Fixed bug in SAM2MS.py where CpGs occuring at the first position in a read where being excluded even if ignore3=0. The fix was to change the strict inequality in the statement 'CpG_index = [pos for pos in CpG_index if pos > ignore5 and pos <= (len(XM) - ignore3)]' to be non-strict, i.e. 'CpG_index = [pos for pos in CpG_index if pos >= ignore5 and pos <= (len(XM) - ignore3)]'
Fixed bug in SAM2MS.py where CpGs occuring at the first position in a read where being excluded even if ignore3=0. The fix was to change the strict inequality in the statement 'CpG_index = [pos for pos in CpG_index if pos > ignore5 and pos <= (len(XM) - ignore3)]' to be non-strict, i.e. 'CpG_index = [pos for pos in CpG_index if pos >= ignore5 and pos <= (len(XM) - ignore3)]'

PeteHaitch/methtuple,PeteHaitch/methtuple,PeteHaitch/methtuple