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
r427: fixed bugs in backtrack

See comments in ksw_global() for details.
print debugging msg to stdout
debugging code only: print seeds
r428: allow to change the default chain_drop_ratio
Merge remote-tracking branch 'upstream/master'