Related Issues (20)
- Handle missing discordant read calls for Af1.x HOT 3
- Upgrade latest_docs.yml to use Node.js 20
- Consider adding more documentation for sample set metadata
- codecov/project CI check fails but seems to require additional coverage on code unrelated to the PR
- Diplotype clustering fails on sample sets without CNV calls HOT 5
- Diplotype clustering title reports the number of amino acid snps, not total snps used in clustering
- Add option to filter samples by max heterozygosity in advanced diplotype clustering HOT 4
- Advanced diplotype clustering orders genes in the CNV section by label rather than by genomic position HOT 6
- Display normal copy number (2) differently from missing CNV call (NaN) in advanced diplotype clustering HOT 3
- Study URL in sample_metadata() is hard-coded rather than sourced from manifest.tsv HOT 1
- SNP browser to replace Panoptes HOT 2
- Add Ag3.cross_metadata() to API docs
- FST plotting function error HOT 5
- Anopheles pca() and plot_njt() functions should have sensible defaults for min_minor_ac and max_missing_an HOT 7
- FAILED tests/anoph/test_g123.py::test_g123_calibration[af1_sim] - IndexError: index -1 is out of bounds for axis 0 with size 0
- Allow fractional value for max_missing_an, e.g. 0.01
- Update docs version switcher
- Cannot always select older versions from docs switcher
- More plotting options in plot_* functions
- Colors in GWSS plots HOT 3
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