/** * HACK: This is used to make a copy of a read. Really, SAMRecord should provide a copy * constructor or a factory method. */ public static SAMRecord cloneSAMRecord(final SAMRecord originalRead) { if (originalRead == null) { return null; } try { return (SAMRecord) originalRead.clone(); } catch (final CloneNotSupportedException e) { throw new IllegalStateException(e); } }