Checkpoint

Works mechanically end-to-end.  Still experimenting with chunk
arrangments and alignment stream processing. Correction not quite
working as expected.
Ready for tests on larger genomes

Reworked the correction pipeline to be target oriented, works a bit
better now with chunking.  The dextract code does not take into
consideration the hole type so may include problematic reads from things
like fiducials, may consider going back to pls2fasta.