r342: bugfix in bwasw - AS is off by one

but I do not understand why the old code does not have the same problem.
r343: bugfix in mem - wrong mate info for unmap

SAM generation is always among the nastiest bits. I would need to refactor at
some point (hardly happening).
gcc wrongly thinks a variable may be uninitialized

It should always be initialized. To avoid a warning, made a change.
r345: bugfix in mem - wrong mate strand for unmap

Received a clean bill from Picard
Updated NEWS; added stddef.h for size_t

I thought size_t is defined in stdlib.h, but it is not always.
Release 0.7.1-r347
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.
Release bwa-0.7.2-r351

For the TLEN sign fix. Sorry for the significant bug in 0.7.0/0.7.1
Merge branch 'master' into master_fixes

Conflicts:
	Makefile