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More bugfixes on the way to a final push with new Exact model framework 

-- UnifiedGenotyperEngine uses only the alleles used in genotyping, not the original alleles, when considering which alleles to include in output
-- AFCalcFactory has a more informative info message when looking for and selecting an exact model to use in genotyping
This commit is contained in:
Mark DePristo 2012-10-12 16:16:45 -04:00
parent 6b639f51f0
commit 1ac09ca81e
2 changed files with 5 additions and 2 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -375,6 +375,8 @@ public class UnifiedGenotyperEngine {
myAlleles.add(vc.getReference());
for ( int i = 0; i < AFresult.getAllelesUsedInGenotyping().size(); i++ ) {
final Allele alternateAllele = AFresult.getAllelesUsedInGenotyping().get(i);
if ( alternateAllele.isReference() )
continue;
// we are non-ref if the probability of being non-ref > the emit confidence.
// the emit confidence is phred-scaled, say 30 => 10^-3.

5
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java
View File

@ -98,7 +98,7 @@ public class AFCalcFactory {
final Logger logger) {
final int maxAltAlleles = Math.max(UAC.MAX_ALTERNATE_ALLELES, UAC.MAX_ALTERNATE_ALLELES_FOR_INDELS);
if ( ! UAC.AFmodel.usableForParams(UAC.samplePloidy, maxAltAlleles) ) {
logger.warn("Requested ploidy / maxAltAlleles " + UAC.samplePloidy + " not supported by requested model " + UAC.AFmodel + " looking for an option");
logger.info("Requested ploidy " + UAC.samplePloidy + " maxAltAlleles " + maxAltAlleles + " not supported by requested model " + UAC.AFmodel + " looking for an option");
final List<Calculation> supportingCalculations = new LinkedList<Calculation>();
for ( final Calculation calc : Calculation.values() ) {
if ( calc.usableForParams(UAC.samplePloidy, maxAltAlleles) )
@ -108,9 +108,10 @@ public class AFCalcFactory {
if ( supportingCalculations.isEmpty() )
throw new UserException("no AFCalculation model found that supports ploidy of " + UAC.samplePloidy + " and max alt alleles " + maxAltAlleles);
else if ( supportingCalculations.size() > 1 )
logger.warn("Warning, multiple supporting AFCalcs found " + Utils.join(",", supportingCalculations) + " choosing first arbitrarily");
logger.debug("Warning, multiple supporting AFCalcs found " + Utils.join(",", supportingCalculations) + " choosing first arbitrarily");
else
UAC.AFmodel = supportingCalculations.get(0);
logger.info("Selecting model " + UAC.AFmodel);
}
final AFCalc calc = createAFCalc(UAC.AFmodel, nSamples, UAC.MAX_ALTERNATE_ALLELES, UAC.MAX_ALTERNATE_ALLELES_FOR_INDELS, UAC.samplePloidy);