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Shame on me: UG was emitting negative QUALs (-0) in all_bases mode. Thanks, Matt. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3732 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-07-07 20:30:22 +00:00
parent 30714ec8d9
commit 4bc3ad2194
2 changed files with 2 additions and 2 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
View File

@ -352,7 +352,7 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
break;
sum += log10PofDgivenAFi[indexOfMax][i];
}
phredScaledConfidence = -10.0 * sum;
phredScaledConfidence = (MathUtils.compareDoubles(sum, 0.0) == 0 ? 0 : -10.0 * sum);
}
}

2
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -86,7 +86,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testParameter() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "-genotype", "0f6b11868a057db246145c98119cb8f7" );
e.put( "-all_bases", "e45b5efc4aa285a7cebfb771da49ebe2" );
e.put( "-all_bases", "73dc78e157881e9f19fdcb121f29a758" );
e.put( "--min_base_quality_score 26", "a132bdcd9300b6483f78bd34d99bd794" );
e.put( "--min_mapping_quality_score 26", "edce61eba0e6e65156452fe3476d6cfc" );
e.put( "--max_mismatches_in_40bp_window 5", "56d3c59532b6e81e835f55bc1135f990" );