Bug fix for non-paired reads (wrong variable name)
Also adjust position of placed but unmapped reads
Dedup using updated POS. Update PNEXT too
Support pairing via FLAG or /1 and /2 suffices
Cope with REF being * (i.e. allow unmapped reads in input)
Hold FLAG as an int; ignore unmapped reads in coverage calc
Tweak output message (counts may now include unmapped partners)