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Add overlapping reads support to bam2bw, bam2bwbases and bam2bedgraph via commandline flag --overlap-a
If the same readname is encountered twice at a position it is considred an overlapping read pair.
Where the same base [ACGT] was encountered on each of the reads it will only be counted once. If a different base was encountered then the coverage count is incremented once for each base.