The SAMv1 spec document defines newer CIGAR codes. In most cases it is preferred to use the '=' and 'X' characters to denote matches or mismatches rather than the older 'M' character, which is ambiguous.
The SAMv1 spec document defines newer CIGAR codes In most cases it is preferred to use the '=' and 'X' characters to denote matches or mismatches rather than the older 'M' character, which is ambiguous.