Fixes to handle when non-ACGT is in ref fasta

iqbal-lab-org / minos

Variant call adjudication

MIT License

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Fixes to handle when non-ACGT is in ref fasta #108

Closed martinghunt closed 3 years ago

martinghunt commented 3 years ago

Gramtools stops if there is anything other than A,G,C,T in the ref seq. This fixes minos, by replacing every non A,C,G,T with a C in the reference before running anything else so that gramtools will work ok.