import java.util.ArrayList;
import net.sf.samtools.SAMSequenceDictionary;
import net.sf.samtools.SAMSequenceRecord;
public class MonolithicShard implements Shard {
private final ShardType shardType;
<BUG>private final List<GenomeLoc> locs = new ArrayList<GenomeLoc>();
public MonolithicShard(ShardType shardType, SAMSequenceDictionary sequenceDictionary) {
if(shardType != ShardType.LOCUS && shardType != ShardType.READ)</BUG>
throw new StingException("Invalid shard type for monolithic shard: " + shardType);
<BUG>this.shardType = shardType;
for(SAMSequenceRecord sequenceRecord: sequenceDictionary.getSequences())
locs.add(GenomeLocParser.createGenomeLoc(sequenceRecord.getSequenceName(),1,sequenceRecord.getSequenceLength()));</BUG>
}

import java.util.ArrayList;
import net.sf.samtools.SAMSequenceDictionary;
import net.sf.samtools.SAMSequenceRecord;
public class MonolithicShard implements Shard {
private final ShardType shardType;
private final List<GenomeLoc> locs;
public MonolithicShard(ShardType shardType, List<GenomeLoc> locs) {
if(shardType != ShardType.LOCUS && shardType != ShardType.READ)
throw new StingException("Invalid shard type for monolithic shard: " + shardType);
this.shardType = shardType;
this.locs = locs;
}
