File lastFile = null;
VariantContext lastContext = null;
for (final File f : inputFiles) {
final VCFFileReader in = new VCFFileReader(f, false);
dict.assertSameDictionary(in.getFileHeader().getSequenceDictionary());
final List<String> theseSamples = in.getFileHeader().getGenotypeSamples();
if (!samples.equals(theseSamples)) {
final SortedSet<String> s1 = new TreeSet<String>(samples);
final SortedSet<String> s2 = new TreeSet<String>(theseSamples);