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).
In the
validateBED()method (Line94), there is a chance of theFAILcountvariable 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
continuefollowing theFAILcount++(Line112) in the firstifstatement (alternatively bundle the twoifstatements into one).