From 4df71a3ca1ef38420fd91b0b10804d1449db2c7d Mon Sep 17 00:00:00 2001
From: Samuel Friedman <sam@broadinstitute.org>
Date: Tue, 2 May 2017 12:05:10 -0400
Subject: [PATCH] expect floats in the report

---
 .../variantrecalibration/VariantRecalibrator.java      | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrator.java
index f305c780b..8e473b5d5 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrator.java
@@ -600,7 +600,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
                         MultivariateGaussian mg = new MultivariateGaussian(numAnnotations);
                         gaussianList.add(mg);
                     }
-                    gaussianList.get(row).mu[curAnnotation] =  Double.parseDouble( (String)muTable.get(row, reportColumn.getColumnName()));
+                    gaussianList.get(row).mu[curAnnotation] = (Double) muTable.get(row, reportColumn.getColumnName());
                 }
                 curAnnotation++;
             }
@@ -609,7 +609,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         for (GATKReportColumn reportColumn : pmixTable.getColumnInfo() ) {
             if (reportColumn.getColumnName().equals("pMixLog10")) {
                 for (int row = 0; row < pmixTable.getNumRows(); row++) {
-                    gaussianList.get(row).pMixtureLog10 =  Double.parseDouble( (String)pmixTable.get(row, reportColumn.getColumnName()));
+                    gaussianList.get(row).pMixtureLog10 =  (Double) pmixTable.get(row, reportColumn.getColumnName());
                 }
             }
         }
@@ -622,7 +622,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
             for (int row = 0; row < sigmaTable.getNumRows(); row++) {
                 int curGaussian = row / numAnnotations;
                 int curI = row % numAnnotations;
-                double curVal = Double.parseDouble( (String)sigmaTable.get(row, reportColumn.getColumnName()));
+                double curVal = (Double) sigmaTable.get(row, reportColumn.getColumnName());
                 gaussianList.get(curGaussian).sigma.set(curI, curJ, curVal);
 
             }
@@ -641,7 +641,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
             if (reportColumn.getColumnName().equals("Standarddeviation")) {
                 stdVector = new double[astdTable.getNumRows()];
                 for (int row = 0; row < astdTable.getNumRows(); row++) {
-                    stdVector[row] =  Double.parseDouble( (String)astdTable.get(row, reportColumn.getColumnName()));
+                    stdVector[row] =  (Double) astdTable.get(row, reportColumn.getColumnName());
                 }
             }
         }
@@ -656,7 +656,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
             if (reportColumn.getColumnName().equals("Mean")) {
                 meanVector = new double[amTable.getNumRows()];
                 for (int row = 0; row < amTable.getNumRows(); row++) {
-                    meanVector[row] =   Double.parseDouble( (String)amTable.get(row, reportColumn.getColumnName()));
+                    meanVector[row] = (Double) amTable.get(row, reportColumn.getColumnName());
                 }
             }
         }