if (readGroups != null && readGroups.size() > 0){
sampleID = readGroups.get(0).getSample();
}
if (sampleID == null){
sampleID = file.getName().replace(".sam", "").replace(".bam","");
<BUG>}
if (contained)</BUG>
os.print(sep + sampleID + "_contained");
<BUG>if (overlap)
os.print(sep + sampleID + "_overlap");</BUG>
if (span)

if (readGroups != null && readGroups.size() > 0){
sampleID = readGroups.get(0).getSample();
}
if (sampleID == null){
sampleID = file.getName().replace(".sam", "").replace(".bam","");
}
if (overlap)
os.print(sep + sampleID + "_overlap");
if (contained)
os.print(sep + sampleID + "_contained");
if (span)
