Fixes segfault in mpileup when alignment is outside of the ref.

If a read is aligned outside of the reference (possibly due to
reference mismatch or truncation), samtools mpileup will segfault. It
should instead warn, and continue on.  This commit fixes this.

Author: Don Armstrong <don@debian.org>
Date: Thu, 22 Dec 2011 17:42:44 -0800
Debian-Bug: https://bugs.debian.org/653042
Forwarded: https://sourceforge.net/p/samtools/mailman/samtools-help/thread/20111223160030.GC30099@chouca.igloo/