diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlignedReadsHistoWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlignedReadsHistoWalker.java index 7657d71b7..10bd5ad3c 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlignedReadsHistoWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlignedReadsHistoWalker.java @@ -45,7 +45,7 @@ public class AlignedReadsHistoWalker extends ReadWalker { return value + sum; } - public void onTraversalDone() { + public void onTraversalDone(Integer result) { int curTotal = 0; for ( int i = 0; i < alignCounts.length; i++ ) { curTotal += alignCounts[i]; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyMetricsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyMetricsWalker.java index 2c0c9b42d..5ef12ef87 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyMetricsWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyMetricsWalker.java @@ -159,7 +159,7 @@ public class AlleleFrequencyMetricsWalker extends LocusWalker { diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityHistoWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityHistoWalker.java index 74c4358b4..f0767bbdb 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityHistoWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityHistoWalker.java @@ -43,7 +43,7 @@ public class BaseQualityHistoWalker extends ReadWalker { return value + sum; } - public void onTraversalDone() { + public void onTraversalDone(Integer result) { int lastNonZero = -1; for ( int i = this.qualCounts.length-1; i >= 0; i-- ) { if ( this.qualCounts[i] > 0 ) { diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java index 4a5c8051a..9165ac8cd 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java @@ -70,7 +70,7 @@ public class MismatchHistoWalker extends ReadWalker { return value + sum; } - public void onTraversalDone() { + public void onTraversalDone(Integer result) { for ( int i = 0; i < mismatchCounts.length; i++ ) out.println((i+1) + "\t" + mismatchCounts[i]); }