final byte[] reference = isSoftClipped ? softClippedReference : genome.getSequence(chr, start, end);
boolean haveBases = (block.hasBases() && block.getLength() > 0);
ShadeBasesOption shadeBasesOption = renderOptions.shadeBasesOption;
ColorOption colorOption = renderOptions.getColorOption();
// Disable showAllBases in bisulfite mode
boolean showAllBases = renderOptions.showAllBases &&
!(colorOption == ColorOption.BISULFITE || colorOption == ColorOption.NOMESEQ);