/**
* For each variant in the file, determine the phasing for the child and replace the child's
* genotype with the trio's genotype
*
* @param tracker the reference meta-data tracker
* @param ref the reference context
* @param context the alignment context
* @return null
*/
@Override
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if (tracker != null) {
for (VariantContext vc :
tracker.getValues(variantCollection.variants, context.getLocation())) {
vc = vc.subContextFromSamples(samples);
if (!vc.isPolymorphicInSamples()) continue;
double log10pSomatic = calcLog10pSomatic(vc);
// write in the somatic status probability
Map<String, Object> attrs = new HashMap<String, Object>(); // vc.getAttributes());
if (!minimalVCF) attrs.putAll(vc.getAttributes());
attrs.put(SOMATIC_LOD_TAG_NAME, log10pSomatic);
if (log10pSomatic > somaticMinLOD) {
attrs.put(VCFConstants.SOMATIC_KEY, true);
attrs.put(SOMATIC_NONREF_TAG_NAME, calculateTumorNNR(vc));
attrs.put(SOMATIC_AC_TAG_NAME, calculateTumorAC(vc));
}
final VariantContextBuilder builder = new VariantContextBuilder(vc).attributes(attrs);
VariantContextUtils.calculateChromosomeCounts(builder, false);
VariantContext newvc = builder.make();
vcfWriter.add(newvc);
}
return null;
}
return null;
}
