closing vcf file before writing index, hopefully this will make the stale index problem go away (unable to test, but tests pass)

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1511 8bce386e-0d6e-43e0-b1ca-608082c0432d
Always shutdown the basecalling threadpool.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1512 8bce386e-0d6e-43e0-b1ca-608082c0432d
Merge remote-tracking branch 'upstream'