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Removed evidence of a previous incarnation of data sharding. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@766 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-05-20 20:48:33 +00:00
parent 3cad580655
commit e7a6f8cdc4
1 changed files with 0 additions and 48 deletions
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48
java/src/org/broadinstitute/sting/gatk/dataSources/ReadDataSource.java
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@ -1,48 +0,0 @@
package org.broadinstitute.sting.gatk.dataSources;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMRecord;
import java.util.Iterator;
import java.io.File;
import org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator;
import org.broadinstitute.sting.gatk.iterators.ReferenceIterator;
import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
/**
* User: aaron
* Date: Mar 26, 2009
* Time: 10:35:40 AM
* <p/>
* 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.
* <p/>
* 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.
*/
public class ReadDataSource {
/**
* our SAM data files
*/
// our SAM reader
private SAMFileReader samReader = null;
// iterator over the sam records in the readsFile
private Iterator<SAMRecord> samReadIter = null;
// The verifying iterator, it does checking
VerifyingSamIterator verifyingSamReadIter = null;
/**
* our reference data source
*/
// The reference data -- filename, refSeqFile, and iterator
private File refFileName = null; // the name of the reference file
//private ReferenceSequenceFile refFile = null;
private FastaSequenceFile2 refFile = null; // todo: merge FastaSequenceFile2 into picard!
private ReferenceIterator refIter = null;
}