Full Code of dib-lab/sourmash for AI

gitextract_wdvkn2_7/

├── .cargo/
│   └── config.toml
├── .envrc
├── .git-blame-ignore-revs
├── .git_archival.txt
├── .gitattributes
├── .github/
│   ├── PULL_REQUEST_TEMPLATE.md
│   ├── dependabot.yml
│   └── workflows/
│       ├── asv.yml
│       ├── build_wheel.yml
│       ├── build_wheel_all_archs.yml
│       ├── codspeed.yml
│       ├── dev_envs.yml
│       ├── draft-pdf.yml
│       ├── hypothesis.yml
│       ├── metadata.yml
│       ├── python.yml
│       └── rust.yml
├── .gitignore
├── .pre-commit-config.yaml
├── .readthedocs.yml
├── .sonarcloud.properties
├── .zenodo.json
├── CITATION.cff
├── CODE_OF_CONDUCT.rst
├── CONTRIBUTING.md
├── Cargo.toml
├── LICENSE
├── MANIFEST.in
├── Makefile
├── README.md
├── asv.conf.json
├── benchmarks/
│   ├── README.md
│   ├── __init__.py
│   └── benchmarks.py
├── binder/
│   ├── README.md
│   └── environment.yml
├── codecov.yml
├── codemeta.json
├── data/
│   └── README.md
├── default.nix
├── deny.toml
├── dev.yml
├── doc/
│   ├── Makefile
│   ├── README.md
│   ├── _static/
│   │   ├── custom.css
│   │   ├── ecoli-cmp.Rmd
│   │   ├── ecoli-cmp.html
│   │   └── ecoli.cmp.csv
│   ├── _templates/
│   │   └── .empty
│   ├── api-example.md
│   ├── api.md
│   ├── cite.md
│   ├── classifying-signatures.md
│   ├── command-line.md
│   ├── conf.py
│   ├── databases-advanced.md
│   ├── databases-md/
│   │   ├── gtdb220.md
│   │   ├── gtdb226.md
│   │   ├── ncbi_euks_2025_01.md
│   │   └── ncbi_viruses_2025_01.md
│   ├── databases.md
│   ├── dev_plugins.md
│   ├── developer.md
│   ├── faq.md
│   ├── funding.md
│   ├── howto-rocksdb.md
│   ├── index.md
│   ├── kmers-and-minhash.ipynb
│   ├── legacy-databases.md
│   ├── more-info.md
│   ├── other-languages.md
│   ├── plotting-compare.ipynb
│   ├── podar-lineage.csv
│   ├── publications.md
│   ├── release-notes/
│   │   ├── releases.md
│   │   ├── sourmash-2.0.md
│   │   ├── sourmash-3.0.md
│   │   ├── sourmash-4.0.md
│   │   └── sourmash-5.0.md
│   ├── release.md
│   ├── requirements.md
│   ├── runtime.txt
│   ├── sidebar.md
│   ├── sourmash-collections.ipynb
│   ├── sourmash-examples.ipynb
│   ├── sourmash-internals.md
│   ├── sourmash-sketch.md
│   ├── storage.md
│   ├── support.md
│   ├── toc.md
│   ├── tutorial-basic.md
│   ├── tutorial-install.md
│   ├── tutorial-lemonade.md
│   ├── tutorial-lin-taxonomy.md
│   ├── tutorial-long.md
│   ├── tutorials-lca.md
│   ├── tutorials.md
│   ├── using-LCA-database-API.ipynb
│   └── using-sourmash-a-guide.md
├── flake.nix
├── include/
│   └── sourmash.h
├── matplotlibrc
├── paper.bib
├── paper.md
├── pyproject.toml
├── requirements.txt
├── shell.nix
├── src/
│   ├── core/
│   │   ├── CHANGELOG.md
│   │   ├── Cargo.toml
│   │   ├── README.md
│   │   ├── benches/
│   │   │   ├── compute.rs
│   │   │   ├── gather.rs
│   │   │   ├── minhash.rs
│   │   │   └── nodegraph.rs
│   │   ├── build.rs
│   │   ├── cbindgen.toml
│   │   ├── examples/
│   │   │   └── generate_mqfs.rs
│   │   ├── src/
│   │   │   ├── ani_utils.rs
│   │   │   ├── cmd.rs
│   │   │   ├── collection.rs
│   │   │   ├── encodings.rs
│   │   │   ├── errors.rs
│   │   │   ├── ffi/
│   │   │   │   ├── cmd/
│   │   │   │   │   ├── compute.rs
│   │   │   │   │   └── mod.rs
│   │   │   │   ├── hyperloglog.rs
│   │   │   │   ├── index/
│   │   │   │   │   ├── mod.rs
│   │   │   │   │   └── revindex.rs
│   │   │   │   ├── manifest.rs
│   │   │   │   ├── minhash.rs
│   │   │   │   ├── mod.rs
│   │   │   │   ├── nodegraph.rs
│   │   │   │   ├── signature.rs
│   │   │   │   ├── storage.rs
│   │   │   │   └── utils.rs
│   │   │   ├── index/
│   │   │   │   ├── linear.rs
│   │   │   │   ├── mod.rs
│   │   │   │   ├── revindex/
│   │   │   │   │   ├── disk_revindex.rs
│   │   │   │   │   ├── mem_revindex.rs
│   │   │   │   │   └── mod.rs
│   │   │   │   └── search.rs
│   │   │   ├── lib.rs
│   │   │   ├── manifest.rs
│   │   │   ├── prelude.rs
│   │   │   ├── selection.rs
│   │   │   ├── signature.rs
│   │   │   ├── sketch/
│   │   │   │   ├── hyperloglog/
│   │   │   │   │   ├── estimators.rs
│   │   │   │   │   └── mod.rs
│   │   │   │   ├── minhash.rs
│   │   │   │   ├── mod.rs
│   │   │   │   └── nodegraph.rs
│   │   │   ├── storage/
│   │   │   │   ├── mod.rs
│   │   │   │   └── rocksdb.rs
│   │   │   └── wasm.rs
│   │   └── tests/
│   │       ├── dedicated_worker.rs
│   │       ├── finch.rs
│   │       ├── minhash.rs
│   │       ├── node.rs
│   │       ├── service_worker.rs
│   │       ├── shared_worker.rs
│   │       ├── storage.rs
│   │       ├── test.rs
│   │       └── web.rs
│   └── sourmash/
│       ├── __init__.py
│       ├── __main__.py
│       ├── cli/
│       │   ├── .gitignore
│       │   ├── __init__.py
│       │   ├── categorize.py
│       │   ├── compare.py
│       │   ├── compute.py
│       │   ├── gather.py
│       │   ├── import_csv.py
│       │   ├── index.py
│       │   ├── info.py
│       │   ├── lca/
│       │   │   ├── __init__.py
│       │   │   ├── classify.py
│       │   │   ├── compare_csv.py
│       │   │   ├── index.py
│       │   │   ├── rankinfo.py
│       │   │   └── summarize.py
│       │   ├── migrate.py
│       │   ├── multigather.py
│       │   ├── plot.py
│       │   ├── prefetch.py
│       │   ├── sbt_combine.py
│       │   ├── scripts/
│       │   │   └── __init__.py
│       │   ├── search.py
│       │   ├── sig/
│       │   │   ├── __init__.py
│       │   │   ├── cat.py
│       │   │   ├── check.py
│       │   │   ├── collect.py
│       │   │   ├── describe.py
│       │   │   ├── downsample.py
│       │   │   ├── export.py
│       │   │   ├── extract.py
│       │   │   ├── fileinfo.py
│       │   │   ├── filter.py
│       │   │   ├── flatten.py
│       │   │   ├── grep.py
│       │   │   ├── inflate.py
│       │   │   ├── ingest.py
│       │   │   ├── intersect.py
│       │   │   ├── kmers.py
│       │   │   ├── manifest.py
│       │   │   ├── merge.py
│       │   │   ├── overlap.py
│       │   │   ├── rename.py
│       │   │   ├── split.py
│       │   │   └── subtract.py
│       │   ├── sketch/
│       │   │   ├── __init__.py
│       │   │   ├── dna.py
│       │   │   ├── fromfile.py
│       │   │   ├── protein.py
│       │   │   └── translate.py
│       │   ├── storage/
│       │   │   ├── __init__.py
│       │   │   └── convert.py
│       │   ├── tax/
│       │   │   ├── __init__.py
│       │   │   ├── annotate.py
│       │   │   ├── genome.py
│       │   │   ├── grep.py
│       │   │   ├── metagenome.py
│       │   │   ├── prepare.py
│       │   │   └── summarize.py
│       │   ├── utils.py
│       │   └── watch.py
│       ├── command_compute.py
│       ├── command_sketch.py
│       ├── commands.py
│       ├── compare.py
│       ├── distance_utils.py
│       ├── exceptions.py
│       ├── fig.py
│       ├── hll.py
│       ├── index/
│       │   ├── __init__.py
│       │   ├── revindex.py
│       │   └── sqlite_index.py
│       ├── lca/
│       │   ├── __init__.py
│       │   ├── __main__.py
│       │   ├── command_classify.py
│       │   ├── command_compare_csv.py
│       │   ├── command_index.py
│       │   ├── command_rankinfo.py
│       │   ├── command_summarize.py
│       │   ├── lca_db.py
│       │   └── lca_utils.py
│       ├── logging.py
│       ├── manifest.py
│       ├── minhash.py
│       ├── nodegraph.py
│       ├── np_utils.py
│       ├── picklist.py
│       ├── plugins.py
│       ├── save_load.py
│       ├── sbt.py
│       ├── sbt_storage.py
│       ├── sbtmh.py
│       ├── search.py
│       ├── sig/
│       │   ├── __init__.py
│       │   ├── __main__.py
│       │   └── grep.py
│       ├── signature.py
│       ├── sketchcomparison.py
│       ├── sourmash_args.py
│       ├── sqlite_utils.py
│       ├── tax/
│       │   ├── __init__.py
│       │   ├── __main__.py
│       │   └── tax_utils.py
│       └── utils.py
├── tests/
│   ├── conftest.py
│   ├── sourmash_tst_utils.py
│   ├── test-data/
│   │   ├── .sbt.leaves/
│   │   │   ├── 0107d767a345eff67ecdaed2ee5cd7ba
│   │   │   ├── 4e94e60265e04f0763142e20b52c0da1
│   │   │   ├── 60f7e23c24a8d94791cc7a8680c493f9
│   │   │   ├── 6d6e87e1154e95b279e5e7db414bc37b
│   │   │   ├── b59473c94ff2889eca5d7165936e64b3
│   │   │   ├── f0c834bc306651d2b9321fb21d3e8d8f
│   │   │   └── f71e78178af9e45e6f1d87a0c53c465c
│   │   ├── .sbt.subset/
│   │   │   ├── 004459575e3657bca8a3d0424545f082
│   │   │   ├── 01bb2bac3849b82dee57a6ecf8725432
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│   │   │   ├── 0418b8351b86bb41c8224d9d15474614
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│   │   │   ├── fcc0a2c84b265a77211ff0d4bd4a413a
│   │   │   ├── internal.0
│   │   │   ├── internal.1
│   │   │   ├── internal.10
│   │   │   ├── internal.11
│   │   │   ├── internal.12
│   │   │   ├── internal.13
│   │   │   ├── internal.14
│   │   │   ├── internal.15
│   │   │   ├── internal.16
│   │   │   ├── internal.17
│   │   │   ├── internal.18
│   │   │   ├── internal.19
│   │   │   ├── internal.2
│   │   │   ├── internal.20
│   │   │   ├── internal.21
│   │   │   ├── internal.22
│   │   │   ├── internal.23
│   │   │   ├── internal.24
│   │   │   ├── internal.25
│   │   │   ├── internal.26
│   │   │   ├── internal.27
│   │   │   ├── internal.28
│   │   │   ├── internal.29
│   │   │   ├── internal.3
│   │   │   ├── internal.30
│   │   │   ├── internal.31
│   │   │   ├── internal.32
│   │   │   ├── internal.33
│   │   │   ├── internal.34
│   │   │   ├── internal.35
│   │   │   ├── internal.36
│   │   │   ├── internal.37
│   │   │   ├── internal.38
│   │   │   ├── internal.39
│   │   │   ├── internal.4
│   │   │   ├── internal.40
│   │   │   ├── internal.41
│   │   │   ├── internal.42
│   │   │   ├── internal.43
│   │   │   ├── internal.44
│   │   │   ├── internal.45
│   │   │   ├── internal.46
│   │   │   ├── internal.47
│   │   │   ├── internal.48
│   │   │   ├── internal.49
│   │   │   ├── internal.5
│   │   │   ├── internal.50
│   │   │   ├── internal.51
│   │   │   ├── internal.52
│   │   │   ├── internal.53
│   │   │   ├── internal.54
│   │   │   ├── internal.55
│   │   │   ├── internal.56
│   │   │   ├── internal.57
│   │   │   ├── internal.58
│   │   │   ├── internal.59
│   │   │   ├── internal.6
│   │   │   ├── internal.60
│   │   │   ├── internal.61
│   │   │   ├── internal.62
│   │   │   ├── internal.63
│   │   │   ├── internal.64
│   │   │   ├── internal.65
│   │   │   ├── internal.66
│   │   │   ├── internal.67
│   │   │   ├── internal.68
│   │   │   ├── internal.69
│   │   │   ├── internal.7
│   │   │   ├── internal.70
│   │   │   ├── internal.71
│   │   │   ├── internal.72
│   │   │   ├── internal.73
│   │   │   ├── internal.74
│   │   │   ├── internal.75
│   │   │   ├── internal.76
│   │   │   ├── internal.77
│   │   │   ├── internal.78
│   │   │   ├── internal.79
│   │   │   ├── internal.8
│   │   │   ├── internal.80
│   │   │   ├── internal.81
│   │   │   ├── internal.82
│   │   │   ├── internal.83
│   │   │   ├── internal.84
│   │   │   ├── internal.85
│   │   │   ├── internal.86
│   │   │   ├── internal.87
│   │   │   ├── internal.88
│   │   │   ├── internal.89
│   │   │   ├── internal.9
│   │   │   ├── internal.90
│   │   │   ├── internal.91
│   │   │   ├── internal.92
│   │   │   ├── internal.93
│   │   │   ├── internal.94
│   │   │   ├── internal.95
│   │   │   ├── internal.96
│   │   │   ├── internal.97
│   │   │   └── internal.98
│   │   ├── .sbt.v2/
│   │   │   ├── v2.0107d767a345eff67ecdaed2ee5cd7ba.sbt
│   │   │   ├── v2.4e94e60265e04f0763142e20b52c0da1.sbt
│   │   │   ├── v2.60f7e23c24a8d94791cc7a8680c493f9.sbt
│   │   │   ├── v2.6d6e87e1154e95b279e5e7db414bc37b.sbt
│   │   │   ├── v2.b59473c94ff2889eca5d7165936e64b3.sbt
│   │   │   ├── v2.f0c834bc306651d2b9321fb21d3e8d8f.sbt
│   │   │   ├── v2.f71e78178af9e45e6f1d87a0c53c465c.sbt
│   │   │   ├── v2.internal.0.sbt
│   │   │   ├── v2.internal.1.sbt
│   │   │   ├── v2.internal.2.sbt
│   │   │   ├── v2.internal.3.sbt
│   │   │   ├── v2.internal.4.sbt
│   │   │   └── v2.internal.5.sbt
│   │   ├── .sbt.v3/
│   │   │   ├── 0107d767a345eff67ecdaed2ee5cd7ba
│   │   │   ├── 4e94e60265e04f0763142e20b52c0da1
│   │   │   ├── 60f7e23c24a8d94791cc7a8680c493f9
│   │   │   ├── 6d6e87e1154e95b279e5e7db414bc37b
│   │   │   ├── b59473c94ff2889eca5d7165936e64b3
│   │   │   ├── f0c834bc306651d2b9321fb21d3e8d8f
│   │   │   ├── f71e78178af9e45e6f1d87a0c53c465c
│   │   │   ├── internal.0
│   │   │   ├── internal.1
│   │   │   ├── internal.2
│   │   │   ├── internal.3
│   │   │   ├── internal.4
│   │   │   └── internal.5
│   │   ├── .sbt.v5_mhmt/
│   │   │   ├── 0107d767a345eff67ecdaed2ee5cd7ba
│   │   │   ├── 4e94e60265e04f0763142e20b52c0da1
│   │   │   ├── 60f7e23c24a8d94791cc7a8680c493f9
│   │   │   ├── 6d6e87e1154e95b279e5e7db414bc37b
│   │   │   ├── b59473c94ff2889eca5d7165936e64b3
│   │   │   ├── f0c834bc306651d2b9321fb21d3e8d8f
│   │   │   ├── f71e78178af9e45e6f1d87a0c53c465c
│   │   │   ├── internal.0
│   │   │   ├── internal.1
│   │   │   ├── internal.2
│   │   │   ├── internal.3
│   │   │   ├── internal.4
│   │   │   └── internal.5
│   │   ├── 10x-example/
│   │   │   ├── barcodes.tsv
│   │   │   ├── barcodes_renamer.tsv
│   │   │   ├── possorted_genome_bam.bam
│   │   │   ├── possorted_genome_bam.bam.bai
│   │   │   └── possorted_genome_bam_filtered.bam
│   │   ├── 2sigs.branch_0913.rocksdb/
│   │   │   ├── 000008.log
│   │   │   ├── 000009.sst
│   │   │   ├── 000010.sst
│   │   │   ├── CURRENT
│   │   │   ├── IDENTITY
│   │   │   ├── LOCK
│   │   │   ├── MANIFEST-000005
│   │   │   └── OPTIONS-000007
│   │   ├── 3sigs.branch_0913.rocksdb/
│   │   │   ├── 000008.log
│   │   │   ├── 000009.sst
│   │   │   ├── 000010.sst
│   │   │   ├── CURRENT
│   │   │   ├── IDENTITY
│   │   │   ├── LOCK
│   │   │   ├── MANIFEST-000005
│   │   │   └── OPTIONS-000007
│   │   ├── compare/
│   │   │   └── labels_from-test.csv
│   │   ├── duplicate-sigs/
│   │   │   └── README.md
│   │   ├── ecoli.faa
│   │   ├── ecoli.genes.fna
│   │   ├── fake-abund/
│   │   │   └── README.md
│   │   ├── gather/
│   │   │   ├── all-picklist.csv
│   │   │   ├── campy-picklist.csv
│   │   │   ├── salmonella-picklist-diffcolumn.csv
│   │   │   ├── salmonella-picklist.csv
│   │   │   └── thermotoga-picklist.csv
│   │   ├── genome-s11.fa.gz.msh.json_dump
│   │   ├── hmp-sigs/
│   │   │   ├── G36354-matches.lineages.csv
│   │   │   └── README.md
│   │   ├── lca/
│   │   │   ├── 47+63.lca.json
│   │   │   ├── bad-spreadsheet-2.csv
│   │   │   ├── bad-spreadsheet-3.csv
│   │   │   ├── bad-spreadsheet.csv
│   │   │   ├── both.lca.json
│   │   │   ├── classify-by-both.csv
│   │   │   ├── delmont-1.csv
│   │   │   ├── delmont-1.lca.json
│   │   │   ├── delmont-1.tsv
│   │   │   ├── delmont-2.csv
│   │   │   ├── delmont-2.lca.json
│   │   │   ├── delmont-3.csv
│   │   │   ├── delmont-4.csv
│   │   │   ├── delmont-5.csv
│   │   │   ├── delmont-6.csv
│   │   │   ├── dir1.lca.json
│   │   │   ├── dir2.lca.json
│   │   │   ├── old-db-format-1.json
│   │   │   ├── podar-lineage.csv
│   │   │   ├── separate.csv
│   │   │   ├── tara-delmont-SuppTable3.csv
│   │   │   ├── tully-genome-sigs.classify.csv
│   │   │   └── tully-query.delmont-db.sigs.classify.csv
│   │   ├── lca-root/
│   │   │   └── tax.csv
│   │   ├── leaves.sbt.json
│   │   ├── picklist/
│   │   │   └── empty.csv
│   │   ├── prot/
│   │   │   ├── build.sh
│   │   │   ├── dayhoff.rocksdb/
│   │   │   │   ├── 000008.log
│   │   │   │   ├── 000009.sst
│   │   │   │   ├── 000010.sst
│   │   │   │   ├── CURRENT
│   │   │   │   ├── IDENTITY
│   │   │   │   ├── LOCK
│   │   │   │   ├── MANIFEST-000005
│   │   │   │   └── OPTIONS-000007
│   │   │   ├── dna-sig.noext
│   │   │   ├── gtdb-subset-lineages.csv
│   │   │   ├── hp.rocksdb/
│   │   │   │   ├── 000008.log
│   │   │   │   ├── 000009.sst
│   │   │   │   ├── 000010.sst
│   │   │   │   ├── CURRENT
│   │   │   │   ├── IDENTITY
│   │   │   │   ├── LOCK
│   │   │   │   ├── MANIFEST-000005
│   │   │   │   └── OPTIONS-000007
│   │   │   └── protein.rocksdb/
│   │   │       ├── 000008.log
│   │   │       ├── 000009.sst
│   │   │       ├── 000010.sst
│   │   │       ├── CURRENT
│   │   │       ├── IDENTITY
│   │   │       ├── LOCK
│   │   │       ├── MANIFEST-000005
│   │   │       └── OPTIONS-000007
│   │   ├── scaled/
│   │   │   ├── all.lca.json
│   │   │   ├── empty-lineage.csv
│   │   │   ├── mf.csv
│   │   │   └── pathlist.txt
│   │   ├── shewanella.faa
│   │   ├── short.fa.msh.dump
│   │   ├── sketch_fromfile/
│   │   │   ├── salmonella-badseq.csv
│   │   │   ├── salmonella-missing.csv
│   │   │   ├── salmonella-mult.csv
│   │   │   ├── salmonella-noname.csv
│   │   │   └── salmonella.csv
│   │   ├── sqlite/
│   │   │   ├── README.md
│   │   │   ├── delmont-6.csv
│   │   │   ├── index.sqldb
│   │   │   ├── lca-2.sqldb
│   │   │   ├── lca.sqldb
│   │   │   ├── prot.sqlmf
│   │   │   └── shewanella-lineage.csv
│   │   ├── subset.sbt.json
│   │   ├── tax/
│   │   │   ├── 47+63_x_gtdb-rs202.gather.csv
│   │   │   ├── bacteria_refseq_lineage.csv
│   │   │   ├── lemonade-MAG3.x.gtdb.csv
│   │   │   ├── lemonade-MAG3.x.gtdb.matches.tax.csv
│   │   │   ├── protozoa_genbank_lineage.csv
│   │   │   ├── test-empty-line.taxonomy.csv
│   │   │   ├── test-empty-ranks-2.taxonomy.csv
│   │   │   ├── test-empty-ranks-3.taxonomy.csv
│   │   │   ├── test-empty-ranks.taxonomy.csv
│   │   │   ├── test-missing-ranks.taxonomy.csv
│   │   │   ├── test-strain.taxonomy.csv
│   │   │   ├── test.LIN-taxonomy.csv
│   │   │   ├── test.ictv-taxonomy.csv
│   │   │   ├── test.ncbi-taxonomy.csv
│   │   │   ├── test.taxonomy.csv
│   │   │   ├── test1.gather.csv
│   │   │   ├── test1.gather.v450.csv
│   │   │   ├── test1.gather.with-lineages.csv
│   │   │   ├── test1.gather_old.csv
│   │   │   └── test1_x_gtdbrs202_genbank_euks.gather.csv
│   │   ├── track_abund/
│   │   │   └── 47+63.abund.rocksdb/
│   │   │       ├── 000008.log
│   │   │       ├── 000009.sst
│   │   │       ├── 000010.sst
│   │   │       ├── CURRENT
│   │   │       ├── IDENTITY
│   │   │       ├── LOCK
│   │   │       ├── MANIFEST-000005
│   │   │       └── OPTIONS-000007
│   │   ├── v1.sbt.json
│   │   ├── v2.sbt.json
│   │   ├── v3.sbt.json
│   │   ├── v4.sbt.json
│   │   ├── v5.sbt.json
│   │   ├── v5_mhmt.sbt.json
│   │   ├── v6.sbt.json
│   │   └── v6.sbt.zip.mf.csv
│   ├── test__minhash_hypothesis.py
│   ├── test_api.py
│   ├── test_bugs.py
│   ├── test_cmd_index.py
│   ├── test_cmd_signature.py
│   ├── test_cmd_signature_collect.py
│   ├── test_cmd_signature_fileinfo.py
│   ├── test_cmd_signature_grep.py
│   ├── test_compare.py
│   ├── test_deprecated.py
│   ├── test_distance_utils.py
│   ├── test_hll.py
│   ├── test_index.py
│   ├── test_index_protocol.py
│   ├── test_jaccard.py
│   ├── test_lca.py
│   ├── test_lca_db_protocol.py
│   ├── test_lca_functions.py
│   ├── test_manifest.py
│   ├── test_manifest_protocol.py
│   ├── test_minhash.py
│   ├── test_moltypes.py
│   ├── test_nodegraph.py
│   ├── test_np_utils.py
│   ├── test_picklist.py
│   ├── test_plugin_framework.py
│   ├── test_prefetch.py
│   ├── test_revindex.py
│   ├── test_rustobj.py
│   ├── test_sbt.py
│   ├── test_search.py
│   ├── test_signature.py
│   ├── test_sketchcomparison.py
│   ├── test_sourmash.py
│   ├── test_sourmash_args.py
│   ├── test_sourmash_compute.py
│   ├── test_sourmash_sketch.py
│   ├── test_sqlite_index.py
│   ├── test_tax.py
│   ├── test_tax_utils.py
│   └── test_test_framework.py
├── tox.ini
└── utils/
    ├── .gitignore
    ├── README.md
    ├── cardinality_estimate_confidence.py
    ├── check-tree.py
    ├── compute-dna-mh-another-way.py
    ├── compute-input-prot-another-way.py
    ├── compute-prot-mh-another-way.py
    ├── toml-to-zenodo-json.py
    └── trim-noV.sh

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_alia

[
  {
    "path": ".cargo/config.toml",
    "chars": 170,
    "preview": "[target.x86_64-unknown-linux-musl]\nrustflags = [\"-C\", \"target-feature=-crt-static\"]\n\n[target.aarch64-unknown-linux-musl]"
  },
  {
    "path": ".envrc",
    "chars": 83,
    "preview": "#use flake\n\nPATH=~/.pixi/bin:$PATH\n\nwatch_file pixi.lock\neval \"$(pixi shell-hook)\"\n"
  },
  {
    "path": ".git-blame-ignore-revs",
    "chars": 70,
    "preview": "# Pre-commit updates (#2427)\nfee62922d8857ce93f1d4e90fd7240629d606997\n"
  },
  {
    "path": ".git_archival.txt",
    "chars": 23,
    "preview": "ref-names: $Format:%D$\n"
  },
  {
    "path": ".gitattributes",
    "chars": 282,
    "preview": ".git_archival.txt  export-subst\ntests/test-data/*.sig  linguist-detectable=false\ntests/test-data/*/*.sig  linguist-detec"
  },
  {
    "path": ".github/PULL_REQUEST_TEMPLATE.md",
    "chars": 675,
    "preview": "Please replace this text with:\n\n* a brief description of your changes in this PR\n* which issues this fixes in the issue "
  },
  {
    "path": ".github/dependabot.yml",
    "chars": 824,
    "preview": "version: 2\nupdates:\n- package-ecosystem: pip\n  directory: \"/\"\n  schedule:\n    interval: weekly\n  open-pull-requests-limi"
  },
  {
    "path": ".github/workflows/asv.yml",
    "chars": 763,
    "preview": "name: asv benchmarks\n\npermissions:\n  contents: read\n\non:\n  push:\n    branches: [latest]\n  pull_request:\n  merge_group:\n "
  },
  {
    "path": ".github/workflows/build_wheel.yml",
    "chars": 2607,
    "preview": "name: cibuildwheel\npermissions:\n  contents: write\n\non:\n  push:\n    branches: [latest]\n    tags: v*\n  pull_request:\n  mer"
  },
  {
    "path": ".github/workflows/build_wheel_all_archs.yml",
    "chars": 2090,
    "preview": "name: maturin wheels\npermissions:\n  contents: write\n\non:\n  pull_request:        # use for testing modifications to this "
  },
  {
    "path": ".github/workflows/codspeed.yml",
    "chars": 998,
    "preview": "name: codspeed-benchmarks\n\npermissions:\n  contents: read\n\non:\n  # Run on pushes to the main branch\n  push:\n    branches:"
  },
  {
    "path": ".github/workflows/dev_envs.yml",
    "chars": 1880,
    "preview": "name: \"Dev env instructions\"\non:\n  pull_request:\n  merge_group:\n  push:\n    branches: [latest]\nconcurrency:\n  group: ${{"
  },
  {
    "path": ".github/workflows/draft-pdf.yml",
    "chars": 689,
    "preview": "on: [push]\n\npermissions:\n  contents: read\n\njobs:\n  paper:\n    runs-on: ubuntu-latest\n    name: Paper Draft\n    steps:\n  "
  },
  {
    "path": ".github/workflows/hypothesis.yml",
    "chars": 811,
    "preview": "name: Hypothesis tests\n\npermissions:\n  contents: read\n\non:\n  push:\n    branches: [latest]\n  pull_request:\n  merge_group:"
  },
  {
    "path": ".github/workflows/metadata.yml",
    "chars": 531,
    "preview": "name: Metadata checks \n\npermissions:\n  contents: read\n\non:\n  push:\n    branches: [latest]\n  pull_request:\n  merge_group:"
  },
  {
    "path": ".github/workflows/python.yml",
    "chars": 2210,
    "preview": "# note: to invalidate caches, adjust the pip-v? number below.\nname: Python tests\n\non:\n  push:\n    branches: [latest]\n  p"
  },
  {
    "path": ".github/workflows/rust.yml",
    "chars": 9289,
    "preview": "name: Rust checks\n\non:\n  push:\n    branches: [latest]\n    tags:\n      - 'r*'\n  pull_request:\n  merge_group:\n  schedule:\n"
  },
  {
    "path": ".gitignore",
    "chars": 369,
    "preview": "*~\n*.fa\n*.fastq.gz\n*.abundtrim\n*.keep\n*.pyc\n*.sig\n*.png\n*.labels.txt\ndistances\n*.npy\ndist\nbuild\nsourmash.egg-info\n.ipynb"
  },
  {
    "path": ".pre-commit-config.yaml",
    "chars": 713,
    "preview": "repos:\n  - repo: https://github.com/pre-commit/pre-commit-hooks\n    rev: v6.0.0\n    hooks:\n      - id: check-ast\n      -"
  },
  {
    "path": ".readthedocs.yml",
    "chars": 463,
    "preview": "# .readthedocs.yml\n# Read the Docs configuration file\n# See https://docs.readthedocs.io/en/stable/config-file/v2.html fo"
  },
  {
    "path": ".sonarcloud.properties",
    "chars": 1,
    "preview": "\n"
  },
  {
    "path": ".zenodo.json",
    "chars": 2175,
    "preview": "{\"creators\": [{\"name\": \"Luiz Irber\", \"orcid\": \"0000-0003-4371-9659\"}, {\"name\": \"N. Tessa Pierce-Ward\", \"orcid\": \"0000-00"
  },
  {
    "path": "CITATION.cff",
    "chars": 6478,
    "preview": "cff-version: \"1.2.0\"\nauthors:\n- family-names: Irber\n  given-names: Luiz\n  orcid: \"https://orcid.org/0000-0003-4371-9659\""
  },
  {
    "path": "CODE_OF_CONDUCT.rst",
    "chars": 1663,
    "preview": "Contributor Code of Conduct\n===========================\n\nAs contributors and maintainers of this project, we pledge to r"
  },
  {
    "path": "CONTRIBUTING.md",
    "chars": 349,
    "preview": "We welcome contributions!  We use\n[GitHub Flow style development](https://guides.github.com/introduction/flow/).\nPlease "
  },
  {
    "path": "Cargo.toml",
    "chars": 116,
    "preview": "[workspace]\nmembers = [\n  \"src/core\",\n]\ndefault-members = [\"src/core\"]\nresolver = \"2\"\n\n[profile.test]\nopt-level = 1\n"
  },
  {
    "path": "LICENSE",
    "chars": 1889,
    "preview": "=======\nLicense\n=======\n\nFiles: *\nCopyright: 2016, The Regents of the University of California.\nLicense: BSD-3-Clause\n R"
  },
  {
    "path": "MANIFEST.in",
    "chars": 238,
    "preview": "include LICENSE Makefile README.md requirements.txt\ninclude Cargo.toml\ninclude include/sourmash.h\nprune .eggs\nglobal-exc"
  },
  {
    "path": "Makefile",
    "chars": 1490,
    "preview": "PYTHON ?= python\n\nall: build\n\n.PHONY:\n\nbuild: .PHONY\n\t$(PYTHON) -m pip install -e .\n\nclean:\n\t$(PYTHON) -m pip uninstall "
  },
  {
    "path": "README.md",
    "chars": 6262,
    "preview": "# sourmash\n\nQuickly search, compare, and analyze genomic and metagenomic data sets.\n\n[![Project Status: Active – The pro"
  },
  {
    "path": "asv.conf.json",
    "chars": 549,
    "preview": "{\n    \"version\": 1,\n    \"project\": \"sourmash\",\n    \"project_url\": \"https://github.com/sourmash-bio/sourmash\",\n    \"repo\""
  },
  {
    "path": "benchmarks/README.md",
    "chars": 230,
    "preview": "# benchmarks for asv ([airspeed velocity](https://asv.readthedocs.io/en/stable/index.html))\n\nThe code in here is run by "
  },
  {
    "path": "benchmarks/__init__.py",
    "chars": 1,
    "preview": "\n"
  },
  {
    "path": "benchmarks/benchmarks.py",
    "chars": 6360,
    "preview": "import random\nfrom tempfile import NamedTemporaryFile\n\nfrom sourmash.sbt_storage import ZipStorage\nfrom sourmash.minhash"
  },
  {
    "path": "binder/README.md",
    "chars": 78,
    "preview": "# binder directory\n\nConfiguration files for [mybinder](https://mybinder.org).\n"
  },
  {
    "path": "binder/environment.yml",
    "chars": 191,
    "preview": "channels:\n  - conda-forge\n  - bioconda\n  - defaults\ndependencies:\n  - python>=3.11\n  - sourmash>=4.8.11\n  - screed\n  - m"
  },
  {
    "path": "codecov.yml",
    "chars": 311,
    "preview": "# config file for codecov, https://app.codecov.io/gh/sourmash-bio/sourmash/\n\n# use path fixing to properly report code c"
  },
  {
    "path": "codemeta.json",
    "chars": 516,
    "preview": "{\n  \"@context\": \"https://raw.githubusercontent.com/mbjones/codemeta/master/codemeta.jsonld\",\n  \"@type\": \"Code\",\n  \"autho"
  },
  {
    "path": "data/README.md",
    "chars": 316,
    "preview": "# The data subdir\n\nData files for various and sundry purposes.\n\nThe following files are used by the doctests in doc/ & m"
  },
  {
    "path": "default.nix",
    "chars": 259,
    "preview": "(import\n  (\n    fetchTarball {\n      url = \"https://github.com/edolstra/flake-compat/archive/99f1c2157fba4bfe6211a321fd0"
  },
  {
    "path": "deny.toml",
    "chars": 1024,
    "preview": "all-features = true\nfeature-depth = 1\n\n[advisories]\ndb-path = \"~/.cargo/advisory-db\"\ndb-urls = [\"https://github.com/rust"
  },
  {
    "path": "dev.yml",
    "chars": 243,
    "preview": "name: sourmash_dev\nchannels:\n  - conda-forge\ndependencies:\n  - clangdev >=16.0.6,<16.1\n  - cxx-compiler >=1.7.0,<1.8\n  -"
  },
  {
    "path": "doc/Makefile",
    "chars": 8085,
    "preview": "# Makefile for Sphinx documentation\n#\n\nall: html\n\n# You can set these variables from the command line.\nSPHINXOPTS    =\nS"
  },
  {
    "path": "doc/README.md",
    "chars": 547,
    "preview": "# Documentation on the docs\n\nWe use\n[MyST](https://myst-parser.readthedocs.io/en/latest/sphinx/intro.html)\nto generate S"
  },
  {
    "path": "doc/_static/custom.css",
    "chars": 163,
    "preview": "div.sphinxsidebar ul {\n    list-style-type: disc;\n    list-style: disc;\n    margin-left: 10px;\n}\n\ndiv.sphinxsidebar ul l"
  },
  {
    "path": "doc/_static/ecoli-cmp.Rmd",
    "chars": 1206,
    "preview": "---\ntitle: \"Working with matrix output by sourmash compare\"\noutput: html_document\n---\n\n```{r setup, include=FALSE}\nknitr"
  },
  {
    "path": "doc/_static/ecoli-cmp.html",
    "chars": 1360669,
    "preview": "<!DOCTYPE html>\n\n<html xmlns=\"http://www.w3.org/1999/xhtml\">\n\n<head>\n\n<meta charset=\"utf-8\" />\n<meta http-equiv=\"Content"
  },
  {
    "path": "doc/_static/ecoli.cmp.csv",
    "chars": 51527,
    "preview": "\"NZ_JHDG01000001.1 Escherichia coli 1-176-05_S3_C1 e117605S3C1.contig.0_1, whole genome shotgun sequence\",\"NZ_JSMW010000"
  },
  {
    "path": "doc/_templates/.empty",
    "chars": 0,
    "preview": ""
  },
  {
    "path": "doc/api-example.md",
    "chars": 27720,
    "preview": "# `sourmash` Python API examples\n\nAll of sourmash's functionality is available via its [Python API](api.md). Below are b"
  },
  {
    "path": "doc/api.md",
    "chars": 757,
    "preview": "# `sourmash` Python API\n\nThe primary programmatic way of interacting with `sourmash` is via\nits Python API.\n\n**Please al"
  },
  {
    "path": "doc/cite.md",
    "chars": 283,
    "preview": "# How to cite sourmash\n\nThe primary citation for the sourmash software is:\n\nIrber et al., (2024). sourmash v4: A multito"
  },
  {
    "path": "doc/classifying-signatures.md",
    "chars": 33103,
    "preview": "# Classifying signatures: `search`, `gather`, and `lca` methods.\n\nsourmash provides several different techniques for doi"
  },
  {
    "path": "doc/command-line.md",
    "chars": 114121,
    "preview": "# Using sourmash from the command line\n\n```{contents} Contents\n:depth: 3\n```\n\nFrom the command line, sourmash can be use"
  },
  {
    "path": "doc/conf.py",
    "chars": 10484,
    "preview": "#!/usr/bin/env python3\n#\n# sourmash documentation build configuration file, created by\n# sphinx-quickstart on Sat Jun  4"
  },
  {
    "path": "doc/databases-advanced.md",
    "chars": 12581,
    "preview": "# sourmash databases - advanced usage information.\n\ntl;dr use `zip` files for heterogeneous collections of sourmash\nsket"
  },
  {
    "path": "doc/databases-md/gtdb220.md",
    "chars": 4386,
    "preview": "<!-- automatically generated by code in https://github.com/sourmash-bio/2025-sourmash-databases-doc-template/ -->\n<!-- t"
  },
  {
    "path": "doc/databases-md/gtdb226.md",
    "chars": 7198,
    "preview": "<!-- automatically generated by code in https://github.com/sourmash-bio/2025-sourmash-databases-doc-template/ -->\n<!-- t"
  },
  {
    "path": "doc/databases-md/ncbi_euks_2025_01.md",
    "chars": 7822,
    "preview": "<!-- automatically generated by code in https://github.com/sourmash-bio/2025-sourmash-databases-doc-template/ -->\n<!-- t"
  },
  {
    "path": "doc/databases-md/ncbi_viruses_2025_01.md",
    "chars": 3439,
    "preview": "<!-- automatically generated by code in https://github.com/sourmash-bio/2025-sourmash-databases-doc-template/ -->\n<!-- t"
  },
  {
    "path": "doc/databases.md",
    "chars": 1213,
    "preview": "# Prepared databases\n\n```{contents}\n```\n\n## Modern databases\n\nWe provide a number of pre-built collections and indexed d"
  },
  {
    "path": "doc/dev_plugins.md",
    "chars": 3907,
    "preview": "# sourmash plugins via Python entry points\n\nAs of version 4.7.0, sourmash has experimental support for Python\nplugins to"
  },
  {
    "path": "doc/developer.md",
    "chars": 11391,
    "preview": "```{contents} Contents\n:depth: 3\n```\n\n# Developer information\n\n## Development environment\n\nYou can get the latest develo"
  },
  {
    "path": "doc/faq.md",
    "chars": 16532,
    "preview": "# Frequently Asked Questions (FAQ)\n\n```{contents} Contents\n:depth: 3\n```\n\n## How is sourmash different from mash?\n\n[mash"
  },
  {
    "path": "doc/funding.md",
    "chars": 623,
    "preview": "# Funding\n\nSourmash development was initiated under award GBMF4551 from the Gordon\nand Betty Moore Foundation to C. Titu"
  },
  {
    "path": "doc/howto-rocksdb.md",
    "chars": 3887,
    "preview": "# A quickstart guide to using RocksDB indexing\n\nThis quickstart shows how to index the GTDB species representatives data"
  },
  {
    "path": "doc/index.md",
    "chars": 6347,
    "preview": "# Welcome to sourmash!\n\nsourmash is a command-line tool and Python/Rust library for\n**metagenome analysis** and **genome"
  },
  {
    "path": "doc/kmers-and-minhash.ipynb",
    "chars": 80952,
    "preview": "{\n \"cells\": [\n  {\n   \"cell_type\": \"markdown\",\n   \"metadata\": {},\n   \"source\": [\n    \"# An introduction to k-mers for gen"
  },
  {
    "path": "doc/legacy-databases.md",
    "chars": 22006,
    "preview": "# Legacy Databases - 2024 and before\n\n## Types of databases\n\nFor each k-mer size, three types of databases may be availa"
  },
  {
    "path": "doc/more-info.md",
    "chars": 5839,
    "preview": "# Additional information on sourmash\n\n## Computational requirements\n\nRead more about the [computational requirements, he"
  },
  {
    "path": "doc/other-languages.md",
    "chars": 1405,
    "preview": "# Using `sourmash` output with R and other languages\n\nMost of the sourmash shell commands output CSV files upon request;"
  },
  {
    "path": "doc/plotting-compare.ipynb",
    "chars": 107966,
    "preview": "{\n \"cells\": [\n  {\n   \"cell_type\": \"markdown\",\n   \"metadata\": {},\n   \"source\": [\n    \"# Building plots from `sourmash com"
  },
  {
    "path": "doc/podar-lineage.csv",
    "chars": 9707,
    "preview": "accession,taxid,superkingdom,phylum,class,order,family,genus,species,strain\r\nAE000782,224325,Archaea,Euryarchaeota,Archa"
  },
  {
    "path": "doc/publications.md",
    "chars": 2817,
    "preview": "# Publications\n\nBelow are publications from the sourmash team.\n\n## sourmash fundamentals\n\n[Lightweight compositional ana"
  },
  {
    "path": "doc/release-notes/releases.md",
    "chars": 244,
    "preview": "# sourmash release notes\n\nPlease see the\n[github releases page](https://github.com/sourmash-bio/sourmash/releases)\nfor d"
  },
  {
    "path": "doc/release-notes/sourmash-2.0.md",
    "chars": 2870,
    "preview": "# sourmash v2.0 release notes\n\nWe are pleased to announce release 2.0 of sourmash!  This release is\nthe first full relea"
  },
  {
    "path": "doc/release-notes/sourmash-3.0.md",
    "chars": 2311,
    "preview": "# sourmash v3.0 release notes\n\nWe are pleased to announce release 3.0 of sourmash!  This release includes internal chang"
  },
  {
    "path": "doc/release-notes/sourmash-4.0.md",
    "chars": 3769,
    "preview": "# sourmash v4.0 release notes\n\n```{contents}\n   :depth: 2\n```\n\nWe are pleased to announce release 4.0 of sourmash! This "
  },
  {
    "path": "doc/release-notes/sourmash-5.0.md",
    "chars": 1624,
    "preview": "# sourmash v5.0 _draft_ release notes\n\n```{contents}\n   :depth: 2\n```\n\nDraft text: We are pleased to announce release 5."
  },
  {
    "path": "doc/release.md",
    "chars": 10448,
    "preview": "# Releasing a new version of sourmash\n\nThese are adapted from the khmer release docs, originally written by\nMichael Crus"
  },
  {
    "path": "doc/requirements.md",
    "chars": 761,
    "preview": "# Computational requirements\n\nsourmash has no particular memory requirements; it will need to hold\nthe largest single se"
  },
  {
    "path": "doc/runtime.txt",
    "chars": 5,
    "preview": "3.11\n"
  },
  {
    "path": "doc/sidebar.md",
    "chars": 1904,
    "preview": "## Tutorials and examples\n\nThese tutorials are command line tutorials that should work on Mac OS\nX and Linux. They requi"
  },
  {
    "path": "doc/sourmash-collections.ipynb",
    "chars": 90073,
    "preview": "{\n \"cells\": [\n  {\n   \"cell_type\": \"markdown\",\n   \"metadata\": {},\n   \"source\": [\n    \"# sourmash: working with private co"
  },
  {
    "path": "doc/sourmash-examples.ipynb",
    "chars": 33432,
    "preview": "{\n \"cells\": [\n  {\n   \"cell_type\": \"markdown\",\n   \"metadata\": {},\n   \"source\": [\n    \"# Some sourmash command line exampl"
  },
  {
    "path": "doc/sourmash-internals.md",
    "chars": 37783,
    "preview": "# A guide to the internal design and structure of sourmash\n\n```{contents} Contents\n:depth: 3\n```\n\nsourmash was created i"
  },
  {
    "path": "doc/sourmash-sketch.md",
    "chars": 19781,
    "preview": "# `sourmash sketch` documentation\n\n```{contents} Contents\n:depth: 3\n```\n\nMost of the commands in sourmash work with **si"
  },
  {
    "path": "doc/storage.md",
    "chars": 1895,
    "preview": "# Storing SBTs\n\nWe support different storage options for the internal SBT data.\n\n\n## Available storages\n\n### FSStorage\n\n"
  },
  {
    "path": "doc/support.md",
    "chars": 13280,
    "preview": "# Support, Versioning, and Migration\n\n```{contents}\n   :depth: 3\n```\n\n## Asking questions and filing bugs\n\nWe do our bes"
  },
  {
    "path": "doc/toc.md",
    "chars": 685,
    "preview": "# Full table of contents\n\n```{toctree}\n---\nmaxdepth: 2\n---\n\napi-example.md\napi.md\ncite.md\nclassifying-signatures.md\ncomm"
  },
  {
    "path": "doc/tutorial-basic.md",
    "chars": 9111,
    "preview": "# The first sourmash tutorial - making signatures, comparing, and searching\n\nYou'll need about 5 GB of free disk space, "
  },
  {
    "path": "doc/tutorial-install.md",
    "chars": 1026,
    "preview": "# Installing sourmash\n\nThis tutorial should run without modification on Linux or Mac OS X,\nunder [Miniforge](https://git"
  },
  {
    "path": "doc/tutorial-lemonade.md",
    "chars": 21146,
    "preview": "# Analyzing the genomic and taxonomic composition of an environmental genome using GTDB and sample-specific MAGs with so"
  },
  {
    "path": "doc/tutorial-lin-taxonomy.md",
    "chars": 24261,
    "preview": "# Analyzing Metagenome Composition using the LIN taxonomic framework  \n\nTessa Pierce Ward\n\nMarch 2023\n\nrequires sourmash"
  },
  {
    "path": "doc/tutorial-long.md",
    "chars": 23290,
    "preview": "# Quick Insights from Sequencing Data with sourmash\n\nNote: this tutorial was developed for and first presented at\n[ANGUS"
  },
  {
    "path": "doc/tutorials-lca.md",
    "chars": 6627,
    "preview": "# Using sourmash LCA to do taxonomic classification\n\nThe `sourmash lca` sub-commands do k-mer classification using an\n\"l"
  },
  {
    "path": "doc/tutorials.md",
    "chars": 2034,
    "preview": "# sourmash tutorials and notebooks\n\n## The first three tutorials!\n\nThese tutorials are command line tutorials that shoul"
  },
  {
    "path": "doc/using-LCA-database-API.ipynb",
    "chars": 23882,
    "preview": "{\n \"cells\": [\n  {\n   \"cell_type\": \"markdown\",\n   \"metadata\": {},\n   \"source\": [\n    \"# Using the `LCA_Database` API\"\n   "
  },
  {
    "path": "doc/using-sourmash-a-guide.md",
    "chars": 9514,
    "preview": "# Using sourmash: a practical guide\n\n```{contents}\n   :depth: 2\n```\n\nSo! You've installed sourmash, run a few of the tut"
  },
  {
    "path": "flake.nix",
    "chars": 4647,
    "preview": "{\n\n  inputs = {\n    nixpkgs.url = \"github:NixOS/nixpkgs/nixpkgs-unstable\";\n    utils.url = \"github:numtide/flake-utils\";"
  },
  {
    "path": "include/sourmash.h",
    "chars": 21242,
    "preview": "/* c bindings to the sourmash library */\n\n#ifndef SOURMASH_H_INCLUDED\n#define SOURMASH_H_INCLUDED\n\n#include <stdarg.h>\n#"
  },
  {
    "path": "matplotlibrc",
    "chars": 14,
    "preview": "backend : Agg\n"
  },
  {
    "path": "paper.bib",
    "chars": 3564,
    "preview": "@article{Ondov:2015,\n  title={Fast genome and metagenome distance estimation using MinHash},\n  author={Ondov, Brian D an"
  },
  {
    "path": "paper.md",
    "chars": 6507,
    "preview": "---\ntitle: 'sourmash v4: A multitool to quickly search, compare, and analyze genomic\nand metagenomic data sets'\ntags:\n  "
  },
  {
    "path": "pyproject.toml",
    "chars": 12164,
    "preview": "[build-system]\nrequires = [\n    \"maturin>=1,<1.14.0\",\n    \"cffi\",\n]\nbuild-backend = 'maturin'\n\n[project]\nname = \"sourmas"
  },
  {
    "path": "requirements.txt",
    "chars": 10,
    "preview": "-e .[all]\n"
  },
  {
    "path": "shell.nix",
    "chars": 257,
    "preview": "(import\n  (\n    fetchTarball {\n      url = \"https://github.com/edolstra/flake-compat/archive/99f1c2157fba4bfe6211a321fd0"
  },
  {
    "path": "src/core/CHANGELOG.md",
    "chars": 20911,
    "preview": "# Changelog\n\nAll notable changes to this project will be documented in this file.\n\nThe format is based on [Keep a Change"
  },
  {
    "path": "src/core/Cargo.toml",
    "chars": 3196,
    "preview": "[package]\nname = \"sourmash\"\nversion = \"0.22.0\"\nauthors = [\"Luiz Irber <luiz@sourmash.bio>\", \"N. Tessa Pierce-Ward <tessa"
  },
  {
    "path": "src/core/README.md",
    "chars": 1552,
    "preview": "<meta charset=\"utf-8\"/>\n\n# sourmash\n\n🦀\n[![](https://img.shields.io/crates/v/sourmash.svg)](https://crates.io/crates/sour"
  },
  {
    "path": "src/core/benches/compute.rs",
    "chars": 4963,
    "preview": "use codspeed_criterion_compat::{Criterion, criterion_group, criterion_main};\n\nuse std::fs::File;\nuse std::io::{Cursor, R"
  },
  {
    "path": "src/core/benches/gather.rs",
    "chars": 2426,
    "preview": "use std::fs::File;\nuse std::io::BufReader;\nuse std::path::PathBuf;\n\nuse sourmash::collection::Collection;\nuse sourmash::"
  },
  {
    "path": "src/core/benches/minhash.rs",
    "chars": 3006,
    "preview": "use std::fs::File;\nuse std::io::BufReader;\nuse std::path::PathBuf;\n\nuse sourmash::signature::{Signature, SigsTrait};\nuse"
  },
  {
    "path": "src/core/benches/nodegraph.rs",
    "chars": 1499,
    "preview": "use std::fs::File;\nuse std::io::{BufWriter, Cursor, Read};\n\nuse sourmash::sketch::nodegraph::Nodegraph;\n\nuse codspeed_cr"
  },
  {
    "path": "src/core/build.rs",
    "chars": 2173,
    "preview": "use std::env;\n\nfn main() {\n    let crate_dir = env::var(\"CARGO_MANIFEST_DIR\").unwrap();\n    copy_c_bindings(&crate_dir);"
  },
  {
    "path": "src/core/cbindgen.toml",
    "chars": 350,
    "preview": "header = \"/* c bindings to the sourmash library */\"\ninclude_guard = \"SOURMASH_H_INCLUDED\"\nlanguage = \"C\"\nstyle = \"type\"\n"
  },
  {
    "path": "src/core/examples/generate_mqfs.rs",
    "chars": 2648,
    "preview": "use std::collections::HashMap;\nuse std::fs::File;\nuse std::io::BufReader;\nuse std::path::PathBuf;\nuse std::result::Resul"
  },
  {
    "path": "src/core/src/ani_utils.rs",
    "chars": 11510,
    "preview": "// Streamlined set of utils for containment --> ANI estimation\n// Equations based off of: https://github.com/KoslickiLab"
  },
  {
    "path": "src/core/src/cmd.rs",
    "chars": 7021,
    "preview": "use getset::{CopyGetters, Getters, Setters};\nuse typed_builder::TypedBuilder;\n\nuse crate::encodings::HashFunctions;\nuse "
  },
  {
    "path": "src/core/src/collection.rs",
    "chars": 21614,
    "preview": "use std::ops::{Deref, DerefMut};\n\nuse camino::Utf8Path as Path;\nuse camino::Utf8PathBuf as PathBuf;\n\nuse crate::encoding"
  },
  {
    "path": "src/core/src/encodings.rs",
    "chars": 19480,
    "preview": "use serde::{Deserialize, Serialize};\nuse std::collections::HashMap;\nuse std::hash::{BuildHasher, BuildHasherDefault, Has"
  },
  {
    "path": "src/core/src/errors.rs",
    "chars": 7614,
    "preview": "use thiserror::Error;\n\n#[derive(Debug, Error)]\n#[non_exhaustive]\npub enum SourmashError {\n    /// Raised for internal er"
  },
  {
    "path": "src/core/src/ffi/cmd/compute.rs",
    "chars": 5820,
    "preview": "use std::slice;\n\nuse crate::ScaledType;\nuse crate::cmd::ComputeParameters;\n\nuse crate::ffi::utils::ForeignObject;\n\npub s"
  },
  {
    "path": "src/core/src/ffi/cmd/mod.rs",
    "chars": 17,
    "preview": "pub mod compute;\n"
  },
  {
    "path": "src/core/src/ffi/hyperloglog.rs",
    "chars": 5696,
    "preview": "use std::ffi::CStr;\nuse std::os::raw::c_char;\nuse std::slice;\n\nuse crate::prelude::*;\nuse crate::signature::SigsTrait;\nu"
  },
  {
    "path": "src/core/src/ffi/index/mod.rs",
    "chars": 1176,
    "preview": "#[cfg(all(feature = \"branchwater\", not(target_arch = \"wasm32\")))]\npub mod revindex;\n\nuse crate::signature::Signature;\n\nu"
  },
  {
    "path": "src/core/src/ffi/index/revindex.rs",
    "chars": 18585,
    "preview": "use std::ffi::CStr;\nuse std::os::raw::c_char;\nuse std::slice;\n\nuse crate::collection::{Collection, CollectionSet};\nuse c"
  },
  {
    "path": "src/core/src/ffi/manifest.rs",
    "chars": 2448,
    "preview": "use crate::manifest::{Manifest, Record};\n\nuse crate::ffi::utils::{ForeignObject, SourmashStr};\n\npub struct SourmashManif"
  },
  {
    "path": "src/core/src/ffi/minhash.rs",
    "chars": 13831,
    "preview": "use std::ffi::CStr;\nuse std::os::raw::c_char;\nuse std::slice;\n\nuse crate::encodings::{aa_to_dayhoff, aa_to_hp, translate"
  },
  {
    "path": "src/core/src/ffi/mod.rs",
    "chars": 2323,
    "preview": "//! # Foreign Function Interface for calling sourmash from a C API\n//!\n//! Primary client for now is the Python version,"
  },
  {
    "path": "src/core/src/ffi/nodegraph.rs",
    "chars": 6605,
    "preview": "use std::ffi::CStr;\nuse std::os::raw::c_char;\nuse std::slice;\n\nuse crate::prelude::*;\nuse crate::sketch::nodegraph::Node"
  },
  {
    "path": "src/core/src/ffi/signature.rs",
    "chars": 9670,
    "preview": "use std::convert::TryInto;\nuse std::ffi::CStr;\nuse std::io;\nuse std::os::raw::c_char;\nuse std::slice;\n\nuse crate::errors"
  },
  {
    "path": "src/core/src/ffi/storage.rs",
    "chars": 3516,
    "preview": "use std::os::raw::c_char;\nuse std::slice;\nuse std::sync::Arc;\n\nuse crate::ffi::utils::{ForeignObject, SourmashStr};\nuse "
  },
  {
    "path": "src/core/src/ffi/utils.rs",
    "chars": 8596,
    "preview": "use std::borrow::Cow;\nuse std::cell::RefCell;\nuse std::ffi::CStr;\nuse std::mem;\nuse std::os::raw::c_char;\nuse std::panic"
  },
  {
    "path": "src/core/src/index/linear.rs",
    "chars": 12094,
    "preview": "use std::collections::HashSet;\nuse std::sync::atomic::{AtomicUsize, Ordering};\n\nuse camino::Utf8PathBuf as PathBuf;\nuse "
  },
  {
    "path": "src/core/src/index/mod.rs",
    "chars": 14591,
    "preview": "//! # Indexing structures for fast similarity search\n//!\n//! An index organizes signatures to allow for fast similarity "
  },
  {
    "path": "src/core/src/index/revindex/disk_revindex.rs",
    "chars": 22865,
    "preview": "use std::cmp::max;\nuse std::collections::HashSet;\nuse std::hash::{BuildHasher, BuildHasherDefault};\nuse std::path::Path;"
  },
  {
    "path": "src/core/src/index/revindex/mem_revindex.rs",
    "chars": 33324,
    "preview": "use std::sync::atomic::{AtomicUsize, Ordering};\n\nuse camino::Utf8Path as Path;\nuse camino::Utf8PathBuf as PathBuf;\nuse l"
  },
  {
    "path": "src/core/src/index/revindex/mod.rs",
    "chars": 44180,
    "preview": "/// Reverse index data structures.\npub mod disk_revindex;\npub mod mem_revindex;\n\nuse std::collections::{HashMap, HashSet"
  },
  {
    "path": "src/core/src/index/search.rs",
    "chars": 856,
    "preview": "use crate::index::Comparable;\n\npub fn search_minhashes<L>(node: &dyn Comparable<L>, query: &L, threshold: f64) -> bool {"
  },
  {
    "path": "src/core/src/lib.rs",
    "chars": 2230,
    "preview": "//! # Compute, compare and search signatures for nucleotide (DNA/RNA) and protein sequences.\n//!\n//! sourmash is a comma"
  },
  {
    "path": "src/core/src/manifest.rs",
    "chars": 19765,
    "preview": "use std::collections::HashSet;\nuse std::fs::File;\nuse std::hash::{Hash, Hasher};\nuse std::io::{BufRead, BufReader, Read,"
  },
  {
    "path": "src/core/src/prelude.rs",
    "chars": 737,
    "preview": "use std::io::Write;\n\nuse crate::Result;\n\npub use crate::selection::{Select, Selection};\npub use crate::signature::Signat"
  },
  {
    "path": "src/core/src/selection.rs",
    "chars": 3047,
    "preview": "use getset::{CopyGetters, Getters, Setters};\nuse typed_builder::TypedBuilder;\n\nuse crate::encodings::HashFunctions;\nuse "
  },
  {
    "path": "src/core/src/signature.rs",
    "chars": 65615,
    "preview": "//! # Compressed representations of genomic data\n//!\n//! A signature is a collection of sketches for a genomic dataset.\n"
  },
  {
    "path": "src/core/src/sketch/hyperloglog/estimators.rs",
    "chars": 7121,
    "preview": "use core::{\n    cmp,\n    ops::{Add, AddAssign, Shl, Sub, SubAssign},\n};\n\npub type CounterType = u8;\n\n/// Trait for types"
  },
  {
    "path": "src/core/src/sketch/hyperloglog/mod.rs",
    "chars": 14759,
    "preview": "/*\nBased on the HyperLogLog implementations in khmer\n  https://github.com/dib-lab/khmer/blob/fb65d21eaedf0d397d49ae3debc"
  },
  {
    "path": "src/core/src/sketch/minhash.rs",
    "chars": 56988,
    "preview": "use std::cmp::Ordering;\nuse std::collections::{BTreeMap, BTreeSet};\nuse std::f64::consts::PI;\nuse std::fmt::Write;\nuse s"
  },
  {
    "path": "src/core/src/sketch/mod.rs",
    "chars": 482,
    "preview": "pub mod hyperloglog;\npub mod minhash;\n\npub mod nodegraph;\n\nuse serde::{Deserialize, Serialize};\n\nuse crate::sketch::hype"
  },
  {
    "path": "src/core/src/sketch/nodegraph.rs",
    "chars": 32873,
    "preview": "use std::fs::File;\nuse std::io;\nuse std::path::Path;\nuse std::slice;\n\nuse byteorder::{BigEndian, ByteOrder, LittleEndian"
  },
  {
    "path": "src/core/src/storage/mod.rs",
    "chars": 19397,
    "preview": "use std::collections::{BTreeMap, HashMap};\nuse std::ffi::OsStr;\nuse std::fs::{DirBuilder, File};\nuse std::io::{BufReader"
  },
  {
    "path": "src/core/src/storage/rocksdb.rs",
    "chars": 4163,
    "preview": "use std::sync::Arc;\n\nuse rocksdb::{ColumnFamilyDescriptor, Options};\n\nuse crate::Result;\nuse crate::storage::{Storage, S"
  },
  {
    "path": "src/core/src/wasm.rs",
    "chars": 7899,
    "preview": "use needletail::parse_fastx_reader;\nuse wasm_bindgen::prelude::*;\n\nuse crate::ScaledType;\nuse crate::cmd::ComputeParamet"
  },
  {
    "path": "src/core/tests/dedicated_worker.rs",
    "chars": 169,
    "preview": "#![cfg(all(target_arch = \"wasm32\", target_os = \"unknown\"))]\n\nuse wasm_bindgen_test::wasm_bindgen_test_configure;\n\nwasm_b"
  },
  {
    "path": "src/core/tests/finch.rs",
    "chars": 1,
    "preview": "\n"
  },
  {
    "path": "src/core/tests/minhash.rs",
    "chars": 31223,
    "preview": "use std::fs::File;\nuse std::io::BufReader;\nuse std::path::PathBuf;\n\nuse proptest::collection::vec;\nuse proptest::num::u6"
  },
  {
    "path": "src/core/tests/node.rs",
    "chars": 145,
    "preview": "#![cfg(all(target_arch = \"wasm32\", target_os = \"unknown\"))]\n\nuse wasm_bindgen_test::*;\n\n#[wasm_bindgen_test]\nfn pass() {"
  },
  {
    "path": "src/core/tests/service_worker.rs",
    "chars": 167,
    "preview": "#![cfg(all(target_arch = \"wasm32\", target_os = \"unknown\"))]\n\nuse wasm_bindgen_test::wasm_bindgen_test_configure;\n\nwasm_b"
  },
  {
    "path": "src/core/tests/shared_worker.rs",
    "chars": 166,
    "preview": "#![cfg(all(target_arch = \"wasm32\", target_os = \"unknown\"))]\n\nuse wasm_bindgen_test::wasm_bindgen_test_configure;\n\nwasm_b"
  },
  {
    "path": "src/core/tests/storage.rs",
    "chars": 4992,
    "preview": "use std::path::PathBuf;\n\nuse tempfile::TempDir;\n\nuse sourmash::signature::Signature;\nuse sourmash::storage::{FSStorage, "
  },
  {
    "path": "src/core/tests/test.rs",
    "chars": 101,
    "preview": "#[test]\nfn test_murmur() {\n    assert_eq!(sourmash::_hash_murmur(b\"ACG\", 42), 1731421407650554201)\n}\n"
  },
  {
    "path": "src/core/tests/web.rs",
    "chars": 160,
    "preview": "#![cfg(all(target_arch = \"wasm32\", target_os = \"unknown\"))]\n\nuse wasm_bindgen_test::wasm_bindgen_test_configure;\n\nwasm_b"
  },
  {
    "path": "src/sourmash/__init__.py",
    "chars": 4251,
    "preview": "\"\"\"A library for creating k-mer sketches from biological sequences, comparing\nthem to each other, and working with the r"
  },
  {
    "path": "src/sourmash/__main__.py",
    "chars": 572,
    "preview": "\"\"\"\nThe main entry point for sourmash, defined in pyproject.toml.\n\nCan also be executed as 'python -m sourmash'.\n\"\"\"\n\n\nd"
  },
  {
    "path": "src/sourmash/cli/.gitignore",
    "chars": 13,
    "preview": "__pycache__/\n"
  },
  {
    "path": "src/sourmash/cli/__init__.py",
    "chars": 5626,
    "preview": "\"\"\"Define the top-level command line interface for sourmash\n\nThis module handles user input when sourmash is invoked fro"
  },
  {
    "path": "src/sourmash/cli/categorize.py",
    "chars": 1184,
    "preview": "\"'sourmash categorize' - query an SBT for bes match, with many signatures.\"\n\nfrom sourmash.cli.utils import add_ksize_ar"
  },
  {
    "path": "src/sourmash/cli/compare.py",
    "chars": 4088,
    "preview": "\"\"\"create a similarity matrix comparing many samples\"\"\"\n\nusage = \"\"\"\n\nThe `compare` subcommand compares one or more sign"
  },
  {
    "path": "src/sourmash/cli/compute.py",
    "chars": 4874,
    "preview": "\"\"\"compute sequence signatures for inputs\"\"\"\n\nusage = \"\"\"\n\n** WARNING: the sourmash compute command is DEPRECATED as of "
  },
  {
    "path": "src/sourmash/cli/gather.py",
    "chars": 6570,
    "preview": "\"\"\"search a metagenome signature against dbs\"\"\"\n\nusage = \"\"\"\n\nThe `gather` subcommand selects the best reference genomes"
  },
  {
    "path": "src/sourmash/cli/import_csv.py",
    "chars": 667,
    "preview": "\"\"\"'sourmash import_csv' description goes here\"\"\"\n\nfrom sourmash.logging import notify\n\n\ndef subparser(subparsers):\n    "
  },
  {
    "path": "src/sourmash/cli/index.py",
    "chars": 2756,
    "preview": "\"\"\"index signatures for rapid search\"\"\"\n\nusage = \"\"\"\n\n   sourmash index -k 31 dbname *.sig -F dbtype\n\nCreate an on-disk "
  },
  {
    "path": "src/sourmash/cli/info.py",
    "chars": 926,
    "preview": "\"\"\"display sourmash version and other information\"\"\"\n\nimport os\nimport screed\nimport sourmash\nfrom sourmash.logging impo"
  },
  {
    "path": "src/sourmash/cli/lca/__init__.py",
    "chars": 1186,
    "preview": "\"\"\"Define the command line interface for sourmash lca\n\nThe top level CLI is defined in ../__init__.py. This module defin"
  },
  {
    "path": "src/sourmash/cli/lca/classify.py",
    "chars": 1414,
    "preview": "\"\"\"classify genomes\"\"\"\n\n\ndef subparser(subparsers):\n    subparser = subparsers.add_parser(\"classify\")\n    subparser.add_"
  },
  {
    "path": "src/sourmash/cli/lca/compare_csv.py",
    "chars": 1442,
    "preview": "\"\"\"compare spreadsheets\"\"\"\n\n\ndef subparser(subparsers):\n    # Dirty hack to simultaneously support new and previous inte"
  },
  {
    "path": "src/sourmash/cli/lca/index.py",
    "chars": 2602,
    "preview": "\"\"\"create LCA database\"\"\"\n\nfrom sourmash.cli.utils import add_ksize_arg, add_moltype_args, add_picklist_args\n\n\ndef subpa"
  },
  {
    "path": "src/sourmash/cli/lca/rankinfo.py",
    "chars": 722,
    "preview": "\"\"\"database rank info\"\"\"\n\n\ndef subparser(subparsers):\n    subparser = subparsers.add_parser(\"rankinfo\")\n    subparser.ad"
  },
  {
    "path": "src/sourmash/cli/lca/summarize.py",
    "chars": 1470,
    "preview": "\"\"\"summarize mixture\"\"\"\n\n\ndef subparser(subparsers):\n    subparser = subparsers.add_parser(\"summarize\")\n    subparser.ad"
  },
  {
    "path": "src/sourmash/cli/migrate.py",
    "chars": 299,
    "preview": "\"'sourmash migrate' - migrate an SBT database to the latest version.\"\n\n\ndef subparser(subparsers):\n    subparser = subpa"
  },
  {
    "path": "src/sourmash/cli/multigather.py",
    "chars": 3705,
    "preview": "\"'sourmash multigather' - gather many signatures against multiple databases.\"\n\nusage = \"\"\"\n\nThe `multigather` subcommand"
  },
  {
    "path": "src/sourmash/cli/plot.py",
    "chars": 2427,
    "preview": "\"\"\"plot distance matrix made by 'compare'\"\"\"\n\n\ndef subparser(subparsers):\n    subparser = subparsers.add_parser(\"plot\")\n"
  },
  {
    "path": "src/sourmash/cli/prefetch.py",
    "chars": 2510,
    "preview": "\"\"\"search a signature against dbs, find all overlaps\"\"\"\n\nfrom sourmash.cli.utils import (\n    add_ksize_arg,\n    add_mol"
  },
  {
    "path": "src/sourmash/cli/sbt_combine.py",
    "chars": 453,
    "preview": "\"\"\"combine multiple Sequence Bloom Trees\"\"\"\n\n\ndef subparser(subparsers):\n    subparser = subparsers.add_parser(\"sbt_comb"
  },
  {
    "path": "src/sourmash/cli/scripts/__init__.py",
    "chars": 1706,
    "preview": "\"\"\"Provide a mechanism to add CLI plugins to sourmash.\n\nSee https://sourmash.readthedocs.io/en/latest/dev_plugins.html f"
  },
  {
    "path": "src/sourmash/cli/search.py",
    "chars": 4483,
    "preview": "\"\"\"search a signature against other signatures\"\"\"\n\nusage = \"\"\"\n\nThe `search` subcommand searches a collection of signatu"
  },
  {
    "path": "src/sourmash/cli/sig/__init__.py",
    "chars": 1613,
    "preview": "\"\"\"Define the command line interface for sourmash sig\n\nThe top level CLI is defined in ../__init__.py. This module defin"
  },
  {
    "path": "src/sourmash/cli/sig/cat.py",
    "chars": 1674,
    "preview": "\"\"\"concatenate signature files\"\"\"\n\nusage = \"\"\"\n\n### `sourmash signature cat` - concatenate multiple signatures together\n"
  },
  {
    "path": "src/sourmash/cli/sig/check.py",
    "chars": 3207,
    "preview": "\"\"\"check signature collections against a picklist\"\"\"\n\nusage = \"\"\"\n\n    sourmash sig check <filenames> --picklist ... -o "
  },
  {
    "path": "src/sourmash/cli/sig/collect.py",
    "chars": 2688,
    "preview": "\"\"\"collect manifest information across many files\"\"\"\n\nusage = \"\"\"\n\n    sourmash sig collect <filenames> -o all.sqlmf\n\nTh"
  },
  {
    "path": "src/sourmash/cli/sig/describe.py",
    "chars": 1595,
    "preview": "\"\"\"show details of signature\"\"\"\n\nusage = \"\"\"\n\n### `sourmash signature describe` - display detailed information about sig"
  },
  {
    "path": "src/sourmash/cli/sig/downsample.py",
    "chars": 1984,
    "preview": "\"\"\"downsample one or more signatures\"\"\"\n\nusage = \"\"\"\n\n### `sourmash signature downsample` - decrease the size of a signa"
  },
  {
    "path": "src/sourmash/cli/sig/export.py",
    "chars": 1025,
    "preview": "\"\"\"export a signature, e.g. to mash\"\"\"\n\nusage = \"\"\"\n\n### `sourmash signature export` - export signatures to mash.\n\nExpor"
  },
  {
    "path": "src/sourmash/cli/sig/extract.py",
    "chars": 2541,
    "preview": "\"\"\"extract one or more signatures\"\"\"\n\nusage = \"\"\"\n\n### `sourmash signature extract` - extract signatures from a collecti"
  },
  {
    "path": "src/sourmash/cli/sig/fileinfo.py",
    "chars": 1173,
    "preview": "\"\"\"provide summary information on the given file\"\"\"\n\nusage = \"\"\"\n\n    sourmash sig fileinfo <filename>\n\nThis will provid"
  },
  {
    "path": "src/sourmash/cli/sig/filter.py",
    "chars": 1911,
    "preview": "\"\"\"filter k-mers on abundance\"\"\"\n\nusage = \"\"\"\n\n### `sourmash signature filter` - remove hashes based on abundance\n\nFilte"
  },
  {
    "path": "src/sourmash/cli/sig/flatten.py",
    "chars": 1687,
    "preview": "\"\"\"remove abundances\"\"\"\n\nusage = \"\"\"\n\n### `sourmash signature flatten` - remove abundance information from signatures\n\nF"
  },
  {
    "path": "src/sourmash/cli/sig/grep.py",
    "chars": 3400,
    "preview": "\"\"\"extract one or more signatures by substr/regex match\"\"\"\n\nusage = \"\"\"\n    sourmash sig grep <pattern> <filename> [... "
  },
  {
    "path": "src/sourmash/cli/sig/inflate.py",
    "chars": 925,
    "preview": "\"\"\"borrow abundances from one signature => one or more other signatures\"\"\"\n\nfrom sourmash.cli.utils import add_moltype_a"
  },
  {
    "path": "src/sourmash/cli/sig/ingest.py",
    "chars": 1320,
    "preview": "\"\"\"ingest/import a mash or other signature\"\"\"\n\nusage = \"\"\"\n\n   sourmash sig ingest --csv <input filename> [ <more inputs"
  }
]

// ... and 507 more files (download for full content)