Making fixes to SomaticSpike.

 Restoring somaticspike.xml which had been corrupted in the transition from git to svn.
 Adding LibraryReadFilter.  This is not necessary to build SomaticSpike, but downstream tools that make use of SomaticSpike expect it.
Merge branch 'master' of github.com:broadinstitute/mutect
Merge pull request #3 from lbergelson/master

Fixing a few things that got lost in the transition to github