From 2cb3e53b0b43b08e91176dd5844dcea38d3fcc79 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 24 Nov 2009 22:01:00 +0000
Subject: [PATCH] Verbose mode shouldn't be printing out 'NaN's and 'Infinity's

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2153 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../JointEstimateGenotypeCalculationModel.java   | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
index 2509218e5..cb7c5abfa 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
@@ -284,9 +284,19 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
             if ( altAllele != ref ) {
                 char base = Character.toLowerCase(altAllele);
                 int baseIndex = BaseUtils.simpleBaseToBaseIndex(altAllele);
-                verboseWriter.println("P(f>0)_" + base + " = " + Math.log10(PofFs[baseIndex]));
-                verboseWriter.println("Qscore_" + base + " = " + (-10.0 * Math.log10(alleleFrequencyPosteriors[baseIndex][0])));
-                verboseWriter.println("LOD_" + base + " = " + (Math.log10(PofFs[baseIndex]) - Math.log10(alleleFrequencyPosteriors[baseIndex][0])));
+                if ( MathUtils.compareDoubles(PofFs[baseIndex], 0.0) != 0 ) {
+                    double phredScaledConfidence = -10.0 * Math.log10(alleleFrequencyPosteriors[baseIndex][0]);
+                    if ( Double.isInfinite(phredScaledConfidence) ) {
+                        phredScaledConfidence = -10.0 * log10PofDgivenAFi[baseIndex][0];
+                        verboseWriter.println("P(f>0)_" + base + " = 1");
+                        verboseWriter.println("Qscore_" + base + " = " + phredScaledConfidence);
+                        verboseWriter.println("LOD_" + base + " = " + phredScaledConfidence);
+                    } else {
+                        verboseWriter.println("P(f>0)_" + base + " = " + Math.log10(PofFs[baseIndex]));
+                        verboseWriter.println("Qscore_" + base + " = " + (-10.0 * Math.log10(alleleFrequencyPosteriors[baseIndex][0])));
+                        verboseWriter.println("LOD_" + base + " = " + (Math.log10(PofFs[baseIndex]) - Math.log10(alleleFrequencyPosteriors[baseIndex][0])));
+                    }
+                }
             }
         }
         verboseWriter.println();