use kthread for multi-threading

Bwa-mem should have better performance with many CPU cores.
r418: use the new mapQ estimator by default
r419: print the @PG line
r420: inferred bandwidth is not used in the final
r421: bw doubling in the final alignment

In some cases, the band width used in the final alignment needs to be larger
than the band width in extension.
r422: matesw hits not sorted
r423: bugfix - SE hits not random
r424: fixed a bw bug in samse/pe
Merge remote-tracking branch 'lh3/master' into java-access

Conflicts:
	Makefile
Fix Makefile