Actually ignore the bad reads...
Export paired vs single mode via commandline API.

Call this v0.0.5; Also reduce the stderr progress verbosity.

TODO - Re-examine SAM input in paired vs single end mode
Overdue commit of fix

Note this does seem to have made this a lot slow...
v0.0.2, ignore unmapped reads

Trying this with BWA-MEM paired output... will need tweaks
Reinstate setting POS module circle length

Trying this with BWA and ignoring mrfast and its problematic output.
Created sam_restore_seq.py to fill in missing SEQ field in BWA output
Explore using this on BWA MEM output.

Working in progress, does not really think about FLAG bits in depth.
Assumes have already used ../sambam/sam_restore_seq.py to fill in the
SEQ (and QUAL) fields otherwise can probably lose the sequence.