Java VariantContext.hasAlternateAllele Examples

Example #1

File: HaplotypeResolver.java Project: jpaul6/gatk-protected

 private static int findOverlap(final VariantContext target, final VariantContext comparison) {
   int overlap = 0;
   for (final Allele allele : target.getAlternateAlleles()) {
     if (comparison.hasAlternateAllele(allele)) overlap++;
   }
   return overlap;
 }