dev-464: preset for pacbio read2read aln
dev-465: a new output format for read overlap

Also moved a few functions to bwamem_extra.c. File bwamem.c is becoming far too
long.
dev-466: simplified chain filtering
dev-467: limit the max #chains to extend
dev-468: fixed a segfault caused by NULL
dev-469: fixed wrong command line prompt
Merge branch 'dev' into mem

Conflicts:
	Makefile