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Lost an import in the merge

This commit is contained in:
Eric Banks 2012-01-25 19:41:41 -05:00
parent cba5f1a8b1
commit 9a60887567
1 changed files with 2 additions and 4 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
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@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.variantcontext.*; import org.broadinstitute.sting.utils.variantcontext.*;
import java.io.PrintStream; import java.io.PrintStream;
@ -38,9 +39,6 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
private final static double MAX_LOG10_ERROR_TO_STOP_EARLY = 6; // we want the calculation to be accurate to 1 / 10^6 private final static double MAX_LOG10_ERROR_TO_STOP_EARLY = 6; // we want the calculation to be accurate to 1 / 10^6
// TODO: PERMITS WALKER USED TO HAVE A TEMPORARY FIX to prevent NullPointerException caused by bug:
public static boolean PRESERVE_AC_DATA = false;
protected ExactAFCalculationModel(UnifiedArgumentCollection UAC, int N, Logger logger, PrintStream verboseWriter) { protected ExactAFCalculationModel(UnifiedArgumentCollection UAC, int N, Logger logger, PrintStream verboseWriter) {
super(UAC, N, logger, verboseWriter); super(UAC, N, logger, verboseWriter);
} }
@ -52,7 +50,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
final int numAlleles = alleles.size(); final int numAlleles = alleles.size();
//linearExact(GLs, log10AlleleFrequencyPriors[0], log10AlleleFrequencyLikelihoods, log10AlleleFrequencyPosteriors); //linearExact(GLs, log10AlleleFrequencyPriors[0], log10AlleleFrequencyLikelihoods, log10AlleleFrequencyPosteriors);
linearExactMultiAllelic(GLs, numAlleles - 1, log10AlleleFrequencyPriors, result, PRESERVE_AC_DATA); linearExactMultiAllelic(GLs, numAlleles - 1, log10AlleleFrequencyPriors, result, false);
} }
private static final ArrayList<double[]> getGLs(GenotypesContext GLs) { private static final ArrayList<double[]> getGLs(GenotypesContext GLs) {