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Slight cleanup for mathutils 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3042 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-03-19 13:18:08 +00:00
parent b221ce94ce
commit 56092a0fc2
2 changed files with 15 additions and 4 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java
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@ -122,7 +122,7 @@ public class TrioGenotyperWalker extends RefWalker<VariantContext, Integer>{
} }
} }
double[] posteriors = MathUtils.log10posteriorsFromLog10L(L); double[] posteriors = MathUtils.normalizeFromLog10(L, true);
log10POfGenotype = posteriors[bestIndex]; log10POfGenotype = posteriors[bestIndex];
} }
//log10POfViolation = Math.min(log10POfViolation, 0); //log10POfViolation = Math.min(log10POfViolation, 0);

17
java/src/org/broadinstitute/sting/utils/MathUtils.java
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@ -277,9 +277,13 @@ public class MathUtils {
/** /**
* normalizes the log10-based array * normalizes the log10-based array
*
* @param array the array to be normalized * @param array the array to be normalized
* @param takeLog10OfOutput if true, the output will be transformed back into log10 units
*
* @return a newly allocated array corresponding the normalized values in array, maybe log10 transformed
*/ */
public static double[] normalizeFromLog10(double[] array) { public static double[] normalizeFromLog10(double[] array, boolean takeLog10OfOutput) {
double[] normalized = new double[array.length]; double[] normalized = new double[array.length];
// for precision purposes, we need to add (or really subtract, since they're // for precision purposes, we need to add (or really subtract, since they're
@ -292,9 +296,16 @@ public class MathUtils {
double sum = 0.0; double sum = 0.0;
for (int i = 0; i < array.length; i++) for (int i = 0; i < array.length; i++)
sum += normalized[i]; sum += normalized[i];
for (int i = 0; i < array.length; i++) for (int i = 0; i < array.length; i++) {
normalized[i] /= sum; double x = normalized[i] / sum;
if ( takeLog10OfOutput ) x = Math.log10(x);
normalized[i] = x;
}
return normalized; return normalized;
} }
public static double[] normalizeFromLog10(double[] array) {
return normalizeFromLog10(array, false);
}
} }