zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

string cast bug

This commit is contained in:
Samuel Friedman 2017-04-28 17:32:36 -04:00
parent f55b932cfc
commit d06a6c7318
1 changed files with 13 additions and 5 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

18
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrator.java
View File

@ -593,7 +593,7 @@ 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] = reportObjectToDouble(muTable.get(row, reportColumn.getColumnName()));
}
curAnnotation++;
}
@ -602,7 +602,7 @@ 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 = reportObjectToDouble(pmixTable.get(row, reportColumn.getColumnName()));
}
}
}
@ -615,7 +615,7 @@ 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 = reportObjectToDouble(sigmaTable.get(row, reportColumn.getColumnName()));
gaussianList.get(curGaussian).sigma.set(curI, curJ, curVal);
}
@ -627,6 +627,14 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
}
private double reportObjectToDouble(Object obj){
if (obj instanceof String){
return Double.parseDouble((String)obj);
} else {
return (Double) obj;
}
}
private double[] getStandardDeviationsFromTable(GATKReportTable astdTable){
double[] stdVector = {};
@ -634,7 +642,7 @@ 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] = reportObjectToDouble(astdTable.get(row, reportColumn.getColumnName()));
}
}
}
@ -649,7 +657,7 @@ 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] = reportObjectToDouble(amTable.get(row, reportColumn.getColumnName()));
}
}
}