applies no mutation data to mutation map . concode_field_sep File allCasesFile concode_elem_sep String MAP_KEY_DELIMETER concode_elem_sep File sequencedCaseFile concode_elem_sep File knownMutationFile concode_elem_sep File sequencedGeneFile concode_field_sep ArrayList<String> getList concode_elem_sep String generateMutationFile concode_elem_sep Map<String,String> getMutationMap concode_elem_sep String createKey concode_elem_sep void applyKnownMutationsData concode_elem_sep void main concode_elem_sep String execute