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The traversal engine now passes the reduce result to OnTraversalDone() in the walker base class 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@210 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-03-27 13:44:46 +00:00
parent d115209e86
commit 826781a760
5 changed files with 10 additions and 7 deletions
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4
java/src/org/broadinstitute/sting/gatk/TraversalEngine.java
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@ -616,7 +616,7 @@ public class TraversalEngine {
} }
printOnTraversalDone("loci", sum); printOnTraversalDone("loci", sum);
walker.onTraversalDone(); walker.onTraversalDone(sum);
return 0; return 0;
} }
@ -738,7 +738,7 @@ public class TraversalEngine {
} }
printOnTraversalDone("reads", sum); printOnTraversalDone("reads", sum);
walker.onTraversalDone(); walker.onTraversalDone(sum);
return 0; return 0;
} }
} }

2
java/src/org/broadinstitute/sting/gatk/WalkerManager.java
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@ -338,7 +338,7 @@ public class WalkerManager {
for (Class<Walker> walkerClass : walkerClasses) { for (Class<Walker> walkerClass : walkerClasses) {
String walkerName = getWalkerName(walkerClass); String walkerName = getWalkerName(walkerClass);
logger.info(String.format("* Adding module %s%n", walkerName)); logger.info(String.format("* Adding module %s", walkerName));
walkers.put(walkerName, walkerClass); walkers.put(walkerName, walkerClass);
} }

2
java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java
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@ -12,7 +12,7 @@ import java.util.List;
* Time: 2:52:28 PM * Time: 2:52:28 PM
* To change this template use File | Settings | File Templates. * To change this template use File | Settings | File Templates.
*/ */
public abstract class LocusWalker<MapType, ReduceType> extends Walker { public abstract class LocusWalker<MapType, ReduceType> extends Walker<ReduceType> {
// Do we actually want to operate on the context? // Do we actually want to operate on the context?
public boolean filter(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) { public boolean filter(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
return true; // We are keeping all the reads return true; // We are keeping all the reads

2
java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java
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@ -10,7 +10,7 @@ import org.broadinstitute.sting.gatk.LocusContext;
* Time: 2:52:28 PM * Time: 2:52:28 PM
* To change this template use File | Settings | File Templates. * To change this template use File | Settings | File Templates.
*/ */
public abstract class ReadWalker<MapType, ReduceType> extends Walker { public abstract class ReadWalker<MapType, ReduceType> extends Walker<ReduceType> {
public boolean requiresOrderedReads() { return false; } public boolean requiresOrderedReads() { return false; }
// Do we actually want to operate on the context? // Do we actually want to operate on the context?

7
java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
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@ -9,7 +9,7 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisTK;
* Time: 1:53:31 PM * Time: 1:53:31 PM
* To change this template use File | Settings | File Templates. * To change this template use File | Settings | File Templates.
*/ */
public abstract class Walker { public abstract class Walker<ReduceType> {
// TODO: Can a walker be templatized so that map and reduce live here? // TODO: Can a walker be templatized so that map and reduce live here?
protected Walker() { protected Walker() {
@ -27,5 +27,8 @@ public abstract class Walker {
} }
public void initialize() { } public void initialize() { }
public void onTraversalDone() { } public void onTraversalDone(ReduceType result) {
// TODO: replace with the correct output stream
System.out.println("[REDUCE RESULT] Traversal result is: " + result);
}
} }