fix: preserve '*' spanning deletion alleles at read time (#65)#104
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fix: preserve '*' spanning deletion alleles at read time (#65)#104jmg421 wants to merge 3 commits into
jmg421 wants to merge 3 commits into
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Convert \itemize blocks that used \item{label}{desc} syntax to \describe,
and replace empty \item{}{} labels in \describe blocks with the function
signature from the body, resolving all checkRd warnings in isSNV-methods,
PolyPhenDb-class, readVcf-methods, SIFTDb-class, summarizeVariants-methods,
VariantType-class, VCF-class, VcfFile-class, VCFHeader-class, VRanges-class,
and VRangesList-class Rd files.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…r#65) VCFs containing '*' (spanning deletion) alleles are now read with a CharacterList ALT column, preserving the '*' character. Previously, .formatALT() converted '*' to an empty string to fit into DNAStringSet, but this made it impossible to write valid VCF output — IGV/htsjdk would reject files with empty alleles. The fix treats '*' as a structural/special allele (like '<DEL>'), which causes .isStructural() to return TRUE and the ALT to be stored as a CharacterList. This is semantically correct per the VCF spec: '*' represents a spanning deletion and is not a DNA sequence. For VCFs without '*' alleles, behavior is unchanged (DNAStringSetList). This supersedes the write-path-only fix in PR Bioconductor#103, which could only handle the multi-allele case. With this read-time fix, both single '*' and multi-allele '*' are correctly round-tripped. Closes Bioconductor#65
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Summary
Fully fixes #65. Supersedes #103 (which only addressed the write-path).
readVcf()now preserves*(spanning deletion) alleles instead of erasing them, enabling faithful VCF round-trips for files containing spanning deletions.Problem
*in VCF ALT fields represents a spanning deletion allele (VCF spec §1.4.2). At read time,.formatALT()converted*to an empty string ("") to fit intoDNAStringSet(since*is not a valid DNA character). At write time, this empty string produced malformed VCF output likeCA,,TTAinstead ofCA,*,TTA, causing IGV/htsjdk to reject the file.Root Cause (per @hpages' analysis in the issue thread)
*is not a DNA sequence — it's a special VCF allele that cannot be stored inDNAStringSet. The package's architecture stores ALT as eitherDNAStringSetList(normal alleles) orCharacterList(structural/special alleles).*should be in the latter category.Fix
One line change: added
grepl("*", x, fixed=TRUE)to.isStructural()inAllUtilities.R. This causes VCFs containing*alleles to be stored with aCharacterListALT column (same treatment as<DEL>,], etc.), preserving the*through read/write.Also removed the now-unnecessary
flat[grepl("*", flat, fixed=TRUE)] <- ""conversion in.formatALT().Behavior Change
*alt()returnsDNAStringSetList*alt()returnsDNAStringSetListwith""for*alt()returnsCharacterListwith"*"preserved**correctly writtenThis is consistent with how structural variants (
<DEL>, breakends) are already handled —alt()is aCharacterListand the special alleles are preserved.Testing
CA,*,TTA→ read → write →CA,*,TTA✓*allele round-trips correctly*still useDNAStringSetList(no change)Agentic 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.