r843: presetting for ONT 2d reads

Somewhat working for 1d reads, but not very well
r844: added intra-species contig mapping mode
r845: updated NEWS

I will use the new version for a while and then release it.
r848: tag alignments with primary ALT
r849: the pa tag now gives a number

... which is the ratio of this hit to the best ALT hit.
added postalt to bwa-helper for post processing
Merge branch 'dev' into bam

Conflicts:
	main.c