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Temp checkin just for experimentation: exposed probabilistic alignment parameters to command line interface to make it easier to experiment on their effects, although a full scrap/rewrite of this should be coming soon. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5218 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2011-02-08 17:33:29 +00:00
parent e5cfc6ae74
commit 3635606cd8
2 changed files with 13 additions and 5 deletions
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7
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java
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@ -48,9 +48,6 @@ import java.util.*;
public class DindelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsCalculationModel { public class DindelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsCalculationModel {
private final int maxReadDeletionLength = 3; private final int maxReadDeletionLength = 3;
private final double insertionStartProbability = 1e-3;
private final double insertionEndProbability = 0.5;
private final double alphaDeletionProbability = 1e-3;
private final int HAPLOTYPE_SIZE = 80; private final int HAPLOTYPE_SIZE = 80;
private final int minIndelCountForGenotyping; private final int minIndelCountForGenotyping;
@ -65,8 +62,8 @@ public class DindelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoo
private List<Allele> alleleList; private List<Allele> alleleList;
protected DindelGenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) { protected DindelGenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) {
super(UAC, logger); super(UAC, logger);
model = new HaplotypeIndelErrorModel(maxReadDeletionLength, insertionStartProbability, model = new HaplotypeIndelErrorModel(maxReadDeletionLength, UAC.INSERTION_START_PROBABILITY,
insertionEndProbability, alphaDeletionProbability, HAPLOTYPE_SIZE, false, DEBUGOUT); UAC.INSERTION_END_PROBABILITY, UAC.ALPHA_DELETION_PROBABILITY, HAPLOTYPE_SIZE, false, DEBUGOUT);
alleleList = new ArrayList<Allele>(); alleleList = new ArrayList<Allele>();
getAlleleListFromVCF = UAC.GET_ALLELES_FROM_VCF; getAlleleListFromVCF = UAC.GET_ALLELES_FROM_VCF;
minIndelCountForGenotyping = UAC.MIN_INDEL_COUNT_FOR_GENOTYPING; minIndelCountForGenotyping = UAC.MIN_INDEL_COUNT_FOR_GENOTYPING;

11
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -99,6 +99,14 @@ public class UnifiedArgumentCollection {
@Argument(fullName = "indel_heterozygosity", shortName = "indelHeterozygosity", doc = "Heterozygosity for indel calling", required = false) @Argument(fullName = "indel_heterozygosity", shortName = "indelHeterozygosity", doc = "Heterozygosity for indel calling", required = false)
public double INDEL_HETEROZYGOSITY = 1.0/8000; public double INDEL_HETEROZYGOSITY = 1.0/8000;
@Argument(fullName = "insertionStartProbability", shortName = "insertionStartProbability", doc = "Heterozygosity for indel calling", required = false)
public double INSERTION_START_PROBABILITY = 1e-3;
@Argument(fullName = "insertionEndProbability", shortName = "insertionEndProbability", doc = "Heterozygosity for indel calling", required = false)
public double INSERTION_END_PROBABILITY = 0.5;
@Argument(fullName = "alphaDeletionProbability", shortName = "alphaDeletionProbability", doc = "Heterozygosity for indel calling", required = false)
public double ALPHA_DELETION_PROBABILITY = 1e-3;
public UnifiedArgumentCollection clone() { public UnifiedArgumentCollection clone() {
UnifiedArgumentCollection uac = new UnifiedArgumentCollection(); UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
@ -121,6 +129,9 @@ public class UnifiedArgumentCollection {
uac.GET_ALLELES_FROM_VCF = GET_ALLELES_FROM_VCF; uac.GET_ALLELES_FROM_VCF = GET_ALLELES_FROM_VCF;
uac.MIN_INDEL_COUNT_FOR_GENOTYPING = MIN_INDEL_COUNT_FOR_GENOTYPING; uac.MIN_INDEL_COUNT_FOR_GENOTYPING = MIN_INDEL_COUNT_FOR_GENOTYPING;
uac.INDEL_HETEROZYGOSITY = INDEL_HETEROZYGOSITY; uac.INDEL_HETEROZYGOSITY = INDEL_HETEROZYGOSITY;
uac.INSERTION_START_PROBABILITY = INSERTION_START_PROBABILITY;
uac.INSERTION_END_PROBABILITY = INSERTION_END_PROBABILITY;
uac.ALPHA_DELETION_PROBABILITY = ALPHA_DELETION_PROBABILITY;
return uac; return uac;
} }