final CloseableIterator<VariantContext> iter2=vcfFileReader.iterator();
final List<VariantContext> inMemoryVariants =  Collections.unmodifiableList(iter2.stream().
		limit(3).
		collect(Collectors.toList())
		);
iter2.close();
vcfFileReader.close();

final VariantContextWriter w = (...)
final VCFHeader header2= (...)
w.writeHeader(header2);
w.add(bestResult.ctx1);
w.add(bestResult.ctx2);
w.close();

java.lang.RuntimeException: Allele C* is not an allele in the variant context
	at htsjdk.variant.vcf.VCFEncoder.writeAllele

final List<Allele> saveAllele = Collections.unmodifiableList(g.getAlleles());
if(!alleleMap.containsKey(g.getAllele(0))) {
                    System.err.println(
                            " boummm3 "+alleleMap+" "+saveAllele+" "+alleleMap.getClass());
                  
                }

inMemoryVariants.forEach(C->{long i=C.getGenotypes().stream().flatMap(G->G.getAlleles().stream()).count();});`