/**
* 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);
}
