import org.broadinstitute.variant.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
<<<<<<< HEAD
import org.broadinstitute.variant.variantcontext.GenotypeLikelihoods;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
=======
import org.broadinstitute.sting.utils.pairhmm.PairHMM;
import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
>>>>>>> 9aaa71527168dc3a62ff7c3d93097c7c9ba05321
import java.io.PrintStream;
import java.util.*; |