Add a method to calculate MD and NM tags.

[nh13]

This is useful for when we perform clipping or other modifications to a SAM record that would affect these values.

For a code example, see htsjdk's calculateMdAndNmTags. I think an additional parameter to make the output compatible with samtools makes sense (i.e. do not treat N->N as a match). See how this is used in fgbio both here and here, which handle unmapped reads.

Bonus points for adding another method that takes a iterator over Templates (and/or pysam.AlignedSegments) and a pysam.FastaFile and updates the records.