don't process hard clipped SEQ

The full read sequence has to be present.
first integration; compiled, but NOT TESTED!
r795: intel's ksw_extend() replacement
r796: more debugging code
don't process hard clipped SEQ

The full read sequence has to be present.
Merge branch 'master' of github.com:lh3/bwa
Fixed a bug related to the score returned.
Merge branch 'master' into new-master