Clarified exception.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1477 8bce386e-0d6e-43e0-b1ca-608082c0432d
Eliminate extraneous open of SAM file.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1478 8bce386e-0d6e-43e0-b1ca-608082c0432d
Merge remote-tracking branch 'upstream'