private String getIdentifier(SAMRecord read) {
String id = read.getReadName();
if (read.getReadPairedFlag() && read.getSecondOfPairFlag()) {
id += "_2";
}
return id;
}
@Override
public boolean nextKeyValue() {
long virtPos;
while ((virtPos = bci.getFilePointer()) < virtualEnd
|| (keepReadPairsTogether && readPair && !lastOfPair)) {
final SAMRecord r = codec.decode();
if (r == null) return false;
// Since we're reading from a BAMRecordCodec directly we have to set the
// validation stringency ourselves.
if (this.stringency != null) r.setValidationStringency(this.stringency);
readPair = r.getReadPairedFlag();
if (readPair) {
boolean first = r.getFirstOfPairFlag(), second = r.getSecondOfPairFlag();
// According to the SAM spec (section 1.4) it is possible for pairs to have
// multiple segments (i.e. more than two), in which case both `first` and
// `second` will be true.
boolean firstOfPair = first && !second;
lastOfPair = !first && second;
// ignore any template that is not first in a pair right at the start of a split
// since it will have been returned in the previous split
if (virtPos == virtualStart && keepReadPairsTogether && !firstOfPair) {
continue;
}
}
if (!overlaps(r)) {
continue;
}
key.set(getKey(r));
record.set(r);
return true;
}
return false;
}
