private final static boolean DEBUG = false;
private final static int MIN_CONTEXT_WING_SIZE = 10;
private final static int MAX_CONSENSUS_HAPLOTYPES_TO_CONSIDER = 50;
private final static char REGEXP_WILDCARD = '.';
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
<BUG>if ( !vc.isBiallelic() || stratifiedContexts.size() == 0 ) // size 0 means that call was made by someone else and we have no data here
return null;</BUG>
final AlignmentContext context = AlignmentContextUtils.joinContexts(stratifiedContexts.values());
final int contextWingSize = Math.min(((int)ref.getWindow().size() - 1)/2, MIN_CONTEXT_WING_SIZE);
final int contextSize = contextWingSize * 2 + 1;

private final static boolean DEBUG = false;
private final static int MIN_CONTEXT_WING_SIZE = 10;
private final static int MAX_CONSENSUS_HAPLOTYPES_TO_CONSIDER = 50;
private final static char REGEXP_WILDCARD = '.';
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if (stratifiedContexts.size() == 0 ) // size 0 means that call was made by someone else and we have no data here
return null;
if (vc.isSNP() && !vc.isBiallelic())
return null;
final AlignmentContext context = AlignmentContextUtils.joinContexts(stratifiedContexts.values());
final int contextWingSize = Math.min(((int)ref.getWindow().size() - 1)/2, MIN_CONTEXT_WING_SIZE);
final int contextSize = contextWingSize * 2 + 1;
