mismatch and gap next to each other

[divy-kangeyan]

Seq2	RNA	CGCCAGCGTCGCAGCGACAGGTNNN	aGCCAGCt-CtCAGCGACAGcTGAG	chr1	91631879	+	3	1

Above is a row of the table from your readme. Why is the mismatch next to the gap is not counted. According to the DNA sequences there should have been 4 mismatches. I see the same in my data. So curious how you decide the mismatch count when the mismatch is next to a gap?

[DORISMO]

Hi, I cannot install the software. It suddenly quit. May I know how to fix it?