if (!AlignmentUtils.compareBases((byte) 'C', readbase) && !AlignmentUtils.compareBases((byte) 'T', readbase)) {
out = CYTOSINE_MISMATCH_COLOR;
} else {
// If we had information about whether this position was a SNP or not, we could
// show cytosines in any context when they are a SNP.
BisulfiteContext matchingContext = contextIsMatching(reference, read, idx, bisulfiteContext);
matchesContext = (matchingContext != null);
if (matchesContext) {
out = getContextColor(readbase, matchingContext);
}
}