41 lines
1.2 KiB
Java
Executable File
41 lines
1.2 KiB
Java
Executable File
package edu.mit.broad.sting.atk.modules;
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import edu.mit.broad.sting.atk.LocusWalker;
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import edu.mit.broad.sting.atk.LocusIterator;
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import edu.mit.broad.sting.utils.ReferenceOrderedDatum;
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import edu.mit.broad.sam.SAMRecord;
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import java.util.List;
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/**
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* Created by IntelliJ IDEA.
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* User: mdepristo
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* Date: Feb 22, 2009
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* Time: 3:22:14 PM
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* To change this template use File | Settings | File Templates.
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*/
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public class CountLociWalker implements LocusWalker<Integer, Integer> {
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public void initialize() {
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}
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public String walkerType() { return "ByLocus"; }
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// Do we actually want to operate on the context?
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public boolean filter(List<ReferenceOrderedDatum> rodData, char ref, LocusIterator context) {
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return true; // We are keeping all the reads
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}
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// Map over the edu.mit.broad.sting.atk.LocusContext
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public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusIterator context) {
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return 1;
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}
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// Given result of map function
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public Integer reduceInit() { return 0; }
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public Integer reduce(Integer value, Integer sum) {
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return value + sum;
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}
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public void onTraveralDone() {
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}
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} |