VcfVariant.php
Immutable value object describing one VCF variant record Freely inspired by BioPHP's project biophp.org Created 30 September 2026 Last modified 9 October 2026
Table of Contents
Classes
- VcfVariant
- POS is 1-based, VCF's own convention (unlike BED) ; 0 and length + 1 are valid too and mark a telomere (VCF 4.3, POS column), typically on a breakend record. getReference()/getAlternates() are kept as raw strings, deliberately not wrapped in a DnaSequence : VCF's ALT column can legitimately hold a symbolic allele ("<DEL>", "<INS>") or breakend notation ("]13:123456]T") for a structural variant, neither of which is a valid DNA alphabet string, so forcing that validation here would wrongly reject real VCF input. Each ALT allele is checked against those forms ; REF, on the other hand, only ever holds bases, and is checked as such.