import java.io.FileNotFoundException;
import java.util.List;
public abstract class MicroScheduler {
<BUG>private List<File> reads;</BUG>
private static long SHARD_SIZE = 100000L;
<BUG>protected static Logger logger = Logger.getLogger(MicroScheduler.class);
protected IndexedFastaSequenceFile reference;

protected TraversalEngine traversalEngine = null;
public static MicroScheduler create( Walker walker, List<File> reads, File ref, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods, int nThreadsToUse ) {</BUG>
if( walker instanceof TreeReducible && nThreadsToUse > 1 ) {

import java.io.FileNotFoundException;
import java.util.List;
public abstract class MicroScheduler {
private static long SHARD_SIZE = 100000L;
protected static Logger logger = Logger.getLogger(MicroScheduler.class);
protected final TraversalEngine traversalEngine;
protected final IndexedFastaSequenceFile reference;
private final SAMDataSource reads;
public static MicroScheduler create( Walker walker, List<File> reads, File ref, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods, int nThreadsToUse ) {
if( walker instanceof TreeReducible && nThreadsToUse > 1 ) {
