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It turns out that Math.log10() can return 0, which leads to QUALs being set to -0, which is off-spec. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5415 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-03-10 03:08:56 +00:00
parent 3596c56602
commit 4baeb5979f
2 changed files with 2 additions and 2 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -29,7 +29,7 @@ import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Hidden; import org.broadinstitute.sting.commandline.Hidden;
public class UnifiedArgumentCollection { public class UnifiedArgumentCollection {
// control the various models to be used // control the various models to be used
@Argument(fullName = "genotype_likelihoods_model", shortName = "glm", doc = "Genotype likelihoods calculation model to employ -- SNP is the default option, while DINDEL is also available for calling indels.", required = false) @Argument(fullName = "genotype_likelihoods_model", shortName = "glm", doc = "Genotype likelihoods calculation model to employ -- SNP is the default option, while DINDEL is also available for calling indels.", required = false)

2
java/src/org/broadinstitute/sting/utils/QualityUtils.java
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@ -78,7 +78,7 @@ public class QualityUtils {
} }
static public double phredScaleErrorRate(double errorRate) { static public double phredScaleErrorRate(double errorRate) {
return -10.0*Math.log10(errorRate); return Math.abs(-10.0*Math.log10(errorRate));
} }
static public double lodToPhredScaleErrorRate(double lod) { static public double lodToPhredScaleErrorRate(double lod) {