Added a couple of methods for 1) doing vector multiplication of two arrays and b) summing values in an array.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1575 8bce386e-0d6e-43e0-b1ca-608082c0432d
Made a few things static that were'nt, but needed to be.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1576 8bce386e-0d6e-43e0-b1ca-608082c0432d
Tided up a little bit and then added a method to be able to query by region from the VCFFileReader.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1577 8bce386e-0d6e-43e0-b1ca-608082c0432d
Merge remote-tracking branch 'upstream'