Comments (1)
daler
commented on July 28, 2024
Actually, there's already a mechanism for checking stderr -- see the check_stderr kwarg in bedtool._wraps, and the existing helpers._check_sequence_stderr(). This latter function only looked for the warning that the .fai needed to be created. I added the additional check for missing chrom to 84690c7. In this case, the sequence file is created, but is empty. You're right that this strategy is sensitive to exactly what BEDTools sends to stderr, but it's easy enough to fix.
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