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Minor reformating for pooled calling 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2063 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-11-17 22:06:11 +00:00
parent ec1a870905
commit 42a0bbaf46
4 changed files with 15 additions and 7 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
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@ -18,6 +18,10 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
return splitContextBySample(context);
}
protected int getNSamples(HashMap<String, AlignmentContextBySample> contexts) {
return contexts.size();
}
protected void initializeLikelihoods(char ref, HashMap<String, AlignmentContextBySample> contexts, StratifiedContext contextType) {
GLs.clear();

4
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
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@ -36,7 +36,7 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
protected abstract void initializeLikelihoods(char ref, HashMap<String, AlignmentContextBySample> contexts, StratifiedContext contextType);
protected abstract double computeLog10PofDgivenAFi(DiploidGenotype refGenotype, DiploidGenotype hetGenotype, DiploidGenotype homGenotype, double f);
protected abstract List<Genotype> makeGenotypeCalls(char ref, HashMap<String, AlignmentContextBySample> contexts, GenomeLoc loc);
protected abstract int getNSamples(HashMap<String, AlignmentContextBySample> contexts);
public Pair<List<Genotype>, GenotypeLocusData> calculateGenotype(RefMetaDataTracker tracker, char ref, AlignmentContext context, DiploidGenotypePriors priors) {
@ -45,7 +45,7 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
if ( contexts == null )
return null;
int numSamples = contexts.size();
int numSamples = getNSamples(contexts);
int frequencyEstimationPoints = (2 * numSamples) + 1; // (add 1 for allele frequency of zero)
initializeAlleleFrequencies(frequencyEstimationPoints);

12
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PooledCalculationModel.java
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@ -10,9 +10,13 @@ import net.sf.samtools.SAMRecord;
public class PooledCalculationModel extends JointEstimateGenotypeCalculationModel {
protected PooledCalculationModel() {}
protected PooledCalculationModel() {
}
protected int getNSamples(HashMap<String, AlignmentContextBySample> contexts) {
return POOL_SIZE;
}
protected HashMap<String, AlignmentContextBySample> createContexts(AlignmentContext context) {
// for testing purposes, we may want to throw multi-samples at pooled mode,
// so we can't use the standard splitContextBySample() method here
@ -48,10 +52,10 @@ public class PooledCalculationModel extends JointEstimateGenotypeCalculationMode
}
protected double computeLog10PofDgivenAFi(DiploidGenotype refGenotype, DiploidGenotype hetGenotype, DiploidGenotype homGenotype, double f) {
System.out.printf("%s %.2f%n", hetGenotype, f);
// TODO -- IMPLEMENT ME
return 0.0;
return -100.0;
}
protected List<Genotype> makeGenotypeCalls(char ref, HashMap<String, AlignmentContextBySample> contexts, GenomeLoc loc) {

2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -77,7 +77,7 @@ public class UnifiedArgumentCollection {
@Argument(fullName = "max_deletions", shortName = "deletions", doc = "Maximum reads with deletions spanning this locus for it to be callable [to disable, set to < 0; default:1]", required = false)
public Integer MAX_DELETIONS = 1;
@Argument(fullName = "max_coverage", shortName = "coverage", doc = "Maximum reads at this locus for it to be callable; to disable, provide value < 1 [default:10,000]", required = false)
@Argument(fullName = "max_coverage", shortName = "mc", doc = "Maximum reads at this locus for it to be callable; to disable, provide value < 1 [default:10,000]", required = false)
public Integer MAX_READS_IN_PILEUP = 10000;
@Argument(fullName = "min_allele_frequency", shortName = "min_freq", doc = "The minimum possible allele frequency in a population (advanced)", required = false)