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Simplifying the interface a bit

This commit is contained in:
Eric Banks 2011-12-19 15:29:46 -05:00
parent 339ef92eac
commit 06d385e619
1 changed files with 11 additions and 7 deletions
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18
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -322,8 +322,9 @@ public class UnifiedGenotyperEngine {
for ( int i = 0; i < vc.getAlternateAlleles().size(); i++ ) { for ( int i = 0; i < vc.getAlternateAlleles().size(); i++ ) {
int indexOfBestAC = MathUtils.maxElementIndex(AFresult.log10AlleleFrequencyPosteriors[i]); int indexOfBestAC = MathUtils.maxElementIndex(AFresult.log10AlleleFrequencyPosteriors[i]);
// if the most likely AC is not 0, then this is a good alternate allele to use // if the most likely AC is not 0, then this is a good alternate allele to use;
if ( indexOfBestAC != 0 && (AFresult.log10AlleleFrequencyPosteriors[i][0] != AlleleFrequencyCalculationModel.VALUE_NOT_CALCULATED || AFresult.log10AlleleFrequencyPosteriors[i][indexOfBestAC] > AFresult.log10PosteriorOfAFzero) ) { // make sure to test against log10PosteriorOfAFzero since that no longer is an entry in the array
if ( indexOfBestAC != 0 && AFresult.log10AlleleFrequencyPosteriors[i][indexOfBestAC] > AFresult.log10PosteriorOfAFzero ) {
altAllelesToUse[i] = true; altAllelesToUse[i] = true;
bestGuessIsRef = false; bestGuessIsRef = false;
} }
@ -392,7 +393,7 @@ public class UnifiedGenotyperEngine {
} }
// create the genotypes // create the genotypes
final GenotypesContext genotypes = assignGenotypes(vc, altAllelesToUse, myAlleles); final GenotypesContext genotypes = assignGenotypes(vc, altAllelesToUse);
// print out stats if we have a writer // print out stats if we have a writer
if ( verboseWriter != null && !limitedContext ) if ( verboseWriter != null && !limitedContext )
@ -771,13 +772,10 @@ public class UnifiedGenotyperEngine {
/** /**
* @param vc variant context with genotype likelihoods * @param vc variant context with genotype likelihoods
* @param allelesToUse bit vector describing which alternate alleles from the vc are okay to use * @param allelesToUse bit vector describing which alternate alleles from the vc are okay to use
* @param newAlleles a list of the final new alleles to use
*
* @return genotypes * @return genotypes
*/ */
public static GenotypesContext assignGenotypes(final VariantContext vc, public static GenotypesContext assignGenotypes(final VariantContext vc,
final boolean[] allelesToUse, final boolean[] allelesToUse) {
final List<Allele> newAlleles) {
// the no-called genotypes // the no-called genotypes
final GenotypesContext GLs = vc.getGenotypes(); final GenotypesContext GLs = vc.getGenotypes();
@ -790,6 +788,12 @@ public class UnifiedGenotyperEngine {
// we need to determine which of the alternate alleles (and hence the likelihoods) to use and carry forward // we need to determine which of the alternate alleles (and hence the likelihoods) to use and carry forward
final int numOriginalAltAlleles = allelesToUse.length; final int numOriginalAltAlleles = allelesToUse.length;
final List<Allele> newAlleles = new ArrayList<Allele>(numOriginalAltAlleles+1);
newAlleles.add(vc.getReference());
for ( int i = 0; i < numOriginalAltAlleles; i++ ) {
if ( allelesToUse[i] )
newAlleles.add(vc.getAlternateAllele(i));
}
final int numNewAltAlleles = newAlleles.size() - 1; final int numNewAltAlleles = newAlleles.size() - 1;
ArrayList<Integer> likelihoodIndexesToUse = null; ArrayList<Integer> likelihoodIndexesToUse = null;