import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMReadGroupRecord;
<BUG>import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.playground.utils.CircularArray;
import org.broadinstitute.sting.utils.StingException;</BUG>
import org.broadinstitute.sting.utils.cmdLine.Argument;

import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.refdata.RODIterator;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.refdata.rodRefSeq;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.playground.utils.CircularArray;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.cmdLine.Argument;
