Emergent bugfix: wrong TLEN sign

It is interesting that Picard did not find the issue.
Match to 'N' costs -1, instead of 0.

This is to prevent alignment through 'N'.
Improving 'properly paired' flag.

If one end has a low quality tail that happens to have a score-20 hit,
the pair won't be flagged as properly paired because bwa-mem thought it has
multiple hits. By filtering with -T, we won't have this problem.