error_too_high(runtmp):
  function test_searchabund_no_ani (line 7520) | def test_searchabund_no_ani(runtmp):
  function test_search_ani_containment (line 7546) | def test_search_ani_containment(runtmp):
  function test_search_ani_containment_asymmetry (line 7589) | def test_search_ani_containment_asymmetry(runtmp):
  function test_search_ani_containment_fail (line 7611) | def test_search_ani_containment_fail(runtmp):
  function test_search_ani_containment_estimate_ci (line 7636) | def test_search_ani_containment_estimate_ci(runtmp):
  function test_search_ani_max_containment (line 7700) | def test_search_ani_max_containment(runtmp):
  function test_search_ani_max_containment_estimate_ci (line 7724) | def test_search_ani_max_containment_estimate_ci(runtmp):
  function test_search_jaccard_ani_downsample (line 7760) | def test_search_jaccard_ani_downsample(runtmp):
  function test_gather_ani_csv (line 7815) | def test_gather_ani_csv(runtmp, linear_gather, prefetch_gather):
  function test_gather_ani_csv_estimate_ci (line 7865) | def test_gather_ani_csv_estimate_ci(runtmp, linear_gather, prefetch_gath...
  function test_compare_containment_ani (line 7937) | def test_compare_containment_ani(runtmp):
  function test_compare_containment_ani_asymmetry (line 7987) | def test_compare_containment_ani_asymmetry(runtmp):
  function test_compare_jaccard_ani (line 8048) | def test_compare_jaccard_ani(runtmp):
  function test_compare_jaccard_protein_parallel_ani_bug (line 8093) | def test_compare_jaccard_protein_parallel_ani_bug(runtmp):
  function test_compare_containment_ani_asymmetry_distance (line 8106) | def test_compare_containment_ani_asymmetry_distance(runtmp):
  function test_compare_jaccard_ani (line 8154) | def test_compare_jaccard_ani(runtmp):
  function test_compare_jaccard_ani_jaccard_error_too_high (line 8196) | def test_compare_jaccard_ani_jaccard_error_too_high(runtmp):
  function test_compare_max_containment_ani (line 8249) | def test_compare_max_containment_ani(runtmp):
  function test_compare_avg_containment_ani (line 8297) | def test_compare_avg_containment_ani(runtmp):
  function test_compare_ANI_require_scaled (line 8346) | def test_compare_ANI_require_scaled(runtmp):

FILE: tests/test_sourmash_args.py
  function test_save_signatures_api_none (line 27) | def test_save_signatures_api_none():
  function test_save_signatures_to_location_1_sig (line 42) | def test_save_signatures_to_location_1_sig(runtmp):
  function test_save_signatures_to_location_1_stdout (line 61) | def test_save_signatures_to_location_1_stdout():
  function test_save_signatures_to_location_1_sig_is_default (line 82) | def test_save_signatures_to_location_1_sig_is_default(runtmp):
  function test_save_signatures_to_location_1_sig_gz (line 101) | def test_save_signatures_to_location_1_sig_gz(runtmp):
  function test_save_signatures_to_location_1_zip (line 125) | def test_save_signatures_to_location_1_zip(runtmp):
  function test_save_signatures_to_location_1_zip_bad (line 148) | def test_save_signatures_to_location_1_zip_bad(runtmp):
  function test_save_signatures_to_location_1_zip_dup (line 169) | def test_save_signatures_to_location_1_zip_dup(runtmp):
  function test_save_signatures_to_location_2_zip_add (line 202) | def test_save_signatures_to_location_2_zip_add(runtmp):
  function test_save_signatures_to_location_2_zip_add_dup (line 235) | def test_save_signatures_to_location_2_zip_add_dup(runtmp):
  function test_save_signatures_to_location_3_zip_add_fail (line 277) | def test_save_signatures_to_location_3_zip_add_fail(runtmp):
  function test_save_signatures_to_location_3_zip_add_with_manifest (line 303) | def test_save_signatures_to_location_3_zip_add_with_manifest(runtmp):
  function test_save_signatures_to_location_1_dirout (line 352) | def test_save_signatures_to_location_1_dirout(runtmp):
  function test_save_signatures_to_location_1_dirout_bug_2751 (line 373) | def test_save_signatures_to_location_1_dirout_bug_2751(runtmp):
  function test_save_signatures_to_location_1_dirout_duplicate (line 396) | def test_save_signatures_to_location_1_dirout_duplicate(runtmp):
  function test_load_empty_zipfile (line 419) | def test_load_empty_zipfile(runtmp):
  function test_load_many_sigs_empty_file (line 428) | def test_load_many_sigs_empty_file(runtmp):
  function test_load_many_sigs_empty_file_force (line 447) | def test_load_many_sigs_empty_file_force(runtmp):
  function test_get_manifest_1 (line 467) | def test_get_manifest_1():
  function test_get_manifest_2_cannot_build (line 476) | def test_get_manifest_2_cannot_build():
  function test_get_manifest_2_cannot_buildno_require (line 487) | def test_get_manifest_2_cannot_buildno_require():
  function test_get_manifest_3_build (line 499) | def test_get_manifest_3_build():
  function test_get_manifest_3_build_2 (line 522) | def test_get_manifest_3_build_2():
  class FakeArgs (line 555) | class FakeArgs:
  function test_pattern_0 (line 561) | def test_pattern_0():
  function test_pattern_1 (line 572) | def test_pattern_1():
  function test_pattern_2 (line 584) | def test_pattern_2():
  function test_pattern_3 (line 596) | def test_pattern_3():
  function test_pattern_4 (line 607) | def test_pattern_4():
  function test_pattern_5 (line 618) | def test_pattern_5():
  function test_fileinput_csv_1_plain (line 629) | def test_fileinput_csv_1_plain():
  function test_fileinput_csv_1_no_such_file (line 639) | def test_fileinput_csv_1_no_such_file(runtmp):
  function test_fileinput_csv_2_gz (line 649) | def test_fileinput_csv_2_gz(runtmp):
  function test_fileinput_csv_2_gz_not_csv (line 664) | def test_fileinput_csv_2_gz_not_csv(runtmp):
  function test_fileinput_csv_2_gz_bad_version_header (line 676) | def test_fileinput_csv_2_gz_bad_version_header(runtmp):
  function test_fileinput_csv_2_zip (line 691) | def test_fileinput_csv_2_zip(runtmp):
  function test_fileinput_csv_3_load_manifest (line 708) | def test_fileinput_csv_3_load_manifest():
  function test_fileinput_csv_3_load_manifest_no_default (line 722) | def test_fileinput_csv_3_load_manifest_no_default():
  function test_fileinput_csv_3_load_manifest_zipfile_obj (line 732) | def test_fileinput_csv_3_load_manifest_zipfile_obj():
  function test_fileinput_csv_3_load_manifest_zipfile_obj_no_defualt (line 747) | def test_fileinput_csv_3_load_manifest_zipfile_obj_no_defualt():
  function test_fileoutput_csv_1 (line 758) | def test_fileoutput_csv_1(runtmp):
  function test_fileoutput_csv_1_gz (line 777) | def test_fileoutput_csv_1_gz(runtmp):
  function test_fileoutput_csv_2_stdout (line 796) | def test_fileoutput_csv_2_stdout():
  function test_add_ksize_arg_no_default (line 806) | def test_add_ksize_arg_no_default():
  function test_add_ksize_arg_no_default_specify (line 814) | def test_add_ksize_arg_no_default_specify():
  function test_add_ksize_arg_default_31 (line 822) | def test_add_ksize_arg_default_31():
  function test_add_ksize_arg_default_31_specify (line 830) | def test_add_ksize_arg_default_31_specify():
  function test_bug_2370 (line 838) | def test_bug_2370(runtmp):
  function test_load_one_signature_1 (line 850) | def test_load_one_signature_1(runtmp):
  function test_load_one_signature_2_fail (line 858) | def test_load_one_signature_2_fail(runtmp):
  function test_load_one_signature_3_fail (line 868) | def test_load_one_signature_3_fail(runtmp):

FILE: tests/test_sourmash_compute.py
  function test_do_sourmash_compute (line 31) | def test_do_sourmash_compute():
  function test_do_sourmash_compute_check_num_bounds_negative (line 45) | def test_do_sourmash_compute_check_num_bounds_negative(runtmp):
  function test_do_sourmash_compute_check_num_bounds_less_than_minimum (line 71) | def test_do_sourmash_compute_check_num_bounds_less_than_minimum(runtmp):
  function test_do_sourmash_compute_check_num_bounds_more_than_maximum (line 96) | def test_do_sourmash_compute_check_num_bounds_more_than_maximum(runtmp):
  function test_do_sourmash_compute_outdir (line 124) | def test_do_sourmash_compute_outdir(c):
  function test_do_sourmash_compute_output_valid_file (line 137) | def test_do_sourmash_compute_output_valid_file():
  function test_do_sourmash_compute_output_stdout_valid (line 164) | def test_do_sourmash_compute_output_stdout_valid():
  function test_do_sourmash_compute_output_and_name_valid_file (line 186) | def test_do_sourmash_compute_output_and_name_valid_file(c):
  function test_do_sourmash_compute_output_and_name_valid_file_outdir (line 237) | def test_do_sourmash_compute_output_and_name_valid_file_outdir(c):
  function test_do_sourmash_compute_singleton (line 263) | def test_do_sourmash_compute_singleton():
  function test_do_sourmash_compute_name (line 279) | def test_do_sourmash_compute_name():
  function test_do_sourmash_compute_name_fail_no_output (line 308) | def test_do_sourmash_compute_name_fail_no_output():
  function test_do_sourmash_compute_merge_fail_no_output (line 320) | def test_do_sourmash_compute_merge_fail_no_output():
  function test_do_sourmash_compute_name_from_first (line 340) | def test_do_sourmash_compute_name_from_first():
  function test_do_sourmash_compute_multik (line 356) | def test_do_sourmash_compute_multik():
  function test_do_sourmash_compute_multik_with_protein (line 373) | def test_do_sourmash_compute_multik_with_protein():
  function test_do_sourmash_compute_multik_with_dayhoff (line 396) | def test_do_sourmash_compute_multik_with_dayhoff():
  function test_do_sourmash_compute_multik_with_dayhoff_and_dna (line 422) | def test_do_sourmash_compute_multik_with_dayhoff_and_dna():
  function test_do_sourmash_compute_multik_with_hp (line 447) | def test_do_sourmash_compute_multik_with_hp():
  function test_do_sourmash_compute_multik_with_hp_and_dna (line 472) | def test_do_sourmash_compute_multik_with_hp_and_dna():
  function test_do_sourmash_compute_multik_with_dayhoff_dna_protein (line 495) | def test_do_sourmash_compute_multik_with_dayhoff_dna_protein():
  function test_do_sourmash_compute_multik_with_dayhoff_hp_dna_protein (line 521) | def test_do_sourmash_compute_multik_with_dayhoff_hp_dna_protein():
  function test_do_sourmash_compute_multik_with_nothing (line 549) | def test_do_sourmash_compute_multik_with_nothing():
  function test_do_sourmash_compute_multik_protein_bad_ksize (line 562) | def test_do_sourmash_compute_multik_protein_bad_ksize():
  function test_do_sourmash_compute_multik_only_protein (line 577) | def test_do_sourmash_compute_multik_only_protein(c):
  function test_do_sourmash_compute_multik_protein_input_bad_ksize (line 594) | def test_do_sourmash_compute_multik_protein_input_bad_ksize():
  function test_do_sourmash_compute_multik_only_protein_no_rna (line 617) | def test_do_sourmash_compute_multik_only_protein_no_rna(c):
  function test_do_sourmash_compute_protein_bad_sequences (line 635) | def test_do_sourmash_compute_protein_bad_sequences():
  function test_do_sourmash_compute_multik_input_is_protein (line 657) | def test_do_sourmash_compute_multik_input_is_protein():
  function test_do_sourmash_compute_multik_outfile (line 682) | def test_do_sourmash_compute_multik_outfile():
  function test_do_sourmash_compute_with_scaled_1 (line 700) | def test_do_sourmash_compute_with_scaled_1():
  function test_do_sourmash_compute_with_scaled_2 (line 719) | def test_do_sourmash_compute_with_scaled_2():
  function test_do_sourmash_compute_with_scaled (line 738) | def test_do_sourmash_compute_with_scaled():
  function test_do_sourmash_compute_with_bad_scaled (line 757) | def test_do_sourmash_compute_with_bad_scaled():
  function test_do_sourmash_compute_with_seed (line 791) | def test_do_sourmash_compute_with_seed():
  function test_do_sourmash_check_protein_comparisons (line 810) | def test_do_sourmash_check_protein_comparisons():
  function test_do_sourmash_check_knowngood_dna_comparisons (line 859) | def test_do_sourmash_check_knowngood_dna_comparisons(c):
  function test_do_sourmash_check_knowngood_dna_comparisons_use_rna (line 879) | def test_do_sourmash_check_knowngood_dna_comparisons_use_rna(c):
  function test_do_sourmash_check_knowngood_input_protein_comparisons (line 895) | def test_do_sourmash_check_knowngood_input_protein_comparisons():
  function test_do_sourmash_check_knowngood_protein_comparisons (line 917) | def test_do_sourmash_check_knowngood_protein_comparisons():
  function test_compute_parameters (line 939) | def test_compute_parameters():

FILE: tests/test_sourmash_sketch.py
  function test_do_sourmash_sketch_check_scaled_bounds_negative (line 34) | def test_do_sourmash_sketch_check_scaled_bounds_negative(runtmp):
  function test_do_sourmash_sketch_check_scaled_bounds_less_than_minimum (line 41) | def test_do_sourmash_sketch_check_scaled_bounds_less_than_minimum(runtmp):
  function test_do_sourmash_sketch_check_scaled_bounds_more_than_maximum (line 50) | def test_do_sourmash_sketch_check_scaled_bounds_more_than_maximum(runtmp):
  function test_do_sourmash_sketch_check_num_bounds_negative (line 59) | def test_do_sourmash_sketch_check_num_bounds_negative(runtmp):
  function test_do_sourmash_sketch_check_num_bounds_less_than_minimum (line 66) | def test_do_sourmash_sketch_check_num_bounds_less_than_minimum(runtmp):
  function test_do_sourmash_sketch_check_num_bounds_more_than_maximum (line 75) | def test_do_sourmash_sketch_check_num_bounds_more_than_maximum(runtmp):
  function test_empty_factory (line 84) | def test_empty_factory():
  function test_no_default_moltype_factory_nonempty (line 89) | def test_no_default_moltype_factory_nonempty():
  function test_factory_no_default_moltype_dna (line 94) | def test_factory_no_default_moltype_dna():
  function test_factory_no_default_moltype_protein (line 103) | def test_factory_no_default_moltype_protein():
  function test_factory_dna_nosplit (line 112) | def test_factory_dna_nosplit():
  function test_factory_dna_split (line 121) | def test_factory_dna_split():
  function test_factory_protein_nosplit (line 132) | def test_factory_protein_nosplit():
  function test_factory_protein_split (line 141) | def test_factory_protein_split():
  function test_factory_dna_equal (line 152) | def test_factory_dna_equal():
  function test_factory_protein_equal (line 167) | def test_factory_protein_equal():
  function test_factory_dna_multi_ksize_eq (line 182) | def test_factory_dna_multi_ksize_eq():
  function test_factory_protein_multi_ksize_eq (line 197) | def test_factory_protein_multi_ksize_eq():
  function test_dna_defaults (line 212) | def test_dna_defaults():
  function test_dna_multiple_ksize (line 234) | def test_dna_multiple_ksize():
  function test_dna_override_1 (line 261) | def test_dna_override_1():
  function test_scaled_param_requires_equal (line 279) | def test_scaled_param_requires_equal():
  function test_k_param_requires_equal (line 284) | def test_k_param_requires_equal():
  function test_k_param_requires_equal_2 (line 289) | def test_k_param_requires_equal_2():
  function test_seed_param_requires_equal (line 294) | def test_seed_param_requires_equal():
  function test_num_param_requires_equal (line 299) | def test_num_param_requires_equal():
  function test_dna_override_bad_1 (line 304) | def test_dna_override_bad_1():
  function test_dna_override_bad_2 (line 309) | def test_dna_override_bad_2():
  function test_protein_defaults (line 314) | def test_protein_defaults():
  function test_protein_override_bad_2 (line 332) | def test_protein_override_bad_2():
  function test_protein_override_bad_rust_foo (line 337) | def test_protein_override_bad_rust_foo():
  function test_dayhoff_defaults (line 361) | def test_dayhoff_defaults():
  function test_dayhoff_override_bad_2 (line 379) | def test_dayhoff_override_bad_2():
  function test_hp_defaults (line 384) | def test_hp_defaults():
  function test_hp_override_bad_2 (line 402) | def test_hp_override_bad_2():
  function test_multiple_moltypes (line 407) | def test_multiple_moltypes():
  function test_compute_parameters_to_param_str (line 479) | def test_compute_parameters_to_param_str(input_param_str, expected_output):
  function test_manifest_row_to_compute_parameters_1 (line 490) | def test_manifest_row_to_compute_parameters_1():
  function test_manifest_row_to_compute_parameters_2 (line 506) | def test_manifest_row_to_compute_parameters_2():
  function test_manifest_row_to_compute_parameters_3 (line 522) | def test_manifest_row_to_compute_parameters_3():
  function test_manifest_row_to_compute_parameters_4 (line 538) | def test_manifest_row_to_compute_parameters_4():
  function test_bad_compute_parameters (line 554) | def test_bad_compute_parameters():
  function test_do_sourmash_sketchdna_empty (line 574) | def test_do_sourmash_sketchdna_empty(c):
  function test_do_sourmash_sketchprotein_empty (line 584) | def test_do_sourmash_sketchprotein_empty(c):
  function test_do_sourmash_sketchtranslate_empty (line 594) | def test_do_sourmash_sketchtranslate_empty(c):
  function test_do_sourmash_sketchdna (line 603) | def test_do_sourmash_sketchdna(runtmp):
  function test_do_sourmash_sketchdna_check_sequence_succeed (line 614) | def test_do_sourmash_sketchdna_check_sequence_succeed(runtmp):
  function test_do_sourmash_sketchdna_check_sequence_fail (line 625) | def test_do_sourmash_sketchdna_check_sequence_fail(runtmp):
  function test_do_sourmash_sketchdna_check_sequence_fail_singleton (line 639) | def test_do_sourmash_sketchdna_check_sequence_fail_singleton(runtmp):
  function test_do_sourmash_sketchdna_from_file (line 653) | def test_do_sourmash_sketchdna_from_file(runtmp):
  function test_do_sourmash_sketchdna_noinput (line 670) | def test_do_sourmash_sketchdna_noinput(c):
  function test_do_sourmash_sketchdna_noinput_singleton (line 685) | def test_do_sourmash_sketchdna_noinput_singleton(c):
  function test_do_sourmash_sketchdna_noinput_merge (line 697) | def test_do_sourmash_sketchdna_noinput_merge(c):
  function test_do_sourmash_sketchdna_outdir (line 709) | def test_do_sourmash_sketchdna_outdir(c):
  function test_do_sourmash_sketchdna_output_dir (line 723) | def test_do_sourmash_sketchdna_output_dir(c):
  function test_do_sourmash_sketchdna_output_valid_file (line 737) | def test_do_sourmash_sketchdna_output_valid_file(runtmp):
  function test_do_sourmash_sketchdna_output_zipfile (line 757) | def test_do_sourmash_sketchdna_output_zipfile(runtmp):
  function test_do_sourmash_sketchdna_output_stdout_valid (line 773) | def test_do_sourmash_sketchdna_output_stdout_valid(runtmp):
  function test_do_sourmash_sketchdna_output_and_name_valid_file (line 788) | def test_do_sourmash_sketchdna_output_and_name_valid_file(c):
  function test_do_sourmash_sketchdna_output_and_name_valid_file_outdir (line 842) | def test_do_sourmash_sketchdna_output_and_name_valid_file_outdir(c):
  function test_do_sourmash_sketchdna_singleton (line 867) | def test_do_sourmash_sketchdna_singleton(runtmp):
  function test_do_sourmash_sketchdna_name (line 878) | def test_do_sourmash_sketchdna_name(runtmp):
  function test_do_sourmash_sketchdna_name_fail_no_output (line 898) | def test_do_sourmash_sketchdna_name_fail_no_output(runtmp):
  function test_do_sourmash_sketchdna_fail_no_output (line 907) | def test_do_sourmash_sketchdna_fail_no_output(runtmp):
  function test_do_sourmash_sketchdna_name_from_first (line 920) | def test_do_sourmash_sketchdna_name_from_first(runtmp):
  function test_do_sourmash_sketchdna_multik (line 931) | def test_do_sourmash_sketchdna_multik(runtmp):
  function test_do_sourmash_sketchdna_multik_output (line 945) | def test_do_sourmash_sketchdna_multik_output(runtmp, sig_save_extension):
  function test_do_sketch_dna_override_protein_fail (line 960) | def test_do_sketch_dna_override_protein_fail(runtmp):
  function test_do_sketch_protein_override_dna_fail (line 972) | def test_do_sketch_protein_override_dna_fail(runtmp):
  function test_do_sketch_translate_multik_with_protein (line 984) | def test_do_sketch_translate_multik_with_protein(runtmp):
  function test_do_sketch_translate_multik_with_protein_from_file (line 1000) | def test_do_sketch_translate_multik_with_protein_from_file(runtmp):
  function test_do_sketch_translate_multik_with_dayhoff (line 1023) | def test_do_sketch_translate_multik_with_dayhoff(runtmp):
  function test_do_sketch_translate_multik_with_hp (line 1042) | def test_do_sketch_translate_multik_with_hp(runtmp):
  function test_do_sourmash_sketch_translate_multik_only_protein (line 1060) | def test_do_sourmash_sketch_translate_multik_only_protein(c):
  function test_do_sourmash_sketch_translate_bad_sequences (line 1076) | def test_do_sourmash_sketch_translate_bad_sequences(runtmp):
  function test_do_sketch_protein_multik_input (line 1093) | def test_do_sketch_protein_multik_input(runtmp):
  function test_do_sketch_protein_multik_input_from_file (line 1113) | def test_do_sketch_protein_multik_input_from_file(runtmp):
  function test_do_sourmash_sketchdna_multik_outfile (line 1140) | def test_do_sourmash_sketchdna_multik_outfile(runtmp):
  function test_do_sourmash_sketchdna_with_scaled_1 (line 1155) | def test_do_sourmash_sketchdna_with_scaled_1(runtmp):
  function test_do_sourmash_sketchdna_with_scaled_2 (line 1173) | def test_do_sourmash_sketchdna_with_scaled_2(runtmp):
  function test_do_sourmash_sketchdna_with_scaled (line 1191) | def test_do_sourmash_sketchdna_with_scaled(runtmp):
  function test_do_sourmash_sketchdna_with_bad_scaled (line 1209) | def test_do_sourmash_sketchdna_with_bad_scaled(runtmp):
  function test_do_sketch_with_seed (line 1243) | def test_do_sketch_with_seed(runtmp):
  function test_do_sourmash_check_protein_comparisons (line 1261) | def test_do_sourmash_check_protein_comparisons(runtmp):
  function test_do_sourmash_check_knowngood_dna_comparisons (line 1306) | def test_do_sourmash_check_knowngood_dna_comparisons(c):
  function test_do_sourmash_check_knowngood_dna_comparisons_use_rna (line 1327) | def test_do_sourmash_check_knowngood_dna_comparisons_use_rna(c):
  function test_do_sourmash_check_knowngood_input_protein_comparisons (line 1343) | def test_do_sourmash_check_knowngood_input_protein_comparisons(runtmp):
  function test_do_sourmash_check_knowngood_protein_comparisons (line 1362) | def test_do_sourmash_check_knowngood_protein_comparisons(runtmp):
  function test_do_sourmash_singleton_multiple_files_no_out_specified (line 1383) | def test_do_sourmash_singleton_multiple_files_no_out_specified(runtmp):
  function test_do_sourmash_singleton_multiple_files_output (line 1428) | def test_do_sourmash_singleton_multiple_files_output(runtmp):
  function test_do_sourmash_singleton_multiple_files_output_zip (line 1469) | def test_do_sourmash_singleton_multiple_files_output_zip(runtmp):
  function test_protein_with_stop_codons (line 1508) | def test_protein_with_stop_codons(runtmp):
  function test_hp_with_stop_codons (line 1574) | def test_hp_with_stop_codons(runtmp):
  function test_dayhoff_with_stop_codons (line 1640) | def test_dayhoff_with_stop_codons(runtmp):
  function test_fromfile_dna (line 1709) | def test_fromfile_dna(runtmp):
  function test_fromfile_dna (line 1738) | def test_fromfile_dna(runtmp):
  function test_fromfile_skipm1n3 (line 1767) | def test_fromfile_skipm1n3(runtmp):
  function test_fromfile_skipm2n3 (line 1796) | def test_fromfile_skipm2n3(runtmp):
  function test_fromfile_dna_empty (line 1825) | def test_fromfile_dna_empty(runtmp):
  function test_fromfile_dna_check_sequence_succeed (line 1856) | def test_fromfile_dna_check_sequence_succeed(runtmp):
  function test_fromfile_dna_check_sequence_fail (line 1886) | def test_fromfile_dna_check_sequence_fail(runtmp):
  function test_fromfile_dna_and_protein (line 1913) | def test_fromfile_dna_and_protein(runtmp):
  function test_fromfile_dna_and_protein_and_hp_and_dayhoff (line 1952) | def test_fromfile_dna_and_protein_and_hp_and_dayhoff(runtmp):
  function test_fromfile_dna_and_protein_noname (line 2007) | def test_fromfile_dna_and_protein_noname(runtmp):
  function test_fromfile_dna_and_protein_dup_name (line 2033) | def test_fromfile_dna_and_protein_dup_name(runtmp):
  function test_fromfile_dna_and_protein_dup_name_report (line 2061) | def test_fromfile_dna_and_protein_dup_name_report(runtmp):
  function test_fromfile_dna_and_protein_missing (line 2090) | def test_fromfile_dna_and_protein_missing(runtmp):
  function test_fromfile_dna_and_protein_missing_ignore (line 2120) | def test_fromfile_dna_and_protein_missing_ignore(runtmp):
  function test_fromfile_no_overwrite (line 2154) | def test_fromfile_no_overwrite(runtmp):
  function test_fromfile_force_overwrite (line 2192) | def test_fromfile_force_overwrite(runtmp):
  function test_fromfile_need_params (line 2237) | def test_fromfile_need_params(runtmp):
  function test_fromfile_seed_not_allowed (line 2254) | def test_fromfile_seed_not_allowed(runtmp):
  function test_fromfile_license_not_allowed (line 2274) | def test_fromfile_license_not_allowed(runtmp):
  function test_fromfile_dna_and_protein_csv_output (line 2296) | def test_fromfile_dna_and_protein_csv_output(runtmp):
  function test_fromfile_dna_and_protein_already_exists (line 2349) | def test_fromfile_dna_and_protein_already_exists(runtmp):
  function test_fromfile_dna_and_protein_partly_already_exists (line 2385) | def test_fromfile_dna_and_protein_partly_already_exists(runtmp):
  function test_fromfile_dna_and_protein_already_exists_noname (line 2414) | def test_fromfile_dna_and_protein_already_exists_noname(runtmp):

FILE: tests/test_sqlite_index.py
  function test_sqlite_index_prefetch_empty (line 29) | def test_sqlite_index_prefetch_empty():
  function test_sqlite_index_bad_version (line 45) | def test_sqlite_index_bad_version(runtmp):
  function test_sqlite_index_bad_version_unique (line 66) | def test_sqlite_index_bad_version_unique(runtmp):
  function test_index_search_subj_scaled_is_lower (line 83) | def test_index_search_subj_scaled_is_lower():
  function test_sqlite_index_save_load (line 107) | def test_sqlite_index_save_load(runtmp):
  function test_sqlite_index_multik_select (line 133) | def test_sqlite_index_multik_select():
  function test_sqlite_index_num_select (line 151) | def test_sqlite_index_num_select():
  function test_sqlite_index_abund_select (line 158) | def test_sqlite_index_abund_select():
  function test_sqlite_index_insert_num_fail (line 165) | def test_sqlite_index_insert_num_fail():
  function test_sqlite_index_insert_abund_fail (line 179) | def test_sqlite_index_insert_abund_fail():
  function test_sqlite_index_moltype_multi_fail (line 192) | def test_sqlite_index_moltype_multi_fail():
  function test_sqlite_index_picklist_select (line 212) | def test_sqlite_index_picklist_select():
  function test_sqlite_index_picklist_select_exclude (line 235) | def test_sqlite_index_picklist_select_exclude():
  function test_sqlite_jaccard_ordering (line 264) | def test_sqlite_jaccard_ordering():
  function test_sqlite_index_scaled1 (line 310) | def test_sqlite_index_scaled1():
  function test_sqlite_index_load_existing (line 353) | def test_sqlite_index_load_existing():
  function test_sqlite_index_create_load_existing (line 363) | def test_sqlite_index_create_load_existing(runtmp):
  function test_sqlite_index_create_load_insert_existing (line 378) | def test_sqlite_index_create_load_insert_existing(runtmp):
  function test_sqlite_index_create_load_insert_existing_cli (line 402) | def test_sqlite_index_create_load_insert_existing_cli(runtmp):
  function test_sqlite_manifest_bad_version (line 425) | def test_sqlite_manifest_bad_version(runtmp):
  function test_sqlite_manifest_bad_version_unique (line 446) | def test_sqlite_manifest_bad_version_unique(runtmp):
  function test_sqlite_manifest_basic (line 463) | def test_sqlite_manifest_basic():
  function test_sqlite_manifest_round_trip (line 495) | def test_sqlite_manifest_round_trip():
  function test_sqlite_manifest_create (line 525) | def test_sqlite_manifest_create(runtmp):
  function test_sqlite_manifest_create_noload_sigs (line 557) | def test_sqlite_manifest_create_noload_sigs(runtmp):
  function test_sqlite_manifest_create_yesload_sigs (line 569) | def test_sqlite_manifest_create_yesload_sigs(runtmp):
  function test_sqlite_manifest_num (line 582) | def test_sqlite_manifest_num(runtmp):
  function test_sqlite_manifest_num_select (line 600) | def test_sqlite_manifest_num_select(runtmp):
  function test_sqlite_manifest_locations (line 617) | def test_sqlite_manifest_locations(runtmp):
  function test_sqlite_manifest_create_insert (line 639) | def test_sqlite_manifest_create_insert(runtmp):
  function test_sqlite_manifest_create_insert_2 (line 660) | def test_sqlite_manifest_create_insert_2(runtmp):
  function test_sqlite_manifest_existing (line 681) | def test_sqlite_manifest_existing(runtmp):
  function test_sqlite_manifest_existing_insert (line 693) | def test_sqlite_manifest_existing_insert(runtmp):
  function test_sqlite_manifest_existing_mf_only (line 718) | def test_sqlite_manifest_existing_mf_only(runtmp):
  function test_sqlite_manifest_existing_mfonly_insert (line 737) | def test_sqlite_manifest_existing_mfonly_insert(runtmp):
  function test_sqlite_manifest_load_existing_index (line 761) | def test_sqlite_manifest_load_existing_index():
  function test_sqlite_manifest_load_existing_index_insert_fail (line 770) | def test_sqlite_manifest_load_existing_index_insert_fail():
  function test_sqlite_manifest_create_load_empty (line 788) | def test_sqlite_manifest_create_load_empty(runtmp):
  function test_sqlite_lca_db_load_existing (line 798) | def test_sqlite_lca_db_load_existing():
  function test_sqlite_lca_db_select (line 808) | def test_sqlite_lca_db_select():
  function test_sqlite_lca_db_create_load_existing (line 819) | def test_sqlite_lca_db_create_load_existing(runtmp):
  function test_sqlite_lca_db_load_empty (line 838) | def test_sqlite_lca_db_load_empty(runtmp):
  function test_sqlite_lca_db_create_readonly (line 855) | def test_sqlite_lca_db_create_readonly(runtmp):
  function test_sqlite_lca_db_try_load_sqlite_index (line 882) | def test_sqlite_lca_db_try_load_sqlite_index():
  function test_sqlite_lca_db_supply_lineage_db (line 892) | def test_sqlite_lca_db_supply_lineage_db():
  function test_bad_sqlite_internal_version (line 914) | def test_bad_sqlite_internal_version():

FILE: tests/test_tax.py
  function test_run_sourmash_tax (line 24) | def test_run_sourmash_tax():
  function test_metagenome_stdout_0 (line 29) | def test_metagenome_stdout_0(runtmp, cli_v4_and_v5):
  function test_metagenome_stdout_0_default_v4 (line 150) | def test_metagenome_stdout_0_default_v4(runtmp, cli_v4_only):
  function test_metagenome_stdout_0_db (line 183) | def test_metagenome_stdout_0_db(runtmp, cli_v4_and_v5):
  function test_metagenome_summary_csv_out_v4 (line 305) | def test_metagenome_summary_csv_out_v4(runtmp, cli_v4_only):
  function test_metagenome_summary_csv_out_v5 (line 431) | def test_metagenome_summary_csv_out_v5(runtmp, cli_v5_only):
  function test_metagenome_summary_csv_out_abund (line 559) | def test_metagenome_summary_csv_out_abund(runtmp):
  function test_metagenome_summary_csv_out_empty_gather_force (line 687) | def test_metagenome_summary_csv_out_empty_gather_force(runtmp, cli_v4_an...
  function test_metagenome_kreport_out (line 734) | def test_metagenome_kreport_out(runtmp):
  function test_metagenome_kreport_ncbi_taxid_out (line 825) | def test_metagenome_kreport_ncbi_taxid_out(runtmp):
  function test_metagenome_kreport_out_lemonade_v4 (line 921) | def test_metagenome_kreport_out_lemonade_v4(runtmp, cli_v4_only):
  function test_metagenome_kreport_out_lemonade_ignore_abund (line 982) | def test_metagenome_kreport_out_lemonade_ignore_abund(runtmp):
  function test_metagenome_kreport_out_lemonade_no_abund_error_v5 (line 1044) | def test_metagenome_kreport_out_lemonade_no_abund_error_v5(runtmp, cli_v...
  function test_metagenome_kreport_out_lemonade_no_abund_use_abund (line 1077) | def test_metagenome_kreport_out_lemonade_no_abund_use_abund(runtmp):
  function test_metagenome_kreport_out_fail (line 1110) | def test_metagenome_kreport_out_fail(runtmp):
  function test_metagenome_bioboxes_stdout (line 1145) | def test_metagenome_bioboxes_stdout(runtmp):
  function test_metagenome_bioboxes_outfile (line 1238) | def test_metagenome_bioboxes_outfile(runtmp):
  function test_metagenome_bioboxes_stdout_missing_ranktaxinfo (line 1283) | def test_metagenome_bioboxes_stdout_missing_ranktaxinfo(runtmp):
  function test_metagenome_krona_tsv_out (line 1399) | def test_metagenome_krona_tsv_out(runtmp):
  function test_metagenome_lineage_summary_out (line 1484) | def test_metagenome_lineage_summary_out(runtmp):
  function test_metagenome_human_format_out (line 1538) | def test_metagenome_human_format_out(runtmp):
  function test_metagenome_human_format_out_default_v5 (line 1595) | def test_metagenome_human_format_out_default_v5(runtmp, cli_v4_and_v5):
  function test_metagenome_human_format_out_default_v5_simple (line 1657) | def test_metagenome_human_format_out_default_v5_simple(runtmp, cli_v5_on...
  function test_metagenome_no_taxonomy_fail (line 1706) | def test_metagenome_no_taxonomy_fail(runtmp):
  function test_metagenome_no_rank_lineage_summary (line 1717) | def test_metagenome_no_rank_lineage_summary(runtmp):
  function test_metagenome_no_rank_krona (line 1742) | def test_metagenome_no_rank_krona(runtmp):
  function test_metagenome_bad_rank_krona (line 1767) | def test_metagenome_bad_rank_krona(runtmp):
  function test_metagenome_ictv (line 1815) | def test_metagenome_ictv(runtmp):
  function test_genome_no_rank_krona (line 1940) | def test_genome_no_rank_krona(runtmp):
  function test_metagenome_rank_not_available (line 1961) | def test_metagenome_rank_not_available(runtmp):
  function test_metagenome_duplicated_taxonomy_fail (line 1981) | def test_metagenome_duplicated_taxonomy_fail(runtmp):
  function test_metagenome_duplicated_taxonomy_force (line 2002) | def test_metagenome_duplicated_taxonomy_force(runtmp, cli_v4_and_v5):
  function test_metagenome_missing_taxonomy (line 2062) | def test_metagenome_missing_taxonomy(runtmp, cli_v4_and_v5):
  function test_metagenome_missing_fail_taxonomy (line 2127) | def test_metagenome_missing_fail_taxonomy(runtmp):
  function test_metagenome_multiple_taxonomy_files_missing (line 2156) | def test_metagenome_multiple_taxonomy_files_missing(runtmp, cli_v4_and_v5):
  function test_metagenome_multiple_taxonomy_files (line 2225) | def test_metagenome_multiple_taxonomy_files(runtmp, cli_v4_and_v5):
  function test_metagenome_multiple_taxonomy_files_multiple_taxonomy_args (line 2293) | def test_metagenome_multiple_taxonomy_files_multiple_taxonomy_args(runtmp):
  function test_metagenome_multiple_taxonomy_files_multiple_taxonomy_args_empty_force (line 2357) | def test_metagenome_multiple_taxonomy_files_multiple_taxonomy_args_empty...
  function test_metagenome_empty_gather_results (line 2440) | def test_metagenome_empty_gather_results(runtmp):
  function test_metagenome_bad_gather_header (line 2458) | def test_metagenome_bad_gather_header(runtmp):
  function test_metagenome_empty_tax_lineage_input (line 2481) | def test_metagenome_empty_tax_lineage_input(runtmp):
  function test_metagenome_empty_tax_lineage_input_force (line 2503) | def test_metagenome_empty_tax_lineage_input_force(runtmp):
  function test_metagenome_perfect_match_warning (line 2525) | def test_metagenome_perfect_match_warning(runtmp):
  function test_metagenome_over100percent_error (line 2562) | def test_metagenome_over100percent_error(runtmp):
  function test_metagenome_gather_duplicate_query (line 2599) | def test_metagenome_gather_duplicate_query(runtmp):
  function test_metagenome_gather_duplicate_query_force (line 2628) | def test_metagenome_gather_duplicate_query_force(runtmp):
  function test_metagenome_two_queries_human_output (line 2661) | def test_metagenome_two_queries_human_output(runtmp):
  function test_metagenome_two_queries_csv_summary_output (line 2705) | def test_metagenome_two_queries_csv_summary_output(runtmp, cli_v4_only):
  function test_metagenome_two_queries_csv_summary_output_v5 (line 2839) | def test_metagenome_two_queries_csv_summary_output_v5(runtmp, cli_v5_only):
  function test_metagenome_two_queries_with_single_query_output_formats_fail (line 2974) | def test_metagenome_two_queries_with_single_query_output_formats_fail(ru...
  function test_metagenome_two_queries_skip_single_query_output_formats (line 3022) | def test_metagenome_two_queries_skip_single_query_output_formats(runtmp):
  function test_metagenome_two_queries_krona (line 3093) | def test_metagenome_two_queries_krona(runtmp):
  function test_metagenome_gather_duplicate_filename (line 3138) | def test_metagenome_gather_duplicate_filename(runtmp, cli_v4_and_v5):
  function test_metagenome_gather_duplicate_filename_2 (line 3177) | def test_metagenome_gather_duplicate_filename_2(runtmp, cli_v4_and_v5):
  function test_metagenome_gather_duplicate_filename_from_file (line 3216) | def test_metagenome_gather_duplicate_filename_from_file(runtmp, cli_v4_a...
  function test_genome_empty_gather_results (line 3256) | def test_genome_empty_gather_results(runtmp):
  function test_genome_bad_gather_header (line 3276) | def test_genome_bad_gather_header(runtmp):
  function test_genome_empty_tax_lineage_input (line 3298) | def test_genome_empty_tax_lineage_input(runtmp):
  function test_genome_rank_stdout_0 (line 3318) | def test_genome_rank_stdout_0(runtmp):
  function test_genome_rank_stdout_0_db (line 3353) | def test_genome_rank_stdout_0_db(runtmp):
  function test_genome_rank_csv_0 (line 3412) | def test_genome_rank_csv_0(runtmp):
  function test_genome_rank_krona (line 3458) | def test_genome_rank_krona(runtmp):
  function test_genome_rank_human_output (line 3519) | def test_genome_rank_human_output(runtmp):
  function test_genome_rank_lineage_csv_output (line 3571) | def test_genome_rank_lineage_csv_output(runtmp):
  function test_genome_gather_from_file_rank (line 3620) | def test_genome_gather_from_file_rank(runtmp):
  function test_genome_gather_two_files (line 3656) | def test_genome_gather_two_files(runtmp):
  function test_genome_gather_two_files_empty_force (line 3702) | def test_genome_gather_two_files_empty_force(runtmp):
  function test_genome_gather_two_files_one_classif_fail (line 3757) | def test_genome_gather_two_files_one_classif_fail(runtmp):
  function test_genome_gather_two_files_one_classif (line 3812) | def test_genome_gather_two_files_one_classif(runtmp):
  function test_genome_gather_duplicate_filename (line 3866) | def test_genome_gather_duplicate_filename(runtmp):
  function test_genome_gather_from_file_duplicate_filename (line 3902) | def test_genome_gather_from_file_duplicate_filename(runtmp):
  function test_genome_gather_from_file_duplicate_query (line 3940) | def test_genome_gather_from_file_duplicate_query(runtmp):
  function test_genome_gather_from_file_duplicate_query_force (line 3976) | def test_genome_gather_from_file_duplicate_query_force(runtmp):
  function test_genome_gather_cli_and_from_file (line 4016) | def test_genome_gather_cli_and_from_file(runtmp):
  function test_genome_gather_cli_and_from_file_duplicate_filename (line 4069) | def test_genome_gather_cli_and_from_file_duplicate_filename(runtmp):
  function test_genome_gather_from_file_below_threshold (line 4111) | def test_genome_gather_from_file_below_threshold(runtmp):
  function test_genome_gather_two_queries (line 4141) | def test_genome_gather_two_queries(runtmp):
  function test_genome_gather_ictv (line 4188) | def test_genome_gather_ictv(runtmp, cli_v4_and_v5):
  function test_genome_gather_ictv_twoqueries (line 4225) | def test_genome_gather_ictv_twoqueries(runtmp):
  function test_genome_gather_ictv_fail (line 4272) | def test_genome_gather_ictv_fail(runtmp):
  function test_genome_rank_duplicated_taxonomy_fail (line 4309) | def test_genome_rank_duplicated_taxonomy_fail(runtmp):
  function test_genome_rank_duplicated_taxonomy_fail_lineages (line 4336) | def test_genome_rank_duplicated_taxonomy_fail_lineages(runtmp):
  function test_genome_rank_duplicated_taxonomy_force (line 4368) | def test_genome_rank_duplicated_taxonomy_force(runtmp):
  function test_genome_missing_taxonomy_ignore_threshold (line 4409) | def test_genome_missing_taxonomy_ignore_threshold(runtmp):
  function test_genome_missing_taxonomy_recover_with_second_tax_file (line 4450) | def test_genome_missing_taxonomy_recover_with_second_tax_file(runtmp):
  function test_genome_missing_taxonomy_ignore_rank (line 4493) | def test_genome_missing_taxonomy_ignore_rank(runtmp):
  function test_genome_multiple_taxonomy_files (line 4527) | def test_genome_multiple_taxonomy_files(runtmp):
  function test_genome_multiple_taxonomy_files_empty_force (line 4583) | def test_genome_multiple_taxonomy_files_empty_force(runtmp):
  function test_genome_missing_taxonomy_fail_threshold (line 4633) | def test_genome_missing_taxonomy_fail_threshold(runtmp):
  function test_genome_missing_taxonomy_fail_rank (line 4668) | def test_genome_missing_taxonomy_fail_rank(runtmp):
  function test_genome_rank_not_available (line 4703) | def test_genome_rank_not_available(runtmp):
  function test_genome_empty_gather_results_with_header_single (line 4735) | def test_genome_empty_gather_results_with_header_single(runtmp):
  function test_genome_empty_gather_results_single (line 4768) | def test_genome_empty_gather_results_single(runtmp):
  function test_genome_empty_gather_results_single_force (line 4791) | def test_genome_empty_gather_results_single_force(runtmp):
  function test_genome_empty_gather_results_with_empty_csv_force (line 4818) | def test_genome_empty_gather_results_with_empty_csv_force(runtmp):
  function test_genome_empty_gather_results_with_csv_force (line 4859) | def test_genome_empty_gather_results_with_csv_force(runtmp):
  function test_genome_containment_threshold_bounds (line 4909) | def test_genome_containment_threshold_bounds(runtmp):
  function test_genome_containment_threshold_type (line 4951) | def test_genome_containment_threshold_type(runtmp):
  function test_genome_over100percent_error (line 4975) | def test_genome_over100percent_error(runtmp):
  function test_genome_ani_threshold_input_errors (line 5009) | def test_genome_ani_threshold_input_errors(runtmp):
  function test_genome_ani_threshold (line 5070) | def test_genome_ani_threshold(runtmp):
  function test_genome_ani_oldgather (line 5130) | def test_genome_ani_oldgather(runtmp):
  function test_genome_ani_lemonade_classify (line 5145) | def test_genome_ani_lemonade_classify(runtmp):
  function test_genome_ani_lemonade_classify_estimate_ani_ci (line 5213) | def test_genome_ani_lemonade_classify_estimate_ani_ci(runtmp):
  function test_metagenome_no_gather_csv (line 5289) | def test_metagenome_no_gather_csv(runtmp):
  function test_genome_no_gather_csv (line 5300) | def test_genome_no_gather_csv(runtmp):
  function test_annotate_no_gather_csv (line 5311) | def test_annotate_no_gather_csv(runtmp):
  function test_genome_LIN (line 5322) | def test_genome_LIN(runtmp):
  function test_genome_LIN_lingroups (line 5400) | def test_genome_LIN_lingroups(runtmp):
  function test_annotate_0 (line 5473) | def test_annotate_0(runtmp):
  function test_annotate_gzipped_gather (line 5516) | def test_annotate_gzipped_gather(runtmp):
  function test_annotate_0_ictv (line 5571) | def test_annotate_0_ictv(runtmp):
  function test_annotate_0_LIN (line 5622) | def test_annotate_0_LIN(runtmp):
  function test_annotate_gather_argparse (line 5661) | def test_annotate_gather_argparse(runtmp):
  function test_annotate_0_db (line 5708) | def test_annotate_0_db(runtmp):
  function test_annotate_empty_gather_results (line 5750) | def test_annotate_empty_gather_results(runtmp):
  function test_annotate_prefetch_or_other_header (line 5766) | def test_annotate_prefetch_or_other_header(runtmp):
  function test_annotate_bad_header (line 5792) | def test_annotate_bad_header(runtmp):
  function test_annotate_no_tax_matches (line 5818) | def test_annotate_no_tax_matches(runtmp):
  function test_annotate_missed_tax_matches (line 5853) | def test_annotate_missed_tax_matches(runtmp):
  function test_annotate_empty_tax_lineage_input (line 5876) | def test_annotate_empty_tax_lineage_input(runtmp):
  function test_annotate_empty_tax_lineage_input_recover_with_second_taxfile (line 5895) | def test_annotate_empty_tax_lineage_input_recover_with_second_taxfile(ru...
  function test_annotate_empty_tax_lineage_input_recover_with_second_taxfile_2 (line 5923) | def test_annotate_empty_tax_lineage_input_recover_with_second_taxfile_2(...
  function test_tax_prepare_1_csv_to_csv (line 5952) | def test_tax_prepare_1_csv_to_csv(runtmp, keep_identifiers, keep_versions):
  function test_tax_prepare_1_combine_csv (line 5985) | def test_tax_prepare_1_combine_csv(runtmp):
  function test_tax_prepare_1_csv_to_csv_empty_ranks (line 6004) | def test_tax_prepare_1_csv_to_csv_empty_ranks(runtmp, keep_identifiers, ...
  function test_tax_prepare_1_csv_to_csv_empty_file (line 6037) | def test_tax_prepare_1_csv_to_csv_empty_file(runtmp, keep_identifiers, k...
  function test_tax_prepare_1_csv_to_csv_empty_ranks_2 (line 6089) | def test_tax_prepare_1_csv_to_csv_empty_ranks_2(
  function test_tax_prepare_1_csv_to_csv_empty_ranks_3 (line 6124) | def test_tax_prepare_1_csv_to_csv_empty_ranks_3(
  function test_tax_prepare_2_csv_to_sql (line 6159) | def test_tax_prepare_2_csv_to_sql(runtmp, keep_identifiers, keep_versions):
  function test_tax_prepare_2_csv_to_sql_empty_ranks (line 6198) | def test_tax_prepare_2_csv_to_sql_empty_ranks(runtmp, keep_identifiers, ...
  function test_tax_prepare_3_db_to_csv (line 6230) | def test_tax_prepare_3_db_to_csv(runtmp):
  function test_tax_prepare_3_db_to_csv_gz (line 6253) | def test_tax_prepare_3_db_to_csv_gz(runtmp):
  function test_tax_prepare_2_csv_to_sql_empty_ranks_2 (line 6276) | def test_tax_prepare_2_csv_to_sql_empty_ranks_2(
  function test_tax_prepare_2_csv_to_sql_empty_ranks_3 (line 6310) | def test_tax_prepare_2_csv_to_sql_empty_ranks_3(
  function test_tax_prepare_3_db_to_csv_empty_ranks (line 6344) | def test_tax_prepare_3_db_to_csv_empty_ranks(runtmp):
  function test_tax_prepare_3_db_to_csv_empty_ranks_2 (line 6367) | def test_tax_prepare_3_db_to_csv_empty_ranks_2(runtmp):
  function test_tax_prepare_3_db_to_csv_empty_ranks_3 (line 6390) | def test_tax_prepare_3_db_to_csv_empty_ranks_3(runtmp):
  function test_tax_prepare_sqlite_lineage_version (line 6413) | def test_tax_prepare_sqlite_lineage_version(runtmp):
  function test_tax_prepare_sqlite_no_lineage (line 6433) | def test_tax_prepare_sqlite_no_lineage():
  function test_tax_grep_exists (line 6441) | def test_tax_grep_exists(runtmp):
  function test_tax_grep_search_shew (line 6451) | def test_tax_grep_search_shew(runtmp):
  function test_tax_grep_search_shew_out (line 6471) | def test_tax_grep_search_shew_out(runtmp):
  function test_tax_grep_search_shew_sqldb_out (line 6491) | def test_tax_grep_search_shew_sqldb_out(runtmp):
  function test_tax_grep_search_shew_lowercase (line 6511) | def test_tax_grep_search_shew_lowercase(runtmp):
  function test_tax_grep_search_shew_out_use_picklist (line 6536) | def test_tax_grep_search_shew_out_use_picklist(runtmp):
  function test_tax_grep_search_shew_invert (line 6559) | def test_tax_grep_search_shew_invert(runtmp):
  function test_tax_grep_search_shew_invert_select_phylum (line 6587) | def test_tax_grep_search_shew_invert_select_phylum(runtmp):
  function test_tax_grep_search_shew_invert_select_bad_rank (line 6614) | def test_tax_grep_search_shew_invert_select_bad_rank(runtmp):
  function test_tax_grep_search_shew_count (line 6627) | def test_tax_grep_search_shew_count(runtmp):
  function test_tax_grep_multiple_csv (line 6642) | def test_tax_grep_multiple_csv(runtmp):
  function test_tax_grep_multiple_csv_empty_force (line 6667) | def test_tax_grep_multiple_csv_empty_force(runtmp):
  function test_tax_grep_duplicate_csv (line 6708) | def test_tax_grep_duplicate_csv(runtmp):
  function test_tax_summarize (line 6731) | def test_tax_summarize(runtmp):
  function test_tax_summarize_multiple (line 6749) | def test_tax_summarize_multiple(runtmp):
  function test_tax_summarize_empty_line (line 6768) | def test_tax_summarize_empty_line(runtmp):
  function test_tax_summarize_empty (line 6786) | def test_tax_summarize_empty(runtmp):
  function test_tax_summarize_csv (line 6797) | def test_tax_summarize_csv(runtmp):
  function test_tax_summarize_on_annotate (line 6823) | def test_tax_summarize_on_annotate(runtmp):
  function test_tax_summarize_strain_csv (line 6860) | def test_tax_summarize_strain_csv(runtmp):
  function test_tax_summarize_strain_csv_with_lineages (line 6890) | def test_tax_summarize_strain_csv_with_lineages(runtmp):
  function test_tax_summarize_ictv (line 6929) | def test_tax_summarize_ictv(runtmp):
  function test_tax_summarize_LINS (line 6967) | def test_tax_summarize_LINS(runtmp):
  function test_metagenome_LIN (line 7011) | def test_metagenome_LIN(runtmp, cli_v4_and_v5):
  function test_metagenome_LIN_lingroups (line 7088) | def test_metagenome_LIN_lingroups(runtmp):
  function test_metagenome_LIN_lingroups_summary (line 7137) | def test_metagenome_LIN_lingroups_summary(runtmp):
  function test_metagenome_LIN_human_summary_no_lin_position (line 7223) | def test_metagenome_LIN_human_summary_no_lin_position(runtmp):
  function test_metagenome_LIN_human_summary_lin_position_5 (line 7259) | def test_metagenome_LIN_human_summary_lin_position_5(runtmp):
  function test_metagenome_LIN_krona_lin_position_5 (line 7293) | def test_metagenome_LIN_krona_lin_position_5(runtmp):
  function test_metagenome_LIN_krona_bad_rank (line 7329) | def test_metagenome_LIN_krona_bad_rank(runtmp):
  function test_metagenome_LIN_lingroups_empty_lg_file (line 7361) | def test_metagenome_LIN_lingroups_empty_lg_file(runtmp):
  function test_metagenome_LIN_lingroups_bad_cli_inputs (line 7394) | def test_metagenome_LIN_lingroups_bad_cli_inputs(runtmp):
  function test_metagenome_mult_outputs_stdout_fail (line 7472) | def test_metagenome_mult_outputs_stdout_fail(runtmp):
  function test_genome_mult_outputs_stdout_fail (line 7499) | def test_genome_mult_outputs_stdout_fail(runtmp):
  function test_metagenome_LIN_lingroups_lg_only_header (line 7526) | def test_metagenome_LIN_lingroups_lg_only_header(runtmp):
  function test_metagenome_abund_reporting_default (line 7557) | def test_metagenome_abund_reporting_default(runtmp, cli_v4_and_v5):
  function test_metagenome_abund_reporting_no_abund_fail_v4 (line 7643) | def test_metagenome_abund_reporting_no_abund_fail_v4(runtmp, cli_v4_only):
  function test_metagenome_abund_reporting_no_abund_fail_v5 (line 7678) | def test_metagenome_abund_reporting_no_abund_fail_v5(runtmp, cli_v5_only):
  function test_metagenome_abund_reporting_use_abund (line 7714) | def test_metagenome_abund_reporting_use_abund(runtmp, cli_v4_and_v5):
  function test_metagenome_abund_reporting_ignore_abund (line 7786) | def test_metagenome_abund_reporting_ignore_abund(runtmp, cli_v4_and_v5):
  function test_metagenome_abund_reporting_use_abund_fail (line 7856) | def test_metagenome_abund_reporting_use_abund_fail(runtmp, cli_v4_and_v5):
  function test_metagenome_abund_reporting_ignore_abund (line 7890) | def test_metagenome_abund_reporting_ignore_abund(runtmp, cli_v4_and_v5):
  function test_metagenome_abund_reporting_ignore_abund_pass (line 7960) | def test_metagenome_abund_reporting_ignore_abund_pass(runtmp, cli_v4_and...

FILE: tests/test_tax_utils.py
  function make_mini_taxonomy (line 48) | def make_mini_taxonomy(tax_info, LIN=False):
  function make_mini_taxonomy_with_taxids (line 60) | def make_mini_taxonomy_with_taxids(tax_info, LIN=False):
  function make_GatherRow (line 80) | def make_GatherRow(gather_dict=None, exclude_cols=[]):
  function make_TaxResult (line 105) | def make_TaxResult(
  function make_QueryTaxResults (line 126) | def make_QueryTaxResults(
  function test_ascending_taxlist_1 (line 182) | def test_ascending_taxlist_1():
  function test_ascending_taxlist_2 (line 195) | def test_ascending_taxlist_2():
  function test_QueryInfo_basic (line 207) | def test_QueryInfo_basic():
  function test_QueryInfo_no_hash_info (line 227) | def test_QueryInfo_no_hash_info():
  function test_QueryInfo_missing (line 243) | def test_QueryInfo_missing():
  function test_SummarizedGatherResult (line 259) | def test_SummarizedGatherResult():
  function test_SummarizedGatherResult_withtaxids (line 337) | def test_SummarizedGatherResult_withtaxids():
  function test_SummarizedGatherResult_LINs (line 419) | def test_SummarizedGatherResult_LINs():
  function test_SummarizedGatherResult_set_query_ani (line 465) | def test_SummarizedGatherResult_set_query_ani():
  function test_SummarizedGatherResult_greater_than_1 (line 531) | def test_SummarizedGatherResult_greater_than_1():
  function test_SummarizedGatherResult_0_fraction (line 557) | def test_SummarizedGatherResult_0_fraction():
  function test_SummarizedGatherResult_species_kreport (line 582) | def test_SummarizedGatherResult_species_kreport():
  function test_SummarizedGatherResult_summary_dict_limit_float (line 615) | def test_SummarizedGatherResult_summary_dict_limit_float():
  function test_ClassificationResult (line 667) | def test_ClassificationResult():
  function test_ClassificationResult_greater_than_1 (line 708) | def test_ClassificationResult_greater_than_1():
  function test_ClassificationResult_0_fraction (line 734) | def test_ClassificationResult_0_fraction():
  function test_ClassificationResult_build_krona_result (line 759) | def test_ClassificationResult_build_krona_result():
  function test_ClassificationResult_build_krona_result_no_rank (line 786) | def test_ClassificationResult_build_krona_result_no_rank():
  function test_GatherRow_old_gather (line 808) | def test_GatherRow_old_gather():
  function test_GatherRow_match_name_not_name (line 817) | def test_GatherRow_match_name_not_name():
  function test_GatherRow_extra_cols (line 825) | def test_GatherRow_extra_cols():
  function test_get_ident_default (line 832) | def test_get_ident_default():
  function test_TaxResult_get_ident_default (line 838) | def test_TaxResult_get_ident_default():
  function test_AnnotateTaxResult_get_ident_default (line 845) | def test_AnnotateTaxResult_get_ident_default():
  function test_AnnotateTaxResult_get_ident_idcol (line 852) | def test_AnnotateTaxResult_get_ident_idcol():
  function test_AnnotateTaxResult_get_ident_idcol_fail (line 873) | def test_AnnotateTaxResult_get_ident_idcol_fail():
  function test_get_ident_split_but_keep_version (line 886) | def test_get_ident_split_but_keep_version():
  function test_TaxResult_get_ident_split_but_keep_version (line 892) | def test_TaxResult_get_ident_split_but_keep_version():
  function test_AnnotateTaxResult_get_ident_split_but_keep_version (line 902) | def test_AnnotateTaxResult_get_ident_split_but_keep_version():
  function test_get_ident_no_split (line 912) | def test_get_ident_no_split():
  function test_TaxResult_get_ident_keep_full (line 918) | def test_TaxResult_get_ident_keep_full():
  function test_AnnotateTaxResult_get_ident_keep_full (line 928) | def test_AnnotateTaxResult_get_ident_keep_full():
  function test_collect_gather_csvs (line 938) | def test_collect_gather_csvs(runtmp):
  function test_check_and_load_gather_csvs_empty (line 950) | def test_check_and_load_gather_csvs_empty(runtmp):
  function test_check_and_load_gather_csvs_with_empty_force (line 966) | def test_check_and_load_gather_csvs_with_empty_force(runtmp):
  function test_check_and_load_gather_lineage_csvs_empty (line 999) | def test_check_and_load_gather_lineage_csvs_empty(runtmp):
  function test_check_and_load_gather_lineage_csvs_bad_header (line 1010) | def test_check_and_load_gather_lineage_csvs_bad_header(runtmp):
  function test_check_and_load_gather_lineage_csvs_dne (line 1024) | def test_check_and_load_gather_lineage_csvs_dne(runtmp):
  function test_check_and_load_gather_lineage_csvs_isdir (line 1033) | def test_check_and_load_gather_lineage_csvs_isdir(runtmp):
  function test_check_and_load_gather_lineage_csvs_name (line 1043) | def test_check_and_load_gather_lineage_csvs_name(runtmp):
  function test_check_and_load_gather_lineage_csvs_match_name (line 1051) | def test_check_and_load_gather_lineage_csvs_match_name(runtmp):
  function test_check_and_load_gather_csvs_fail_on_missing (line 1066) | def test_check_and_load_gather_csvs_fail_on_missing(runtmp):
  function test_load_gather_results (line 1091) | def test_load_gather_results():
  function test_load_gather_results_gzipped (line 1104) | def test_load_gather_results_gzipped(runtmp):
  function test_load_gather_results_bad_header (line 1124) | def test_load_gather_results_bad_header(runtmp):
  function test_load_gather_results_empty (line 1152) | def test_load_gather_results_empty(runtmp):
  function test_load_taxonomy_csv (line 1172) | def test_load_taxonomy_csv():
  function test_load_taxonomy_csv_LIN (line 1187) | def test_load_taxonomy_csv_LIN():
  function test_load_taxonomy_csv_LIN_fail (line 1205) | def test_load_taxonomy_csv_LIN_fail():
  function test_load_taxonomy_csv_LIN_mismatch_in_taxfile (line 1215) | def test_load_taxonomy_csv_LIN_mismatch_in_taxfile(runtmp):
  function test_load_taxonomy_csv_gzip (line 1237) | def test_load_taxonomy_csv_gzip(runtmp):
  function test_load_taxonomy_csv_split_id (line 1260) | def test_load_taxonomy_csv_split_id():
  function test_load_taxonomy_csv_with_ncbi_id (line 1277) | def test_load_taxonomy_csv_with_ncbi_id(runtmp):
  function test_load_taxonomy_csv_split_id_ncbi (line 1302) | def test_load_taxonomy_csv_split_id_ncbi(runtmp):
  function test_load_taxonomy_csv_duplicate (line 1335) | def test_load_taxonomy_csv_duplicate(runtmp):
  function test_load_taxonomy_csv_duplicate_force (line 1351) | def test_load_taxonomy_csv_duplicate_force(runtmp):
  function test_format_for_krona_summarization (line 1373) | def test_format_for_krona_summarization():
  function test_format_for_krona_classification (line 1413) | def test_format_for_krona_classification():
  function test_format_for_krona_improper_rank (line 1449) | def test_format_for_krona_improper_rank():
  function test_format_for_krona_summarization_two_queries (line 1482) | def test_format_for_krona_summarization_two_queries():
  function test_write_krona (line 1530) | def test_write_krona(runtmp):
  function test_write_lineage_sample_frac (line 1545) | def test_write_lineage_sample_frac(runtmp):
  function test_write_lineage_sample_frac_format_lineage (line 1569) | def test_write_lineage_sample_frac_format_lineage(runtmp):
  function test_tax_multi_load_files (line 1599) | def test_tax_multi_load_files(runtmp):
  function test_tax_sql_load_new_file (line 1631) | def test_tax_sql_load_new_file(runtmp):
  function test_tax_multi_load_files_shadowed (line 1642) | def test_tax_multi_load_files_shadowed(runtmp):
  function test_tax_multi_save_files (line 1667) | def test_tax_multi_save_files(runtmp, keep_identifiers, keep_versions):
  function test_lineage_db_csv_load (line 1730) | def test_lineage_db_csv_load(runtmp):
  function test_lineage_db_sql_load (line 1768) | def test_lineage_db_sql_load(runtmp):
  function test_LineagePair (line 1795) | def test_LineagePair():
  function test_LineagePair_1 (line 1803) | def test_LineagePair_1():
  function test_BaseLineageInfo_init_empty (line 1811) | def test_BaseLineageInfo_init_empty():
  function test_BaseLineageInfo_init_lineage_str (line 1832) | def test_BaseLineageInfo_init_lineage_str():
  function test_BaseLineageInfo_init_lineage_str_comma_sep (line 1850) | def test_BaseLineageInfo_init_lineage_str_comma_sep():
  function test_BaseLineageInfo_init_lineage_tups (line 1861) | def test_BaseLineageInfo_init_lineage_tups():
  function test_BaseLineageInfo_init_lca_lineage_tups (line 1870) | def test_BaseLineageInfo_init_lca_lineage_tups():
  function test_BaseLineageInfo_init_no_ranks (line 1879) | def test_BaseLineageInfo_init_no_ranks():
  function test_BaseLineageInfo_init_with_wrong_ranks (line 1895) | def test_BaseLineageInfo_init_with_wrong_ranks():
  function test_BaseLineageInfo_init_not_lineagepair (line 1904) | def test_BaseLineageInfo_init_not_lineagepair():
  function test_RankLineageInfo_taxlist (line 1913) | def test_RankLineageInfo_taxlist():
  function test_RankLineageInfo_init_lineage_str (line 1929) | def test_RankLineageInfo_init_lineage_str():
  function test_LINLineageInfo_init_empty (line 1937) | def test_LINLineageInfo_init_empty():
  function test_LINLineageInfo_init_n_pos (line 1946) | def test_LINLineageInfo_init_n_pos():
  function test_LINLineageInfo_init_n_pos_and_lineage_str (line 1957) | def test_LINLineageInfo_init_n_pos_and_lineage_str():
  function test_LINLineageInfo_init_n_pos_and_lineage_str_fail (line 1969) | def test_LINLineageInfo_init_n_pos_and_lineage_str_fail():
  function test_LINLineageInfo_init_lineage_str_only (line 1981) | def test_LINLineageInfo_init_lineage_str_only():
  function test_LINLineageInfo_init_not_lineagepair (line 1992) | def test_LINLineageInfo_init_not_lineagepair():
  function test_LINLineageInfo_init_lineagepair (line 2000) | def test_LINLineageInfo_init_lineagepair():
  function test_lca_LINLineageInfo_diff_n_pos (line 2015) | def test_lca_LINLineageInfo_diff_n_pos():
  function test_lca_LINLineageInfo_no_lca (line 2028) | def test_lca_LINLineageInfo_no_lca():
  function test_lca_RankLineageInfo_no_lca (line 2040) | def test_lca_RankLineageInfo_no_lca():
  function test_ICTVLineageInfo_ranks_input_ignored (line 2052) | def test_ICTVLineageInfo_ranks_input_ignored():
  function test_ICTVLineageInfo_lineagedict_input (line 2058) | def test_ICTVLineageInfo_lineagedict_input():
  function test_incompatibility_LINLineageInfo_RankLineageInfo (line 2068) | def test_incompatibility_LINLineageInfo_RankLineageInfo():
  function test_RankLineageInfo_init_lineage_str_with_ranks_as_list (line 2076) | def test_RankLineageInfo_init_lineage_str_with_ranks_as_list():
  function test_RankLineageInfo_init_lineage_tups (line 2093) | def test_RankLineageInfo_init_lineage_tups():
  function test_RankLineageInfo_init_lineage_dict_fail (line 2104) | def test_RankLineageInfo_init_lineage_dict_fail():
  function test_RankLineageInfo_init_lineage_dict (line 2114) | def test_RankLineageInfo_init_lineage_dict():
  function test_RankLineageInfo_init_lineage_dict_default_ranks (line 2123) | def test_RankLineageInfo_init_lineage_dict_default_ranks():
  function test_RankLineageInfo_init_lineage_dict_withtaxpath (line 2131) | def test_RankLineageInfo_init_lineage_dict_withtaxpath():
  function test_RankLineageInfo_init_lineage_str_lineage_dict_test_eq (line 2144) | def test_RankLineageInfo_init_lineage_str_lineage_dict_test_eq():
  function test_RankLineageInfo_init_lineage_dict_missing_rank (line 2153) | def test_RankLineageInfo_init_lineage_dict_missing_rank():
  function test_RankLineageInfo_init_lineage_dict_missing_rank_with_taxpath (line 2163) | def test_RankLineageInfo_init_lineage_dict_missing_rank_with_taxpath():
  function test_RankLineageInfo_init_lineage_dict_name_taxpath_mismatch (line 2173) | def test_RankLineageInfo_init_lineage_dict_name_taxpath_mismatch():
  function test_RankLineageInfo_init_lineage_dict_name_taxpath_missing_taxids (line 2185) | def test_RankLineageInfo_init_lineage_dict_name_taxpath_missing_taxids():
  function test_RankLineageInfo_init_lineage_dict_taxpath_too_long (line 2198) | def test_RankLineageInfo_init_lineage_dict_taxpath_too_long():
  function test_RankLineageInfo_init_lineage_str_lineage_dict_test_eq (line 2206) | def test_RankLineageInfo_init_lineage_str_lineage_dict_test_eq():
  function test_RankLineageInfo_init_lineage_str_1_truncate (line 2216) | def test_RankLineageInfo_init_lineage_str_1_truncate():
  function test_RankLineageInfo_init_lineage_str_2 (line 2224) | def test_RankLineageInfo_init_lineage_str_2():
  function test_RankLineageInfo_init_lineage_str_2_truncate (line 2232) | def test_RankLineageInfo_init_lineage_str_2_truncate():
  function test_RankLineageInfo_init_lineage_with_incorrect_rank (line 2240) | def test_RankLineageInfo_init_lineage_with_incorrect_rank():
  function test_zip_lineage_1 (line 2252) | def test_zip_lineage_1():
  function test_zip_lineage_2 (line 2260) | def test_zip_lineage_2():
  function test_zip_lineage_3 (line 2268) | def test_zip_lineage_3():
  function test_zip_lineage_3_truncate (line 2278) | def test_zip_lineage_3_truncate():
  function test_zip_lineage_4 (line 2288) | def test_zip_lineage_4():
  function test_display_lineage_1 (line 2294) | def test_display_lineage_1():
  function test_display_lineage_2 (line 2300) | def test_display_lineage_2():
  function test_display_taxid_1 (line 2310) | def test_display_taxid_1():
  function test_display_taxid_2 (line 2317) | def test_display_taxid_2():
  function test_is_lineage_match_1 (line 2328) | def test_is_lineage_match_1():
  function test_is_lineage_match_2 (line 2357) | def test_is_lineage_match_2():
  function test_is_lineage_match_3 (line 2385) | def test_is_lineage_match_3():
  function test_is_lineage_match_incorrect_ranks (line 2407) | def test_is_lineage_match_incorrect_ranks():
  function test_is_lineage_match_improper_rank (line 2429) | def test_is_lineage_match_improper_rank():
  function test_pop_to_rank_1 (line 2441) | def test_pop_to_rank_1():
  function test_pop_to_rank_2 (line 2452) | def test_pop_to_rank_2():
  function test_pop_to_rank_rank_not_avail (line 2459) | def test_pop_to_rank_rank_not_avail():
  function test_lineage_at_rank_norank (line 2467) | def test_lineage_at_rank_norank():
  function test_lineage_at_rank_rank_not_avail (line 2477) | def test_lineage_at_rank_rank_not_avail():
  function test_lineage_at_rank_1 (line 2485) | def test_lineage_at_rank_1():
  function test_lineage_at_rank_below_rank (line 2500) | def test_lineage_at_rank_below_rank():
  function test_TaxResult_get_match_lineage_1 (line 2515) | def test_TaxResult_get_match_lineage_1():
  function test_AnnotateTaxResult_get_match_lineage_1 (line 2525) | def test_AnnotateTaxResult_get_match_lineage_1():
  function test_TaxResult_get_match_lineage_skip_ident (line 2536) | def test_TaxResult_get_match_lineage_skip_ident():
  function test_TaxResult_get_match_lineage_missed_ident_fail_on_missing (line 2553) | def test_TaxResult_get_match_lineage_missed_ident_fail_on_missing():
  function test_TaxResult_get_match_lineage_missed_ident_fail_on_missing (line 2571) | def test_TaxResult_get_match_lineage_missed_ident_fail_on_missing():
  function test_QueryTaxResult (line 2585) | def test_QueryTaxResult():
  function test_QueryTaxResult_add_incompatible (line 2618) | def test_QueryTaxResult_add_incompatible():
  function test_QueryTaxResult_add_without_tax_info (line 2636) | def test_QueryTaxResult_add_without_tax_info():
  function test_QueryTaxResult_add_skipped_ident (line 2651) | def test_QueryTaxResult_add_skipped_ident():
  function test_QueryTaxResult_add_missed_ident (line 2666) | def test_QueryTaxResult_add_missed_ident():
  function test_QueryTaxResult_track_missed_and_skipped (line 2681) | def test_QueryTaxResult_track_missed_and_skipped():
  function test_QueryTaxResult_track_missed_and_skipped_using_fn (line 2713) | def test_QueryTaxResult_track_missed_and_skipped_using_fn():
  function test_QueryTaxResult_summarize_up_ranks_1 (line 2741) | def test_QueryTaxResult_summarize_up_ranks_1():
  function test_QueryTaxResult_summarize_up_ranks_2 (line 2782) | def test_QueryTaxResult_summarize_up_ranks_2():
  function test_QueryTaxResult_summarize_up_ranks_missing_lineage (line 2830) | def test_QueryTaxResult_summarize_up_ranks_missing_lineage():
  function test_QueryTaxResult_summarize_up_ranks_skipped_lineage (line 2865) | def test_QueryTaxResult_summarize_up_ranks_skipped_lineage():
  function test_QueryTaxResult_summarize_up_ranks_perfect_match (line 2903) | def test_QueryTaxResult_summarize_up_ranks_perfect_match():
  function test_QueryTaxResult_summarize_up_ranks_already_summarized (line 2919) | def test_QueryTaxResult_summarize_up_ranks_already_summarized():
  function test_QueryTaxResult_summarize_up_ranks_already_summarized_force (line 2934) | def test_QueryTaxResult_summarize_up_ranks_already_summarized_force():
  function test_QueryTaxResult_summarize_up_ranks_single_rank (line 2980) | def test_QueryTaxResult_summarize_up_ranks_single_rank():
  function test_QueryTaxResult_summarize_up_ranks_single_rank_not_available (line 3010) | def test_QueryTaxResult_summarize_up_ranks_single_rank_not_available():
  function test_QueryTaxResult_summarize_up_ranks_single_rank_not_filled (line 3035) | def test_QueryTaxResult_summarize_up_ranks_single_rank_not_filled():
  function test_QueryTaxResult_build_summarized_result_1 (line 3059) | def test_QueryTaxResult_build_summarized_result_1():
  function test_QueryTaxResult_build_summarized_result_2 (line 3142) | def test_QueryTaxResult_build_summarized_result_2():
  function test_QueryTaxResult_build_summarized_result_missing_lineage (line 3225) | def test_QueryTaxResult_build_summarized_result_missing_lineage():
  function test_QueryTaxResult_build_summarized_result_skipped_lineage (line 3301) | def test_QueryTaxResult_build_summarized_result_skipped_lineage():
  function test_QueryTaxResult_build_summarized_result_over100percent (line 3377) | def test_QueryTaxResult_build_summarized_result_over100percent():
  function test_build_summarized_result_rank_fail_not_available_resummarize (line 3395) | def test_build_summarized_result_rank_fail_not_available_resummarize():
  function test_aggregate_by_lineage_at_rank_noabund (line 3409) | def test_aggregate_by_lineage_at_rank_noabund():
  function test_aggregate_by_lineage_at_rank_abund (line 3443) | def test_aggregate_by_lineage_at_rank_abund():
  function test_aggregate_by_lineage_at_rank_not_available (line 3477) | def test_aggregate_by_lineage_at_rank_not_available():
  function test_aggregate_by_lineage_at_rank_by_query (line 3509) | def test_aggregate_by_lineage_at_rank_by_query():
  function test_build_classification_result_containment_threshold_fail (line 3562) | def test_build_classification_result_containment_threshold_fail():
  function test_build_classification_result_containment_threshold (line 3583) | def test_build_classification_result_containment_threshold():
  function test_build_classification_result_ani_threshold (line 3622) | def test_build_classification_result_ani_threshold():
  function test_build_classification_result_ani_threshold_fail (line 3662) | def test_build_classification_result_ani_threshold_fail():
  function test_build_classification_result_rank_fail_not_filled (line 3679) | def test_build_classification_result_rank_fail_not_filled():
  function test_build_classification_result_rank_fail_not_available_resummarize (line 3694) | def test_build_classification_result_rank_fail_not_available_resummarize():
  function test_build_classification_result_rank_fail_not_available (line 3708) | def test_build_classification_result_rank_fail_not_available():
  function test_build_classification_result_rank_containment_threshold (line 3724) | def test_build_classification_result_rank_containment_threshold():
  function test_build_classification_result_rank_ani_threshold (line 3752) | def test_build_classification_result_rank_ani_threshold():
  function test_krona_classified (line 3779) | def test_krona_classified():
  function test_make_krona_header_basic (line 3803) | def test_make_krona_header_basic():
  function test_make_krona_header_basic_1 (line 3819) | def test_make_krona_header_basic_1():
  function test_make_krona_header_fail (line 3833) | def test_make_krona_header_fail():
  function test_make_human_summary (line 3847) | def test_make_human_summary():
  function test_make_human_summary_2 (line 3885) | def test_make_human_summary_2():
  function test_make_human_summary_classification (line 3923) | def test_make_human_summary_classification():
  function test_make_human_summary_classification_2 (line 3953) | def test_make_human_summary_classification_2():
  function test_make_full_summary (line 3983) | def test_make_full_summary():
  function test_make_full_summary_summarization_fail (line 4192) | def test_make_full_summary_summarization_fail():
  function test_make_full_summary_classification (line 4204) | def test_make_full_summary_classification():
  function test_make_full_summary_classification_limit_float (line 4240) | def test_make_full_summary_classification_limit_float():
  function test_make_full_summary_classification_fail (line 4276) | def test_make_full_summary_classification_fail():
  function test_make_kreport_results (line 4288) | def test_make_kreport_results():
  function test_make_kreport_results_with_taxids (line 4368) | def test_make_kreport_results_with_taxids():
  function test_make_kreport_results_fail (line 4451) | def test_make_kreport_results_fail():
  function test_make_kreport_results_fail_pre_v450 (line 4463) | def test_make_kreport_results_fail_pre_v450():
  function test_make_cami_results_with_taxids (line 4478) | def test_make_cami_results_with_taxids():
  function test_make_cami_results_with_taxids_missing_ranks (line 4504) | def test_make_cami_results_with_taxids_missing_ranks():
  function test_make_lingroup_results (line 4530) | def test_make_lingroup_results():
  function test_make_lingroup_results_fail_pre_v450 (line 4578) | def test_make_lingroup_results_fail_pre_v450():
  function test_read_lingroups (line 4600) | def test_read_lingroups(runtmp):
  function test_read_lingroups_empty_file (line 4612) | def test_read_lingroups_empty_file(runtmp):
  function test_read_lingroups_only_header (line 4622) | def test_read_lingroups_only_header(runtmp):
  function test_read_lingroups_bad_header (line 4632) | def test_read_lingroups_bad_header(runtmp):
  function test_LineageTree_init (line 4642) | def test_LineageTree_init():
  function test_LineageTree_init_mult (line 4652) | def test_LineageTree_init_mult():
  function test_LineageTree_init_and_add_lineage (line 4669) | def test_LineageTree_init_and_add_lineage():
  function test_LineageTree_init_and_add_lineages (line 4690) | def test_LineageTree_init_and_add_lineages():
  function test_build_tree_RankLineageInfo (line 4711) | def test_build_tree_RankLineageInfo():
  function test_build_tree_LINLineageInfo (line 4721) | def test_build_tree_LINLineageInfo():
  function test_build_tree_2 (line 4729) | def test_build_tree_2():
  function test_build_tree_2_LineagePairs (line 4746) | def test_build_tree_2_LineagePairs():
  function test_build_tree_3 (line 4763) | def test_build_tree_3():
  function test_build_tree_3_LineagePairs (line 4771) | def test_build_tree_3_LineagePairs():
  function test_build_tree_5 (line 4781) | def test_build_tree_5():
  function test_build_tree_5b (line 4786) | def test_build_tree_5b():
  function test_build_tree_iterable (line 4791) | def test_build_tree_iterable():
  function test_find_lca (line 4800) | def test_find_lca():
  function test_find_lca_LineagePairs (line 4815) | def test_find_lca_LineagePairs():
  function test_find_lca_2 (line 4828) | def test_find_lca_2():
  function test_find_lca_LIN (line 4840) | def test_find_lca_LIN():
  function test_find_lca_2_LineagePairs (line 4853) | def test_find_lca_2_LineagePairs():
  function test_find_lca_3 (line 4865) | def test_find_lca_3():
  function test_build_tree_with_initial (line 4875) | def test_build_tree_with_initial():
  function test_LineageTree_find_ordered_paths (line 4900) | def test_LineageTree_find_ordered_paths():
  function test_LineageTree_find_ordered_paths_include_internal (line 4930) | def test_LineageTree_find_ordered_paths_include_internal():

FILE: tests/test_test_framework.py
  function test_failed_sourmash_exception (line 6) | def test_failed_sourmash_exception(runtmp):

FILE: utils/cardinality_estimate_confidence.py
  function set_size_chernoff (line 6) | def set_size_chernoff(set_size, scale, relative_error=0.05):
  function get_set_size (line 20) | def get_set_size(scale, num_sketches):
  function set_size_estimate_is_accurate (line 31) | def set_size_estimate_is_accurate(
  function test_set_size_chernoff (line 42) | def test_set_size_chernoff():
  function test_set_size_estimate_is_accurate (line 69) | def test_set_size_estimate_is_accurate():
  function run_tests (line 135) | def run_tests():

FILE: utils/check-tree.py
  function main (line 14) | def main():

FILE: utils/compute-dna-mh-another-way.py
  function complement (line 13) | def complement(s):
  function reverse (line 21) | def reverse(s):
  function kmers (line 29) | def kmers(seq, k):

FILE: utils/compute-input-prot-another-way.py
  function complement (line 81) | def complement(s):
  function reverse (line 89) | def reverse(s):
  function peptides (line 97) | def peptides(seq, start):
  function translate (line 102) | def translate(seq):
  function kmers (line 113) | def kmers(seq, k):

FILE: utils/compute-prot-mh-another-way.py
  function complement (line 81) | def complement(s):
  function reverse (line 89) | def reverse(s):
  function peptides (line 97) | def peptides(seq, start):
  function translate (line 102) | def translate(seq):
  function kmers (line 113) | def kmers(seq, k):

FILE: utils/toml-to-zenodo-json.py
  function main (line 9) | def main():