modbam reads and hardclipping

[jts]

Hi,

Thanks for providing this tool, it is very useful.

I have been testing it on nanopore data and noticed a potential issue in the modbam parser. In the current implementation of MM tags reads that are hardclipped by the aligner are unreliable as it breaks the correspondence between SEQ and the MM tag (if interested there's a discussion here). As far as I can tell ont.cpp doesn't check for this condition so it is possible the .pat output is incorrect for hard clipped records.

Jared