diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java similarity index 98% rename from java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java rename to java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java index e37b0ccc5..e5a9927e4 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java @@ -47,7 +47,7 @@ import org.broadinstitute.sting.utils.sam.ReadUtils; import java.util.*; -public class DindelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsCalculationModel { +public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsCalculationModel { private final int maxReadDeletionLength = 3; private final int HAPLOTYPE_SIZE; @@ -66,7 +66,7 @@ public class DindelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoo private GenomeLoc lastSiteVisited; private List alleleList; - protected DindelGenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) { + protected IndelGenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) { super(UAC, logger); pairModel = new PairHMMIndelErrorModel(UAC.INDEL_GAP_OPEN_PENALTY,UAC.INDEL_GAP_CONTINUATION_PENALTY, UAC.OUTPUT_DEBUG_INDEL_INFO, UAC.DO_CONTEXT_DEPENDENT_PENALTIES, UAC.dovit); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index c0d092afd..db860029b 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -638,7 +638,7 @@ public class UnifiedGenotyperEngine { private static Map getGenotypeLikelihoodsCalculationObject(Logger logger, UnifiedArgumentCollection UAC) { Map glcm = new HashMap(); glcm.put(GenotypeLikelihoodsCalculationModel.Model.SNP, new SNPGenotypeLikelihoodsCalculationModel(UAC, logger)); - glcm.put(GenotypeLikelihoodsCalculationModel.Model.INDEL, new DindelGenotypeLikelihoodsCalculationModel(UAC, logger)); + glcm.put(GenotypeLikelihoodsCalculationModel.Model.INDEL, new IndelGenotypeLikelihoodsCalculationModel(UAC, logger)); return glcm; }