Does anyone know any option in any software that could say:
"In the case a read aligns to the beginning or end of a contig/scaffold of the reference but has an overhang, as long as the matching part is longer than some threshold, do not think of the overhang as mismatch, and calculate mapping just based on the part that actually aligns"
A short example:
REFERENCE CONTIG= AGAGAGAGTTTCCCGAGTATATAGAGACACAGAGTGGTGAGGAT
READ WITH OVERHANG= TTATAGGTTCCGAGAGAGAGTTTCGC
another read= CGAGTATATAGAGACACA
READ WITH OVERHANG= ACAGAGTGGTGAGGGTGGAGAT
ALIGNED READ WITH 2 SNPS= AGAGAGAGTTTCGCGAGTATATAGAGACACAGAGTGGTGAGGGT