Changes

The <code>baseQC</code> option generates the following statistics:  

The <code>baseQC</code> option generates the following statistics:  

A read spans a position if the read starts at or before the position, ends at or after the position and the position is not a clip.  CIGAR operations allowed for the position are M/X/=/D/N.

A read spans a position if the read starts at or before the position, ends at or after the position and the position is not a clip.  CIGAR operations allowed for the position are M/X/=/D/N.  If the CIGAR is '*', only numbers for the specified reference position are incremented.

Currently there is no special logic to exclude positions/reads where the reference base is 'N' or the read base is 'N'.  

Currently there is no special logic to exclude positions/reads where the reference base is 'N' or the read base is 'N'.