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Allow longs and doubles in recalibration report to allow some backward compatibility

This commit is contained in:
Mark DePristo 2012-09-19 19:23:44 -04:00
parent 2267b722b2
commit 087247f1f0
1 changed files with 16 additions and 4 deletions
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20
public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java
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@ -2,11 +2,12 @@ package org.broadinstitute.sting.utils.recalibration;
import org.broadinstitute.sting.gatk.report.GATKReport; import org.broadinstitute.sting.gatk.report.GATKReport;
import org.broadinstitute.sting.gatk.report.GATKReportTable; import org.broadinstitute.sting.gatk.report.GATKReportTable;
import org.broadinstitute.sting.gatk.walkers.bqsr.*; import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection;
import org.broadinstitute.sting.utils.recalibration.covariates.Covariate;
import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.collections.NestedIntegerArray; import org.broadinstitute.sting.utils.collections.NestedIntegerArray;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.recalibration.covariates.Covariate;
import java.io.File; import java.io.File;
import java.io.PrintStream; import java.io.PrintStream;
@ -193,9 +194,20 @@ public class RecalibrationReport {
} }
} }
private double asDouble(final Object o) {
if ( o instanceof Double )
return (Double)o;
else if ( o instanceof Integer )
return (Integer)o;
else if ( o instanceof Long )
return (Long)o;
else
throw new ReviewedStingException("Object " + o + " is expected to be either a double, long or integer but its not either: " + o.getClass());
}
private RecalDatum getRecalDatum(final GATKReportTable reportTable, final int row, final boolean hasEstimatedQReportedColumn) { private RecalDatum getRecalDatum(final GATKReportTable reportTable, final int row, final boolean hasEstimatedQReportedColumn) {
final double nObservations = (Double) reportTable.get(row, RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME); final double nObservations = asDouble(reportTable.get(row, RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME));
final double nErrors = (Double) reportTable.get(row, RecalUtils.NUMBER_ERRORS_COLUMN_NAME); final double nErrors = asDouble(reportTable.get(row, RecalUtils.NUMBER_ERRORS_COLUMN_NAME));
final double empiricalQuality = (Double) reportTable.get(row, RecalUtils.EMPIRICAL_QUALITY_COLUMN_NAME); final double empiricalQuality = (Double) reportTable.get(row, RecalUtils.EMPIRICAL_QUALITY_COLUMN_NAME);
// the estimatedQreported column only exists in the ReadGroup table // the estimatedQreported column only exists in the ReadGroup table