@Override
public GCResult createResult(Result result) {
if (result.getRow() != null) {
GCResult gcResult = new GCResult(result.getRow());
gcResult.setChromosome(result.getValue(Bytes.toBytes("chr"), Bytes.toBytes("name")));
byte[] family = Bytes.toBytes("gc");
gcResult.setMin(result.getValue(family, Bytes.toBytes("min")));
gcResult.setMax(result.getValue(family, Bytes.toBytes("max")));
gcResult.setTotalFragments(result.getValue(Bytes.toBytes("frag"), Bytes.toBytes("total")));
return gcResult;
}
return null;
}
public Map<String, List<GCResult>> getBins() throws IOException {
Map<String, List<GCResult>> byChr = new HashMap<String, List<GCResult>>();
for (GCResult r : this.getRows()) {
if (!byChr.containsKey(r.getChromosome()))
byChr.put(r.getChromosome(), new ArrayList<GCResult>());
byChr.get(r.getChromosome()).add(r);
}
for (String chr : byChr.keySet()) {
Collections.sort(
byChr.get(chr),
new Comparator<GCResult>() {
@Override
public int compare(GCResult a, GCResult b) {
return (a.getMax() < b.getMax()) ? -1 : (a.getMax() > b.getMax()) ? 1 : 0;
}
});
}
return byChr;
}
