staar: strip FORMAT column in GenotypeWriter::push#135
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…push
noodles exposes `Samples<'_>` as everything after the INFO field, which
for VCF includes the FORMAT column ("GT" or "GT:AD:DP"). push was
running its memchr loop over the full string, so the FORMAT bytes
landed in sample[0]'s slot, every real sample shifted by one, and the
last sample was dropped. MAF and dosages were wrong on every ingested
variant.
Fix: skip past the first tab before entering the sample-parsing loop.
Three tests added: correct 3-sample mapping with a bare "GT" format,
multi-field "GT:AD:DP" format, and the missing-samples-field case.
Invariance and ground-truth-vs-R tests unaffected (they feed U/K/MAF
directly from JSON fixtures; neither exercises the VCF→MAF path).
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noodles_vcf::Record::samples()returns everything after INFO, whichin VCF includes the FORMAT column (
"GT"or"GT:AD:DP").pushwas running its memchr loop over the full string, so sample[0]'s slot
got the FORMAT bytes, every real sample shifted by one, and the last
sample was silently dropped. MAF and dosages were wrong on every real
variant.
Fix: skip past the first tab in
samples_strbefore the sample loop.Three tests cover the bare-
GTcase, multi-fieldGT:AD:DP, and themissing-samples case.
Invariance golden and all ground-truth-vs-R tests unaffected. They
feed
U,K,mafsdirectly from the JSON fixture intorun_staar_from_sumstats; neither path touchesGenotypeWriter::push.Nothing to regenerate. 341/341 cargo test, clippy clean.
Surfaced while writing the
VariantReaderunit test in #134.