diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java index 3ff55bab6..dd8cd1c26 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java @@ -24,7 +24,7 @@ import net.sf.samtools.SAMRecord; */ @By(DataSource.REFERENCE) @Reference(window=@Window(start=-3,stop=3)) -public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker,Set> { +public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker,Set> implements TreeReducible> { @Argument(fullName="usePreviousBases", doc="Use previous bases of the reference as part of the calculation, uses the specified number, defaults to 0", required=false) int nPreviousBases = 0; @Argument(fullName="useSecondaryBase",doc="Use the secondary base of a read as part of the calculation", required=false) @@ -111,6 +111,10 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker treeReduce( Set reduce1, Set reduce2 ) { + return reduce(reduce1,reduce2); + } + public void onTraversalDone( Set conditionalTables ) { out.print(createHeaderFromConditions()); for ( BaseTransitionTable t : conditionalTables ) diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaIntegrationTest.java index 5b787dc5d..e908ae339 100644 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaIntegrationTest.java @@ -13,7 +13,7 @@ import java.util.Arrays; * To change this template use File | Settings | File Templates. */ public class BaseTransitionTableCalculatorJavaIntegrationTest extends WalkerTest{ - // MD5s last computed 10/20 at revision 1877 + // MD5s last computed 10/21 at revision 1897 public static final String OUTPUT_MD5_STANDARD = "e88f010ea842bcdb6503a4da24b90edc"; public static final String OUTPUT_MD5_3MISMATCHES = "46f9aadbfe260a286fb6c8cac137dddd"; public static final String OUTPUT_MD5_LOWMAPPINGQUALITY = "0b7447e0a271ffa5c8ff1719db3585e6";