/** * Method that combines the fingerprint evidence across all the read groups for the same library * and then produces a matrix of LOD scores for comparing every library with every other library. */ private void crossCheckLibraries( final Map<SAMReadGroupRecord, Fingerprint> fingerprints, final PrintStream out) { final List<Fingerprint> fixedFps = new ArrayList<>(); for (final SAMReadGroupRecord rg : fingerprints.keySet()) { final Fingerprint old = fingerprints.get(rg); final String name = rg.getSample() + "::" + rg.getLibrary(); final Fingerprint newFp = new Fingerprint(name, old.getSource(), old.getInfo()); newFp.putAll(old); fixedFps.add(newFp); } crossCheckSamples(fixedFps, out); }