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Bug fix to FisherStrand: do not let it output INFINITY. This all needs to be unit tested, but that's coming on the horizon.

This commit is contained in:
Eric Banks 2013-01-16 15:35:04 -05:00
parent 2a42b47e4a
commit 4cf34ee9da
1 changed files with 3 additions and 3 deletions
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6
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
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@ -116,8 +116,8 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
else if (table1 == null) else if (table1 == null)
return annotationForOneTable(pValueForContingencyTable(table2)); return annotationForOneTable(pValueForContingencyTable(table2));
else { // take the one with the best (i.e., least significant pvalue) else { // take the one with the best (i.e., least significant pvalue)
double pvalue1 = Math.max(pValueForContingencyTable(table1), MIN_PVALUE); double pvalue1 = pValueForContingencyTable(table1);
double pvalue2 = Math.max(pValueForContingencyTable(table2), MIN_PVALUE); double pvalue2 = pValueForContingencyTable(table2);
return annotationForOneTable(Math.max(pvalue1, pvalue2)); return annotationForOneTable(Math.max(pvalue1, pvalue2));
} }
} }
@ -129,7 +129,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
* @return a hash map from FS -> phred-scaled pValue * @return a hash map from FS -> phred-scaled pValue
*/ */
private Map<String, Object> annotationForOneTable(final double pValue) { private Map<String, Object> annotationForOneTable(final double pValue) {
final Object value = String.format("%.3f", QualityUtils.phredScaleErrorRate(pValue)); final Object value = String.format("%.3f", QualityUtils.phredScaleErrorRate(Math.max(pValue, MIN_PVALUE))); // prevent INFINITYs
return Collections.singletonMap(FS, value); return Collections.singletonMap(FS, value);
// Map<String, Object> map = new HashMap<String, Object>(); // Map<String, Object> map = new HashMap<String, Object>();
// map.put(FS, String.format("%.3f", QualityUtils.phredScaleErrorRate(pValue))); // map.put(FS, String.format("%.3f", QualityUtils.phredScaleErrorRate(pValue)));