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Pull out RMS calculation into MathUtils for all to use 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1364 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-08-03 17:00:20 +00:00
parent e495b836d3
commit e3b08f245f
5 changed files with 30 additions and 17 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECAlleleBalance.java
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@ -7,7 +7,7 @@ import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.Pair;
public class VECAlleleBalance implements VariantExclusionCriterion { //extends RatioFilter {
final private static GenotypeFeatureData.Tail tail = GenotypeFeatureData.Tail.TwoTailed;
//final private static GenotypeFeatureData.Tail tail = GenotypeFeatureData.Tail.TwoTailed;
private boolean exclude;
private double lowThreshold, highThreshold, ratio;

14
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECMappingQuality.java
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@ -2,6 +2,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.variants;
import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.refdata.rodVariants;
import org.broadinstitute.sting.utils.MathUtils;
import net.sf.samtools.SAMRecord;
import java.util.List;
@ -20,14 +21,11 @@ public class VECMappingQuality implements VariantExclusionCriterion {
public void compute(char ref, LocusContext context, rodVariants variant) {
List<SAMRecord> reads = context.getReads();
rms = 0.0;
for (int readIndex = 0; readIndex < reads.size(); readIndex++) {
int qual = reads.get(readIndex).getMappingQuality();
rms += qual * qual;
}
rms /= reads.size();
rms = Math.sqrt(rms);
int[] qualities = new int[reads.size()];
for (int i=0; i < reads.size(); i++)
qualities[i] = reads.get(i).getMappingQuality();
rms = MathUtils.rms(qualities);
exclude = rms < minQuality;
}
public boolean isExcludable() {

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECOnOffGenotypeRatio.java
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@ -5,7 +5,7 @@ import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.utils.*;
public class VECOnOffGenotypeRatio implements VariantExclusionCriterion { // extends RatioFilter {
final private static GenotypeFeatureData.Tail tail = GenotypeFeatureData.Tail.LeftTailed;
//final private static GenotypeFeatureData.Tail tail = GenotypeFeatureData.Tail.LeftTailed;
private boolean exclude;
private double lowThreshold, highThreshold, ratio;

16
java/src/org/broadinstitute/sting/utils/MathUtils.java
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@ -142,4 +142,20 @@ public class MathUtils {
return multinomialCoefficient*probs;
}
/**
* calculate the Root Mean Square of an array of integers
* @param x an int[] of numbers
* @return the RMS of the specified numbers.
*/
public static double rms(int[] x) {
if ( x.length == 0 )
return 0.0;
double rms = 0.0;
for (int i : x)
rms += i * i;
rms /= x.length;
return Math.sqrt(rms);
}
}

13
java/src/org/broadinstitute/sting/utils/genotype/calls/SSGGenotypeCall.java
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@ -4,6 +4,7 @@ import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.ReadBackedPileup;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.genotype.BasicGenotype;
import org.broadinstitute.sting.utils.genotype.Genotype;
import org.broadinstitute.sting.utils.genotype.GenotypeOutput;
@ -103,13 +104,11 @@ public class SSGGenotypeCall implements GenotypeCall, GenotypeOutput {
* @return
*/
private double calculateRMS(ReadBackedPileup pileup) {
double rms = 0.0;
for (SAMRecord r : pileup.getReads()) {
rms += r.getMappingQuality() * r.getMappingQuality();
}
rms /= pileup.getReads().size();
rms = Math.sqrt(rms);
return rms;
List<SAMRecord> reads = pileup.getReads();
int[] qualities = new int[reads.size()];
for (int i=0; i < reads.size(); i++)
qualities[i] = reads.get(i).getMappingQuality();
return MathUtils.rms(qualities);
}
/**