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Fix for NaNs in the rank sum tests. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4938 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2011-01-05 15:21:30 +00:00
parent 445ae06a7a
commit 4ac0590744
2 changed files with 8 additions and 2 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
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@ -72,7 +72,7 @@ public abstract class RankSumTest implements InfoFieldAnnotation, ExperimentalAn
}
final Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%.3f", QualityUtils.phredScaleErrorRate(pvalue)));
map.put(getKeyNames().get(0), String.format("%.3f", Math.abs(QualityUtils.phredScaleErrorRate(pvalue))));
return map;
}

8
java/src/org/broadinstitute/sting/utils/WilcoxonRankSum.java
View File

@ -124,8 +124,9 @@ public class WilcoxonRankSum {
// calculate normal approximation of the p-value
// returns -1 when unable to calculate it (too few data points)
public double getPValue(WILCOXON_H0 h0) {
if ( observations.size() == 0 )
if ( observations.size() == 0 ) {
return -1.0;
}
// dither to break rank ties
dither();
@ -144,6 +145,11 @@ public class WilcoxonRankSum {
}
int n2 = observations.size() - n1;
if ( n1 == 0 || n2 == 0 ) {
// one of the sets is empty so there is no information
return -1.0;
}
// todo -- these are actually integers
// we want the smaller of U1 and U2
double U1 = sum - (n1 * (n1 + 1.0) / 2.0);