fix: expand() handles NULL geno data in sites-only VCFs (#72)#100
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fix: expand() handles NULL geno data in sites-only VCFs (#72)#100jmg421 wants to merge 1 commit into
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) Sites-only VCFs (e.g., gnomAD allele frequency files) declare FORMAT fields in the header but have no sample columns. This results in geno data stored as empty list-matrices (nrow × 0). When expand() attempted to process Number=R fields (like AD), .expandAD() would call array(NULL, ...) because unlist() on an empty list returns NULL. Fix: add an early return in .expandAD() when the input list is empty or xcols (number of samples) is 0, returning an appropriately-shaped empty array instead. Also adds a sites-only test VCF and corresponding unit test. Closes Bioconductor#72
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Summary
Fixes #72.
expand()errored with'data' must be of a vector type, was 'NULL'when called on sites-only VCFs (e.g., the GATK gnomAD allele frequency resource) that declare FORMAT fields in the header but have no sample columns.Root Cause
Sites-only VCFs have 0 sample columns, but
readVcf()still creates geno slots as list-matrices with dimensions (nrow × 0). Whenexpand()processesNumber=Rfields (like AD), it calls.expandAD()with this empty list-matrix. Inside.expandAD():is.list(AD)→ TRUE (a list-matrix is still a list)length(AD)→ 0 (no elements since 0 columns)unlist(AD)→ NULLarray(NULL, c(idxlen, xcols, 2L))→ ERRORFix
Added an early-return guard in
.expandAD(): when the input list has length 0 orxcols(number of samples) is 0, return an appropriately-shaped emptyarray(integer(0L), c(idxlen, xcols, 2L))instead of attempting to process non-existent allele depth data.Testing
inst/unitTests/cases/sites_only.vcf— a minimal sites-only VCF with multi-allelic variants and FORMAT headers but no sample columns.test_expand_sitesOnly_issue72unit test verifying:expand()succeeds on a 0-sample VCFAgentic tooling disclosure
This PR was produced with the assistance of Kiro CLI (Amazon's AI coding agent). All changes were reviewed and verified by the author.