From aaf952469eab82ffdc7d21517075554b52158c19 Mon Sep 17 00:00:00 2001 From: Laura Gauthier Date: Sun, 1 Mar 2015 14:31:08 -0500 Subject: [PATCH] Change UG @PartitionBy to fix Queue tests --- .../gatk/tools/walkers/genotyper/UnifiedGenotyper.java | 1 + 1 file changed, 1 insertion(+) diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java index b3fe7867a..31999f522 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java @@ -156,6 +156,7 @@ import java.util.*; @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = ReadTransformer.ApplicationTime.ON_INPUT) @ReadFilters( {BadMateFilter.class, MappingQualityUnavailableFilter.class} ) @Reference(window=@Window(start=-200,stop=200)) +@PartitionBy(value = PartitionType.LOCUS, includeUnmapped = false) @By(DataSource.REFERENCE) // TODO -- When LocusIteratorByState gets cleaned up, we should enable multiple @By sources: // TODO -- @By( {DataSource.READS, DataSource.REFERENCE_ORDERED_DATA} )