<BUG>import org.broadinstitute.sting.utils.genotype.Haplotype;import java.util.Arrays;</BUG><CONTEXT>import net.sf.samtools.SAMRecord;import org.broad.tribble.util.variantcontext.VariantContext;import org.broadinstitute.sting.utils.MathUtils;import org.broadinstitute.sting.utils.QualityUtils;import org.broadinstitute.sting.utils.Utils;<extra_id_0>import java.util.List;public class HaplotypeIndelErrorModel {private final int maxReadDeletionLength; // maximum length of deletion on a read</CONTEXT>
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;import java.util.Arrays;