440 fix indelrealigner

Sorry for taking a while to get to this; it's a small patch to fix the bug, but it was tricky to figure out _what_ was causing the bug (partially because of some oddness in the GATK). My patch shows more changes because it is rebased on bigdatagenomics/adam/master; if you rebase your branch you should see 1 file changed, +11/-8.