ValueObject
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.