Perform check for mutation parent integrity while checking tree integrity

[jeromekelleher]

Following up on #3212, we should perform the check on mutation parent integrity at the same time as doing the tree integrity. It'll be easy enough to do. We can probably pull out a small function that does the mutation parent computation for a given site on a given tree, which will mean we're not duplicating any code.

[jeromekelleher]

The overhead then will be minimal I think.