public DataBag exec(Tuple input) throws IOException {
DataBag output = DefaultBagFactory.getInstance().newDefaultBag();
if (input == null || input.size() == 0) return null;
try {
String seq = ((String) input.get(0));
// byte[] ba = ((DataByteArray) input.get(0)).get();
int distance = (Integer) input.get(1);
// int seqLength = SequenceString.numBases(ba);
// String seq = SequenceString.byteArrayToSequence(ba);
Set<String> neighbors = MetaUtils.generateAllNeighborsWithinDistance(seq, distance);
for (String n : neighbors) {
Tuple t = DefaultTupleFactory.getInstance().newTuple(1);
t.set(0, n);
output.add(t);
}
} catch (Exception e) {
System.err.println("HammingDistance: failed to process input; error - " + e.getMessage());
return null;
}
return output;
}
