private Set<String> tumor_samples = new HashSet<String>();
@Override
public void initialize() {
<BUG>coverage = new RunningCoverage(0,WINDOW_SIZE);
int nSams = getToolkit().getArguments().samFiles.size();
if ( call_somatic ) {</BUG>
if ( nSams != 2 ) {
System.out.println("In --somatic mode two input bam files must be specified (normal/tumor)");
System.exit(1);
}

private Set<String> tumor_samples = new HashSet<String>();
@Override
public void initialize() {
coverage = new RunningCoverage(0,WINDOW_SIZE);
ReferenceOrderedData<rodRefSeq> refseq = new ReferenceOrderedData<rodRefSeq>("refseq",
new java.io.File("/humgen/gsa-scr1/GATK_Data/refGene.sorted.txt"),rodRefSeq.class);
refseqIterator = refseq.iterator();
int nSams = getToolkit().getArguments().samFiles.size();
location = new GenomeLoc(0,1);
if ( call_somatic ) {
if ( nSams != 2 ) {
System.out.println("In --somatic mode two input bam files must be specified (normal/tumor)");
System.exit(1);
}
