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Bug fix in ValidationSiteSelector: when input vcf had genotypes and was multiallelic, the parsing of the AF/AC fields was wrong. Better logic to unify parsing of field

This commit is contained in:
Guillermo del Angel 2012-02-06 10:33:12 -05:00
parent 30b937d2af
commit 090d87b48b
1 changed files with 14 additions and 15 deletions
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29
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java
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@ -71,25 +71,24 @@ public class KeepAFSpectrumFrequencySelector extends FrequencyModeSelector {
// recompute AF,AC,AN based on genotypes:
// todo - - maybe too inefficient??
VariantContextUtils.calculateChromosomeCounts(vc, attributes, false);
afArray = new double[] {Double.valueOf((String)attributes.get(VCFConstants.ALLELE_FREQUENCY_KEY))};
} else {
// sites-only vc or we explicitly tell to ignore genotypes; we trust the AF field if present
if ( vc.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY) ) {
String afo = vc.getAttributeAsString(VCFConstants.ALLELE_FREQUENCY_KEY, null);
}
if (afo.contains(",")) {
String[] afs = afo.split(",");
afs[0] = afs[0].substring(1,afs[0].length());
afs[afs.length-1] = afs[afs.length-1].substring(0,afs[afs.length-1].length()-1);
// sites-only vc or we explicitly tell to ignore genotypes; we trust the AF field if present
if ( vc.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY) ) {
String afo = vc.getAttributeAsString(VCFConstants.ALLELE_FREQUENCY_KEY, null);
afArray = new double[afs.length];
if (afo.contains(",")) {
String[] afs = afo.split(",");
afs[0] = afs[0].substring(1,afs[0].length());
afs[afs.length-1] = afs[afs.length-1].substring(0,afs[afs.length-1].length()-1);
for (int k=0; k < afArray.length; k++)
afArray[k] = Double.valueOf(afs[k]);
}
else
afArray = new double[] {Double.valueOf(afo)};
afArray = new double[afs.length];
for (int k=0; k < afArray.length; k++)
afArray[k] = Double.valueOf(afs[k]);
}
else
afArray = new double[] {Double.valueOf(afo)};
}