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Let's not have the indel model emit more than the max possible number of genotypable alt alleles (since we may not be able to subset down to the best ones).

This commit is contained in:
Eric Banks 2012-04-12 15:16:29 -04:00
parent b659b16b31
commit 0dd571928d
3 changed files with 12 additions and 13 deletions
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15
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
View File

@ -261,15 +261,14 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
builder.alleles(vcAlleles);
builder.referenceBaseForIndel(ref.getBase());
builder.noGenotypes();
if (doMultiAllelicCalls)
if (doMultiAllelicCalls) {
vcs.add(builder.make());
if (vcs.size() >= GenotypeLikelihoods.MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED)
break;
} else if (curCnt > maxAlleleCnt) {
maxAlleleCnt = curCnt;
vcs.clear();
vcs.add(builder.make());
else {
if (curCnt > maxAlleleCnt) {
maxAlleleCnt = curCnt;
vcs.clear();
vcs.add(builder.make());
}
}
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -210,8 +210,8 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
**/
public void initialize() {
// check for a bad max alleles value
if ( UAC.MAX_ALTERNATE_ALLELES > GenotypeLikelihoods.MAX_ALLELES_THAT_CAN_BE_GENOTYPED )
throw new UserException.BadArgumentValue("max_alternate_alleles", "the maximum possible value is " + GenotypeLikelihoods.MAX_ALLELES_THAT_CAN_BE_GENOTYPED);
if ( UAC.MAX_ALTERNATE_ALLELES > GenotypeLikelihoods.MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED)
throw new UserException.BadArgumentValue("max_alternate_alleles", "the maximum possible value is " + GenotypeLikelihoods.MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED);
// warn the user for misusing EMIT_ALL_SITES
if ( UAC.OutputMode == UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES &&

6
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
View File

@ -223,12 +223,12 @@ public class GenotypeLikelihoods {
/**
* The maximum number of alleles that we can represent as genotype likelihoods
*/
public final static int MAX_ALLELES_THAT_CAN_BE_GENOTYPED = 500;
public final static int MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED = 500;
/*
* a cache of the PL index to the 2 alleles it represents over all possible numbers of alternate alleles
*/
private final static GenotypeLikelihoodsAllelePair[] PLIndexToAlleleIndex = calculatePLcache(MAX_ALLELES_THAT_CAN_BE_GENOTYPED); // start with data for 10 alternate alleles
private final static GenotypeLikelihoodsAllelePair[] PLIndexToAlleleIndex = calculatePLcache(MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED); // start with data for 10 alternate alleles
private static GenotypeLikelihoodsAllelePair[] calculatePLcache(final int altAlleles) {
final int numLikelihoods = calculateNumLikelihoods(altAlleles);
@ -274,7 +274,7 @@ public class GenotypeLikelihoods {
public static GenotypeLikelihoodsAllelePair getAllelePair(final int PLindex) {
// make sure that we've cached enough data
if ( PLindex >= PLIndexToAlleleIndex.length )
throw new ReviewedStingException("GATK limitation: cannot genotype more than " + MAX_ALLELES_THAT_CAN_BE_GENOTYPED + " alleles");
throw new ReviewedStingException("GATK limitation: cannot genotype more than " + MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED + " alleles");
return PLIndexToAlleleIndex[PLindex];
}