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Optimization: look up diploid genotypes from a static matrix instead of creating them on the fly (with String.format); bases no longer need to be ordered appropriately 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2448 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-12-28 17:28:51 +00:00
parent 57516582c2
commit b1ac4b81d5
2 changed files with 23 additions and 18 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
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@ -46,7 +46,7 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
DiploidGenotype refGenotype = DiploidGenotype.createHomGenotype(ref); DiploidGenotype refGenotype = DiploidGenotype.createHomGenotype(ref);
for ( char alt : BaseUtils.BASES ) { for ( char alt : BaseUtils.BASES ) {
if ( alt != ref ) { if ( alt != ref ) {
DiploidGenotype hetGenotype = DiploidGenotype.unorderedValueOf(ref, alt); DiploidGenotype hetGenotype = DiploidGenotype.createDiploidGenotype(ref, alt);
DiploidGenotype homGenotype = DiploidGenotype.createHomGenotype(alt); DiploidGenotype homGenotype = DiploidGenotype.createHomGenotype(alt);
AFMatrixMap.get(alt).setLikelihoods(posteriors[refGenotype.ordinal()], posteriors[hetGenotype.ordinal()], posteriors[homGenotype.ordinal()], sample); AFMatrixMap.get(alt).setLikelihoods(posteriors[refGenotype.ordinal()], posteriors[hetGenotype.ordinal()], posteriors[homGenotype.ordinal()], sample);
} }
@ -78,7 +78,7 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
// set up some variables we'll need in the loop // set up some variables we'll need in the loop
AlleleFrequencyMatrix matrix = AFMatrixMap.get(alt); AlleleFrequencyMatrix matrix = AFMatrixMap.get(alt);
DiploidGenotype refGenotype = DiploidGenotype.createHomGenotype(ref); DiploidGenotype refGenotype = DiploidGenotype.createHomGenotype(ref);
DiploidGenotype hetGenotype = DiploidGenotype.unorderedValueOf(ref, alt); DiploidGenotype hetGenotype = DiploidGenotype.createDiploidGenotype(ref, alt);
DiploidGenotype homGenotype = DiploidGenotype.createHomGenotype(alt); DiploidGenotype homGenotype = DiploidGenotype.createHomGenotype(alt);
for ( String sample : GLs.keySet() ) { for ( String sample : GLs.keySet() ) {

37
java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java
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@ -1,6 +1,7 @@
package org.broadinstitute.sting.utils.genotype; package org.broadinstitute.sting.utils.genotype;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.BaseUtils;
/** /**
* Created by IntelliJ IDEA. * Created by IntelliJ IDEA.
@ -53,28 +54,32 @@ public enum DiploidGenotype {
* @return the diploid genotype * @return the diploid genotype
*/ */
public static DiploidGenotype createHomGenotype(char hom) { public static DiploidGenotype createHomGenotype(char hom) {
hom = Character.toUpperCase(hom); int index = BaseUtils.simpleBaseToBaseIndex(hom);
switch (hom) { if ( index == -1 )
case 'A': return DiploidGenotype.AA; throw new IllegalArgumentException(hom + " is not a valid base character");
case 'C': return DiploidGenotype.CC; return conversionMatrix[index][index];
case 'G': return DiploidGenotype.GG;
case 'T': return DiploidGenotype.TT;
}
throw new IllegalArgumentException(hom + " is not a valid base character");
} }
/** /**
* get the genotype, given a string of 2 chars which may not necessarily be ordered correctly * create a diploid genotype, given 2 chars which may not necessarily be ordered correctly
* @param base1 base1 * @param base1 base1
* @param base2 base2 * @param base2 base2
* @return the diploid genotype * @return the diploid genotype
*/ */
public static DiploidGenotype unorderedValueOf(char base1, char base2) { public static DiploidGenotype createDiploidGenotype(char base1, char base2) {
if ( base1 > base2 ) { int index1 = BaseUtils.simpleBaseToBaseIndex(base1);
char temp = base1; if ( index1 == -1 )
base1 = base2; throw new IllegalArgumentException(base1 + " is not a valid base character");
base2 = temp; int index2 = BaseUtils.simpleBaseToBaseIndex(base2);
} if ( index2 == -1 )
return valueOf(String.format("%c%c", base1, base2)); throw new IllegalArgumentException(base2 + " is not a valid base character");
return conversionMatrix[index1][index2];
} }
private static final DiploidGenotype[][] conversionMatrix = {
{ DiploidGenotype.AA, DiploidGenotype.AC, DiploidGenotype.AG, DiploidGenotype.AT },
{ DiploidGenotype.AC, DiploidGenotype.CC, DiploidGenotype.CG, DiploidGenotype.CT },
{ DiploidGenotype.AG, DiploidGenotype.CG, DiploidGenotype.GG, DiploidGenotype.GT },
{ DiploidGenotype.AT, DiploidGenotype.CT, DiploidGenotype.GT, DiploidGenotype.TT }
};
} }