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Thanks to Steve Hershman for finding this bug: 

getNegLog10PError() does not equal the confidence score (you need to multiply by 10 as confidence is traditionally phred scaled).  Probably we should change the method to be getNeg10Log10PError().  Anyone have strong feelings on this?



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2207 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-12-02 01:59:03 +00:00
parent bc8f3d58ae
commit ba8a8febc6
2 changed files with 3 additions and 3 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
View File

@ -247,7 +247,7 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
eval = null;
if (eval != null)
if (eval.getNegLog10PError() < minConfidenceScore) eval = null;
if (eval.getNegLog10PError() * 10.0 < minConfidenceScore) eval = null;
if ( eval != null && (eval instanceof RodVCF) && ((RodVCF)eval).mCurrentRecord.isFiltered() ) {
//System.out.printf("Rejecting filtered record %s%n", eval);

4
java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java
View File

@ -75,10 +75,10 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
" -L 1:10,000,000-11,000,000" +
" --outerr %s" +
" --supressDateInformation" +
" -minConfidenceScore 6",
" -minConfidenceScore 60",
1, // just one output file
md5);
List<File> result = executeTest("testEvalVariantRODConfSix", spec).getFirst();
List<File> result = executeTest("testEvalVariantRODConfSixty", spec).getFirst();
}
@Test