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Moving to private

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Eric Banks 2011-10-28 09:29:28 -04:00
parent 1bdd76c2f2
commit 4ba7c0cecd
1 changed files with 0 additions and 70 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignedReadCounter.java
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/*
* Copyright (c) 2010.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.walkers.indels;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.By;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
@By(DataSource.READS)
// walker to count realigned reads
public class RealignedReadCounter extends ReadWalker<Integer, Integer> {
public static final String ORIGINAL_CIGAR_TAG = "OC";
public static final String ORIGINAL_POSITION_TAG = "OP";
private long updatedReads = 0;
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
if ( read.getAttribute(ORIGINAL_CIGAR_TAG) != null ) {
String newCigar = (String)read.getAttribute(ORIGINAL_CIGAR_TAG);
// deal with an old bug
if ( read.getCigar().toString().equals(newCigar) ) {
return 0;
}
updatedReads++;
}
return 0;
}
public Integer reduceInit() {
return 0;
}
public Integer reduce(Integer value, Integer sum) {
return sum + value;
}
public void onTraversalDone(Integer result) {
System.out.println(updatedReads + " reads were updated");
}
}