populationgenomics / automated-interpretation-pipeline

Rare Disease variant prioritisation MVP

MIT License

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Fix failure to export haplo GTs #374

Closed MattWellie closed 1 month ago

MattWellie commented 1 month ago

Fixes

CNV labelling fails - Hail can't export data from MT to VCF when there is only a haploid genotype
example https://batch.hail.populationgenomics.org.au/batches/437009/jobs/2
patched here, but this won't be released for ages

Proposed Changes

Updates haploid genotypes to diploid
[0] -> [0, 0]
[1] -> [1, 1]
doesn't update diploid genotypes

Checklist

[ ] Related Issue created
[x] Tests covering new change
[x] Linting checks pass