diff --git a/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java b/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java index 46ef0b546..e77471aee 100755 --- a/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java @@ -616,7 +616,7 @@ public class TraversalEngine { } printOnTraversalDone("loci", sum); - walker.onTraversalDone(); + walker.onTraversalDone(sum); return 0; } @@ -738,7 +738,7 @@ public class TraversalEngine { } printOnTraversalDone("reads", sum); - walker.onTraversalDone(); + walker.onTraversalDone(sum); return 0; } } diff --git a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java index 360f1d435..030f39e9e 100755 --- a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java +++ b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java @@ -338,7 +338,7 @@ public class WalkerManager { for (Class walkerClass : walkerClasses) { 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); } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java index 83d4f102f..a7e371cbb 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java @@ -12,7 +12,7 @@ import java.util.List; * Time: 2:52:28 PM * To change this template use File | Settings | File Templates. */ -public abstract class LocusWalker extends Walker { +public abstract class LocusWalker extends Walker { // Do we actually want to operate on the context? public boolean filter(List rodData, char ref, LocusContext context) { return true; // We are keeping all the reads diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java index dbc073eb7..093d55916 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java @@ -10,7 +10,7 @@ import org.broadinstitute.sting.gatk.LocusContext; * Time: 2:52:28 PM * To change this template use File | Settings | File Templates. */ -public abstract class ReadWalker extends Walker { +public abstract class ReadWalker extends Walker { public boolean requiresOrderedReads() { return false; } // Do we actually want to operate on the context? diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java b/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java index dc69ab344..101595a1c 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java @@ -9,7 +9,7 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisTK; * Time: 1:53:31 PM * To change this template use File | Settings | File Templates. */ -public abstract class Walker { +public abstract class Walker { // TODO: Can a walker be templatized so that map and reduce live here? protected Walker() { @@ -27,5 +27,8 @@ public abstract class Walker { } 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); + } }