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Break AF histogram into max and min AFs

This commit is contained in:
Eric Banks 2012-02-06 09:01:19 -05:00
parent cef550903e
commit 9d94f310f1
1 changed files with 28 additions and 15 deletions
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43
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java
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@ -90,8 +90,11 @@ public class MultiallelicSummary extends VariantEvaluator { // implements Standa
@DataPoint(description = "Multi-allelic Indel Novelty Rate")
public String indelNoveltyRate = "NA";
@DataPoint(description="Histogram of allele frequencies")
AFHistogram AFhistogram = new AFHistogram();
@DataPoint(description="Histogram of allele frequencies for most common alternate allele")
AFHistogram AFhistogramMax = new AFHistogram();
@DataPoint(description="Histogram of allele frequencies for less common alternate alleles")
AFHistogram AFhistogramMin = new AFHistogram();
/*
* AF histogram table object
@ -130,18 +133,10 @@ public class MultiallelicSummary extends VariantEvaluator { // implements Standa
public String getName() { return "AFHistTable"; }
public void update(VariantContext vc) {
final Object obj = vc.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY, null);
if ( obj == null || !(obj instanceof List) )
return;
List<String> list = (List<String>)obj;
for ( String str : list ) {
final double AF = Double.valueOf(str);
final int bin = (int)(numBins * MathUtils.round(AF, 2));
AFhistogram[bin]++;
}
}
public void update(final double AF) {
final int bin = (int)(numBins * MathUtils.round(AF, 2));
AFhistogram[bin]++;
}
}
public void initialize(VariantEvalWalker walker) {}
@ -180,7 +175,7 @@ public class MultiallelicSummary extends VariantEvaluator { // implements Standa
default:
throw new UserException.BadInput("Unexpected variant context type: " + eval);
}
AFhistogram.update(eval);
updateAFhistogram(eval);
return null; // we don't capture any interesting sites
}
@ -213,6 +208,24 @@ public class MultiallelicSummary extends VariantEvaluator { // implements Standa
private void calculateIndelPairwiseNovelty(VariantContext eval, VariantContext comp) {
}
private void updateAFhistogram(VariantContext vc) {
final Object obj = vc.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY, null);
if ( obj == null || !(obj instanceof List) )
return;
List<String> list = (List<String>)obj;
ArrayList<Double> AFs = new ArrayList<Double>(list.size());
for ( String str : list ) {
AFs.add(Double.valueOf(str));
}
Collections.sort(AFs);
AFhistogramMax.update(AFs.get(AFs.size()-1));
for ( int i = 0; i < AFs.size() - 1; i++ )
AFhistogramMin.update(AFs.get(i));
}
private final String noveltyRate(final int all, final int known) {
final int novel = all - known;
final double rate = (novel / (1.0 * all));