55 lines
1.5 KiB
Java
Executable File
55 lines
1.5 KiB
Java
Executable File
package org.broadinstitute.sting.gatk.walkers;
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import java.io.PrintStream;
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import org.broadinstitute.sting.gatk.GenomeAnalysisTK;
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/**
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* Created by IntelliJ IDEA.
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* User: hanna
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* Date: Mar 17, 2009
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* Time: 1:53:31 PM
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* To change this template use File | Settings | File Templates.
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*/
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public abstract class Walker<MapType, ReduceType> {
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// TODO: Can a walker be templatized so that map and reduce live here?
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/**
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* A stream for writing normal (non-error) output. System.out by default.
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*/
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protected PrintStream out = null;
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/**
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* A stream for writing error output. System.err by default.
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*/
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protected PrintStream err = null;
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protected Walker() {
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if( GenomeAnalysisTK.Instance != null ) {
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GenomeAnalysisTK.Instance.loadArgumentsIntoObject(this);
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out = GenomeAnalysisTK.Instance.out;
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err = GenomeAnalysisTK.Instance.err;
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}
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else {
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out = System.out;
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err = System.err;
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}
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}
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/**
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* Retrieve the toolkit, for peering into internal structures that can't
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* otherwise be read. Use sparingly, and discuss uses with software engineering
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* team.
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* @return The genome analysis toolkit.
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*/
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protected GenomeAnalysisTK getToolkit() {
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return GenomeAnalysisTK.Instance;
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}
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public void initialize() { }
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public void onTraversalDone(ReduceType result) {
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// TODO: replace with the correct output stream
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System.out.println("[REDUCE RESULT] Traversal result is: " + result);
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}
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}
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