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Exact model code cleanup 

-- Fixed up code when fixing a bug detected by aggressive contracts in GenotypesContext.
This commit is contained in:
Mark DePristo 2011-11-21 14:35:15 -05:00
parent 2c501364b8
commit 1561af22af
1 changed files with 45 additions and 59 deletions
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28
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
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@ -42,6 +42,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
private final static double MAX_LOG10_ERROR_TO_STOP_EARLY = 6; // we want the calculation to be accurate to 1 / 10^6 private final static double MAX_LOG10_ERROR_TO_STOP_EARLY = 6; // we want the calculation to be accurate to 1 / 10^6
private final boolean SIMPLE_GREEDY_GENOTYPER = false; private final boolean SIMPLE_GREEDY_GENOTYPER = false;
private final static double SUM_GL_THRESH_NOCALL = -0.001; // if sum(gl) is bigger than this threshold, we treat GL's as non-informative and will force a no-call. private final static double SUM_GL_THRESH_NOCALL = -0.001; // if sum(gl) is bigger than this threshold, we treat GL's as non-informative and will force a no-call.
private final List<Allele> NO_CALL_ALLELES = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
protected ExactAFCalculationModel(UnifiedArgumentCollection UAC, int N, Logger logger, PrintStream verboseWriter) { protected ExactAFCalculationModel(UnifiedArgumentCollection UAC, int N, Logger logger, PrintStream verboseWriter) {
super(UAC, N, logger, verboseWriter); super(UAC, N, logger, verboseWriter);
@ -338,8 +339,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
} }
} }
GenotypesContext calls = GenotypesContext.create(); final GenotypesContext calls = GenotypesContext.create();
int startIdx = AFofMaxLikelihood; int startIdx = AFofMaxLikelihood;
for (int k = sampleIdx; k > 0; k--) { for (int k = sampleIdx; k > 0; k--) {
int bestGTguess; int bestGTguess;
@ -353,6 +353,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
double[] likelihoods = g.getLikelihoods().getAsVector(); double[] likelihoods = g.getLikelihoods().getAsVector();
if (MathUtils.sum(likelihoods) <= SUM_GL_THRESH_NOCALL) {
if (SIMPLE_GREEDY_GENOTYPER || !vc.isBiallelic()) { if (SIMPLE_GREEDY_GENOTYPER || !vc.isBiallelic()) {
bestGTguess = Utils.findIndexOfMaxEntry(likelihoods); bestGTguess = Utils.findIndexOfMaxEntry(likelihoods);
} }
@ -390,28 +391,13 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
} }
final double qual = GenotypeLikelihoods.getQualFromLikelihoods(bestGTguess, likelihoods); final double qual = GenotypeLikelihoods.getQualFromLikelihoods(bestGTguess, likelihoods);
//System.out.println(myAlleles.toString());
calls.add(new Genotype(sample, myAlleles, qual, null, g.getAttributes(), false)); calls.add(new Genotype(sample, myAlleles, qual, null, g.getAttributes(), false));
} else {
final double qual = Genotype.NO_LOG10_PERROR;
calls.add(new Genotype(sample, NO_CALL_ALLELES, qual, null, g.getAttributes(), false));
}
} }
for ( final Genotype genotype : GLs.iterateInSampleNameOrder() ) {
if ( !genotype.hasLikelihoods() )
continue;
Genotype g = GLs.get(genotype.getSampleName());
double[] likelihoods = genotype.getLikelihoods().getAsVector();
if (MathUtils.sum(likelihoods) <= SUM_GL_THRESH_NOCALL)
continue; // regular likelihoods
ArrayList<Allele> myAlleles = new ArrayList<Allele>();
double qual = Genotype.NO_LOG10_PERROR;
myAlleles.add(Allele.NO_CALL);
myAlleles.add(Allele.NO_CALL);
//System.out.println(myAlleles.toString());
calls.add(new Genotype(genotype.getSampleName(), myAlleles, qual, null, g.getAttributes(), false));
}
return calls; return calls;
} }