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expect floats in the report

This commit is contained in:
Samuel Friedman 2017-05-02 12:05:10 -04:00
parent 1b4ac51048
commit 4df71a3ca1
1 changed files with 5 additions and 5 deletions
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10
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrator.java
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@ -600,7 +600,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
MultivariateGaussian mg = new MultivariateGaussian(numAnnotations); MultivariateGaussian mg = new MultivariateGaussian(numAnnotations);
gaussianList.add(mg); 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++; curAnnotation++;
} }
@ -609,7 +609,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
for (GATKReportColumn reportColumn : pmixTable.getColumnInfo() ) { for (GATKReportColumn reportColumn : pmixTable.getColumnInfo() ) {
if (reportColumn.getColumnName().equals("pMixLog10")) { if (reportColumn.getColumnName().equals("pMixLog10")) {
for (int row = 0; row < pmixTable.getNumRows(); row++) { 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++) { for (int row = 0; row < sigmaTable.getNumRows(); row++) {
int curGaussian = row / numAnnotations; int curGaussian = row / numAnnotations;
int curI = 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); gaussianList.get(curGaussian).sigma.set(curI, curJ, curVal);
} }
@ -641,7 +641,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
if (reportColumn.getColumnName().equals("Standarddeviation")) { if (reportColumn.getColumnName().equals("Standarddeviation")) {
stdVector = new double[astdTable.getNumRows()]; stdVector = new double[astdTable.getNumRows()];
for (int row = 0; row < astdTable.getNumRows(); row++) { 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")) { if (reportColumn.getColumnName().equals("Mean")) {
meanVector = new double[amTable.getNumRows()]; meanVector = new double[amTable.getNumRows()];
for (int row = 0; row < amTable.getNumRows(); row++) { 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());
} }
} }
} }