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Don't output -0 as qual value in VariantRecalibrator. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4044 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-08-16 16:47:58 +00:00
parent 3d63302b70
commit 578e7fa36d
2 changed files with 2 additions and 2 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
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@ -203,7 +203,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
final double pVar = theModel.evaluateVariant( vc );
final double lod = (Math.log10(totalPrior) + Math.log10(pVar)) - ((Math.log10(1.0 - totalPrior)) + Math.log10(1.0));
variantDatum.qual = QUALITY_SCALE_FACTOR * QualityUtils.lodToPhredScaleErrorRate(lod);
variantDatum.qual = Math.abs( QUALITY_SCALE_FACTOR * QualityUtils.lodToPhredScaleErrorRate(lod) );
mapList.add( variantDatum );

2
java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
View File

@ -37,7 +37,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testVariantRecalibrator() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "df4e6f55c714b68b13e47b61d4bd0cd5" );
e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "3c5a41567b60b777875d585a379eb231" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String vcf = entry.getKey();