I've filed a bug for this in github:
In the meantime, you'll either have to use my script with the reference fasta file (in which case INDELs will change the length of the generated sequence), or add a dummy SAM line for each sequence in the reference fasta file that covers the entire range of the sequence.
In the meantime, you'll either have to use my script with the reference fasta file (in which case INDELs will change the length of the generated sequence), or add a dummy SAM line for each sequence in the reference fasta file that covers the entire range of the sequence.
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