seqcode/cegr-tools

TagPileup's validateBED() method miscounts fails for specific BED input cases

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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).