The original version of SAM2MRF assumed that the only element in the CIGAR string were N and M, and explicitly requiring xMyNzM, where x and z are the number of matches (M) and y the number of skipped nucleotides (N). Moreover, x+z should have been equal to the read size. This format encoded for a splice junction read, i.e. a read mapped to a splice junction.
However, new alignment tools, such as STAR, reports also soft-clipping (S) and insertions or deletions. The MRF format can handle these situations already, but the conversion from SAM needs to be updated.
The original version of SAM2MRF assumed that the only element in the CIGAR string were N and M, and explicitly requiring xMyNzM, where x and z are the number of matches (M) and y the number of skipped nucleotides (N). Moreover, x+z should have been equal to the read size. This format encoded for a splice junction read, i.e. a read mapped to a splice junction.
However, new alignment tools, such as STAR, reports also soft-clipping (S) and insertions or deletions. The MRF format can handle these situations already, but the conversion from SAM needs to be updated.