public Map<String, Double> methLevels(IupacPatterns patterns) {
Map<String, Double> out = new HashMap<String, Double>();
Map<String, FractionNonidentical> orig = this.methLevelsFractions(patterns);
for (String key : orig.keySet()) {
FractionNonidentical frac = orig.get(key);
out.put(key, frac.doubleValue());
}
return out;
}
public Map<String, FractionNonidentical> methLevelsFractions(IupacPatterns patterns) {
Map<String, FractionNonidentical> out = new HashMap<String, FractionNonidentical>();
Iterator<Cpg> it = this.iterator();
while (it.hasNext()) {
Cpg cpg = it.next();
String contextOrig = cpg.getPrevBasesRef() + "C" + cpg.getNextBasesRef();
String context = patterns.firstMatch(contextOrig);
// System.err.printf("Read at pos %d, cpg at pos %d: contextOrig=%s, context=%s\n",
// this.midpointChromPos(), cpg.chromPos, contextOrig, context);
if (context != null) {
FractionNonidentical frac = out.get(context);
if (frac == null) {
frac = new FractionNonidentical();
}
frac.incDenominator();
if (cpg.cReads > 0) frac.incNumerator();
out.put(context, frac);
}
}
return out;
}