feat: allow snp_allele_frequencies to accept genomic regions#1076
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joshitha1808 wants to merge 2 commits intomalariagen:masterfrom
Open
feat: allow snp_allele_frequencies to accept genomic regions#1076joshitha1808 wants to merge 2 commits intomalariagen:masterfrom
joshitha1808 wants to merge 2 commits intomalariagen:masterfrom
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What problem does this solve:
Previously,
snp_allele_frequencies()required a transcript as input. This meant analyses were limited to coding regions, and users couldn’t easily check SNP allele frequencies for arbitrary genomic regions.How does it solve it:
This PR adds an optional
regionparameter, so users can now specify any genomic region directly. The function will accept either a transcript or a region .When a region is used, SNP calls and allele frequencies are calculated for that region. Effect annotations are still only generated if a transcript is provided. Plot titles are automatically adjusted to work with both transcript- and region-based queries.Issue number:
Closes #805
Testing done:
Added unit tests for region-based queries.
Verified that all existing transcript-based tests still pass.
Confirmed that effect annotations are applied correctly when using transcripts.
Breaking changes or migration notes:
No.