public List<String> buildAlleles(Variant variant, Pair<Integer, Integer> adjustedRange) { String reference = variant.getReference(); String alternate = variant.getAlternate(); List<AlternateCoordinate> secAlts = variant.getStudy(this.studyConfiguration.getStudyName()).getSecondaryAlternates(); List<String> alleles = new ArrayList<>(secAlts.size() + 2); Integer origStart = variant.getStart(); Integer origEnd = variant.getEnd(); alleles.add(buildAllele(variant.getChromosome(), origStart, origEnd, reference, adjustedRange)); alleles.add(buildAllele(variant.getChromosome(), origStart, origEnd, alternate, adjustedRange)); secAlts.forEach(alt -> { alleles.add(buildAllele(variant.getChromosome(), alt.getStart(), alt.getEnd(), alt.getAlternate(), adjustedRange)); }); return alleles; }