Added control id variable

                print_error("Replicate id not an integer!", "Line", line)

            replicate = int(replicate)

            ## Create control identity

            if control != "":

                    is_control = "0"

            else:

                is_control = "1"

            ## Check FastQ file extension

            for fastq in [fastq_1, fastq_2]:

                if fastq:

            ## Auto-detect paired-end/single-end

            sample_info = []

            if sample and fastq_1 and fastq_2:  ## Paired-end short reads

                sample_info = [sample, str(replicate), control, "0", fastq_1, fastq_2, is_control]

                sample_info = [sample, str(replicate), control, "0", fastq_1, fastq_2]

            elif sample and fastq_1 and not fastq_2:  ## Single-end short reads

                sample_info = [sample, str(replicate), control, "1", fastq_1, fastq_2, is_control]

                sample_info = [sample, str(replicate), control, "1", fastq_1, fastq_2]

            else:

                print_error("Invalid combination of columns provided!", "Line", line)

            ## Create sample mapping dictionary = {sample: {replicate : [ single_end, fastq_1, fastq_2 ]}}

            if sample not in sample_run_dict:

                sample_run_dict[sample] = {}

            print_error("Each control entry must match at least one group entry! Unmatched control entry: {}.".format(CTRL))

            sys.exit(1)

    ## Create control identity variable

    for sample in sorted(sample_run_dict.keys()):

        for replicate in sorted(sample_run_dict[sample].keys()):

            sample_info = sample_run_dict[sample][replicate][0]

            if igg_control:

                if sample_info[0] in control_names_list:

                    sample_info.append("1")

                    ## If control column not blanc, raise error

                else:

                    sample_info.append("0")

            else: 

                sample_info.append("0")

            sample_run_dict[sample][replicate][0] = sample_info

    ## Check igg_control parameter is consistent with input groups

    if (igg_control == 'true' and not igg_present):

        print("ERROR: No 'igg' group was found in " + str(file_in) + " If you are not supplying an IgG control, please specify --igg_control 'false' on command line.")