System.exit(1);
}
ArrayList<JapsaFeature> myList = JapsaFeature.readBED(bedFile);
SamReaderFactory.setDefaultValidationStringency(ValidationStringency.SILENT);
SequenceOutputStream os = SequenceOutputStream.makeOutputStream(output);
<BUG>char sep = '\t';
int notCount = 0;
os.print("#H:chrom\tID\tstart\tend");
SamReader [] readers = new SamReader[args.length];</BUG>
for (int i = 0; i < readers.length; i++){

System.exit(1);
}
ArrayList<JapsaFeature> myList = JapsaFeature.readBED(bedFile);
SamReaderFactory.setDefaultValidationStringency(ValidationStringency.SILENT);
SequenceOutputStream os = SequenceOutputStream.makeOutputStream(output);
String sep = "\t";
int notCount = 0;
os.print("#H:chrom\tID\tstart\tend");
args = new String[1];
args[0] = cmdLine.getStringVal("bamFile");
SamReader [] readers = new SamReader[args.length];
for (int i = 0; i < readers.length; i++){
