@Override
public boolean isDone() {
for (PerReadGroupInfo info : readGroupInfo.values()) {
if (info.needsMoreData()) return false;
}
return true;
}
@Override
public Integer map(
ReferenceContext referenceContext,
GATKSAMRecord read,
RefMetaDataTracker RefMetaDataTracker) {
final String rgID = read.getReadGroup().getId();
final PerReadGroupInfo info = readGroupInfo.get(rgID);
if (info.needsMoreData()) {
info.readLength.add(read.getReadLength());
info.nReadsSeen++;
if (read.getReadPairedFlag()) {
info.nReadsPaired++;
if (read.getInferredInsertSize() != 0) {
info.insertSize.add(Math.abs(read.getInferredInsertSize()));
}
}
}
return null;
}