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Further trivial cleanup: Renamed DindelGenotypeLikelihoodsCalculationModel to IndelGenotypeLikelihoodsCalculationModel 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5616 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2011-04-12 18:00:48 +00:00
parent 3b424fd74d
commit 488622041d
2 changed files with 3 additions and 3 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java → java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
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@ -47,7 +47,7 @@ import org.broadinstitute.sting.utils.sam.ReadUtils;
import java.util.*; import java.util.*;
public class DindelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsCalculationModel { public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsCalculationModel {
private final int maxReadDeletionLength = 3; private final int maxReadDeletionLength = 3;
private final int HAPLOTYPE_SIZE; private final int HAPLOTYPE_SIZE;
@ -66,7 +66,7 @@ public class DindelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoo
private GenomeLoc lastSiteVisited; private GenomeLoc lastSiteVisited;
private List<Allele> alleleList; private List<Allele> alleleList;
protected DindelGenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) { protected IndelGenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) {
super(UAC, logger); super(UAC, logger);
pairModel = new PairHMMIndelErrorModel(UAC.INDEL_GAP_OPEN_PENALTY,UAC.INDEL_GAP_CONTINUATION_PENALTY, 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); UAC.OUTPUT_DEBUG_INDEL_INFO, UAC.DO_CONTEXT_DEPENDENT_PENALTIES, UAC.dovit);

2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -638,7 +638,7 @@ public class UnifiedGenotyperEngine {
private static Map<GenotypeLikelihoodsCalculationModel.Model, GenotypeLikelihoodsCalculationModel> getGenotypeLikelihoodsCalculationObject(Logger logger, UnifiedArgumentCollection UAC) { private static Map<GenotypeLikelihoodsCalculationModel.Model, GenotypeLikelihoodsCalculationModel> getGenotypeLikelihoodsCalculationObject(Logger logger, UnifiedArgumentCollection UAC) {
Map<GenotypeLikelihoodsCalculationModel.Model, GenotypeLikelihoodsCalculationModel> glcm = new HashMap<GenotypeLikelihoodsCalculationModel.Model, GenotypeLikelihoodsCalculationModel>(); Map<GenotypeLikelihoodsCalculationModel.Model, GenotypeLikelihoodsCalculationModel> glcm = new HashMap<GenotypeLikelihoodsCalculationModel.Model, GenotypeLikelihoodsCalculationModel>();
glcm.put(GenotypeLikelihoodsCalculationModel.Model.SNP, new SNPGenotypeLikelihoodsCalculationModel(UAC, logger)); 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; return glcm;
} }