Balancing training classes between SNP/Indel and TP/FP.

-- This results in much more consistent distribution of LOD scores for SNPs and Indels.
-- Removing genotype summary stats since they are now produced by default.
-- Added functionality to specify certain subsets of the training data to be used in Tranche file generation, -good:tranche=true set.vcf

public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/MathUtils.java

@@ -1537,6 +1537,9 @@ public class MathUtils {
     * @param N - the number of elements to draw
     */
     public static <T> List<T> randomSample(final List<T> list, final int N) {
+        if (list.isEmpty() ) {
+            return list;
+        }
         return sliceListByIndices(sampleIndicesWithReplacement(list.size(),N),list);
     }