print debugging msg to stdout
debugging code only: print seeds
r428: allow to change the default chain_drop_ratio
fix duplicate PG lines in bwape and bwase
Merge pull request #21 from bpow/fix-duplicate-pg

fix duplicate PG lines in bwape and bwase
r430: fix a bug producing incorrect alignment

Ksw uses two rounds of SSE2-SW to find the boundaries of an alignment. If the
second round gives a different score from the first round, it will fail. The
fix checks if this happens, though I have not dig into an example to understand
why this may happen in the first place.
Merge branch 'master' into mem

Conflicts:
	bwamem.c
	bwape.c
	bwase.c
useless files