/**
* Shallow copy of everything, except for the attribute list and the temporary attributes. A new
* list of the attributes is created for both, but the attributes themselves are copied by
* reference. This should be safe because callers should never modify a mutable value returned by
* any of the get() methods anyway.
*
* @return a shallow copy of the GATKSAMRecord
*/
@Override
public Object clone() {
try {
final GATKSAMRecord clone = (GATKSAMRecord) super.clone();
if (temporaryAttributes != null) {
clone.temporaryAttributes = new HashMap<>();
for (Object attribute : temporaryAttributes.keySet())
clone.setTemporaryAttribute(attribute, temporaryAttributes.get(attribute));
}
return clone;
} catch (final CloneNotSupportedException e) {
throw new RuntimeException(e);
}
}
