diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ReadShardStrategy.java b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ReadShardStrategy.java new file mode 100755 index 000000000..9d7d7287a --- /dev/null +++ b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ReadShardStrategy.java @@ -0,0 +1,82 @@ +package org.broadinstitute.sting.gatk.dataSources.shards; + +import net.sf.samtools.SAMSequenceDictionary; + +import java.util.Iterator; + +/** + * + * User: aaron + * Date: Apr 14, 2009 + * Time: 1:34:28 PM + * + * The Broad Institute + * SOFTWARE COPYRIGHT NOTICE AGREEMENT + * This software and its documentation are copyright 2009 by the + * Broad Institute/Massachusetts Institute of Technology. All rights are reserved. + * + * This software is supplied without any warranty or guaranteed support whatsoever. Neither + * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality. + * + */ + + +/** + * @author aaron + * @version 1.0 + * @date Apr 14, 2009 + *
+ * Class ReadShardStrategy + * + * A descriptions should go here. Blame aaron if it's missing. + */ +public class ReadShardStrategy implements ShardStrategy { + + // do we use unmapped reads in the sharding strategy + private boolean unMappedReads = true; + + // our read bucket size, default + public long readCount = 100000; + + // our sequence dictionary + final private SAMSequenceDictionary dic; + + /** + * the default constructor + * @param dic the dictionary + * @param size the read count to iterate over + */ + ReadShardStrategy(SAMSequenceDictionary dic, long size) { + this.dic = dic; + readCount = size; + } + + /** + * do we have another read shard? + * @return + */ + public boolean hasNext() { + return true; + } + + public Shard next() { + return null; //To change body of implemented methods use File | Settings | File Templates. + } + + public void remove() { + throw new UnsupportedOperationException("Remove not supported"); + } + + public Iterator