Function Coverage Audit
This audit maps source modules in src/ to documentation anchors so newly added capabilities stay discoverable. Counts come from a regex sweep of the Julia sources and should be refreshed after major changes.
Module-Level Coverage
| Source Module | Function Count | Primary Documentation | Coverage Notes |
|---|---|---|---|
assembly.jl | 68 | Assembly Suite | Wrapper coverage for MEGAHIT/metaSPAdes/Flye/hifiasm is documented; link polishing and long-read retries into tutorials. |
quality-control-and-benchmarking.jl | 30 | Quality Control | External filtering and QUAST/BUSCO/MUMmer paths are covered; native metrics (robust_cv, filter_genome_outliers) referenced in the Workflow & Tool Map. |
kmer-analysis.jl | 39 | Sequence Analysis | K-mer spectrum utilities are referenced; add examples for saved-result loaders. |
distance-metrics.jl | 15 | Sequence Analysis | Mash/Jaccard/JS divergence functions are linked from tutorials. |
pangenome-analysis.jl | 8 | Comparative Genomics | PGGB/cactus wrappers present; tutorials pending. |
taxonomy-and-trees.jl | 38 | Workflow & Tool Map | Classification + plotting functions surfaced in the map; needs dedicated taxonomy tutorial. |
variant-analysis.jl | 15 | Workflow & Tool Map | Functions exist but lack tutorial/API detail; planned variant calling tutorial will fill the gap. |
alignments-and-mapping.jl | 25 | Tool Integration | Alignment wrappers (BLAST/DIAMOND/MMSeqs2/minimap2) are referenced from the capability matrix. |
reference-databases.jl | 34 | Data Acquisition | NCBI/SRA helpers documented; ensure coverage of metadata loaders. |
simulation.jl | 41 | Data Acquisition | Read simulators surfaced in tutorials and workflow map. |
plotting-and-visualization.jl | 27 | Visualization Gallery | Embedding/taxa plots linked; gallery currently has some broken refs. |
xam.jl | 22 | Tool Integration | Mapping stats and coverage plotting referenced; align with BAM/CRAM primer. |
alignments-and-mapping.jl | 25 | Tool Integration | Alignment wrappers (BLAST/DIAMOND/MMSeqs2/minimap2) are referenced from the capability matrix. |
reference-databases.jl | 34 | Data Acquisition | NCBI/SRA helpers documented; ensure coverage of metadata loaders. |
simulation.jl | 41 | Data Acquisition | Read simulators surfaced in tutorials and workflow map. |
plotting-and-visualization.jl | 27 | Visualization Gallery | Embedding/taxa plots linked; gallery currently has some broken refs. |
xam.jl | 22 | Tool Integration | Mapping stats and coverage plotting referenced; align with BAM/CRAM primer. |
fastx.jl | 50 | Workflow & Tool Map | FASTA/FASTQ normalization utilities used by tutorials; add quick-start snippet to API reference. |
utility-functions.jl | 102 | Internal | Shared helpers; document only when promoted to user-facing APIs. |
How to Keep This Audit Fresh
- When adding a new function, link it from:
- the nearest workflow page and/or tutorial, and
- the Workflow & Tool Map if it creates a new input/output path.
- For wrappers around external tools, record expected inputs/outputs in the workflow map.
- Periodically update the counts with a small helper script, for example:
rg '^function ' src | awk -F: '{print $1}' | sort | uniq -cand edit the table above.
Cross-check with Complete API
Use the Complete API Surface page as a ground truth index of documented symbols:
If a function appears in the code but not on the Complete API Surface, it is missing a docstring.
If it appears in the API, but not:
- the Workflow & Tool Map, and
- any tutorial,
then it is likely undiscoverable in real workflows and should be linked.
Immediate Documentation Tasks
- Add API snippets and at least one tutorial for
variant-analysis.jl(normalize VCF → evaluate ROC). - Surface taxonomy abundance plotting (
plot_taxa_abundances) in the Comparative Genomics or Tool Integration tutorial. - Expand the Visualization Gallery once broken references are resolved and ensure all plotting helpers appear there.