TagPileup's validateBED() method miscounts fails for specific BED input cases
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owlang commented
In the validateBED()
method (Line94), there is a chance of the FAILcount
variable double-counting failed indexes in cases where a BED file entry has both (1) an unrecognized chromosome name and (2) coordinate start>end. This can potentially lead to the program skipping over the system exit block (Line121).
FIX: All it needs is a continue
following the FAILcount++
(Line112) in the first if
statement (alternatively bundle the two if
statements into one).