/** Note: this is the only getKey function that handles unmapped reads specially! */
public static long getKey(final SAMRecord rec) {
final int refIdx = rec.getReferenceIndex();
final int start = rec.getAlignmentStart();
if (!(rec.getReadUnmappedFlag() || refIdx < 0 || start < 0)) return getKey(refIdx, start);
// Put unmapped reads at the end, but don't give them all the exact same
// key so that they can be distributed to different reducers.
//
// A random number would probably be best, but to ensure that the same
// record always gets the same key we use a fast hash instead.
//
// We avoid using hashCode(), because it's not guaranteed to have the
// same value across different processes.
int hash = 0;
byte[] var;
if ((var = rec.getVariableBinaryRepresentation()) != null) {
// Undecoded BAM record: just hash its raw data.
hash = (int) MurmurHash3.murmurhash3(var, hash);
} else {
// Decoded BAM record or any SAM record: hash a few representative
// fields together.
hash = (int) MurmurHash3.murmurhash3(rec.getReadName(), hash);
hash = (int) MurmurHash3.murmurhash3(rec.getReadBases(), hash);
hash = (int) MurmurHash3.murmurhash3(rec.getBaseQualities(), hash);
hash = (int) MurmurHash3.murmurhash3(rec.getCigarString(), hash);
}
return getKey0(Integer.MAX_VALUE, hash);
}
