all_sample_IGH_chain_all_metrics_wide_format_dataframe
                        a dataframe of wide format
all_sample_IGH_chain_all_metrics_wide_format_dataframe_list
                        a dataframe list to combine rowwise.
all_sample_IGH_chain_individual_metrics_dataframe_list
                        a list of dataframes
all_sample_all_chain_all_metrics_wide_format_dataframe
                        a dataframe of wide format
all_sample_all_chain_all_metrics_wide_format_dataframe_list
                        a dataframe list to combine rowwise.
all_sample_all_chain_individual_metrics_dataframe_list
                        a list of dataframes
annotate_chain_name_and_isotype_name
                        Annotate chain name and isotype name
calculate_IGH_isotype_proportion
                        calculate_IGH_isotype_proportion
calculate_repertoire_metrics
                        calculate_repertoire_metrics
calibrate_proportion_by_clones
                        calibrate_proportion_by_clones
chain_separated_dataframe
                        a dataframe separated by chain name
combine_all_sample_repertoire_metrics
                        combine_all_sample_repertoire_metrics
compute_repertoire_metrics_by_chain_name
                        compute_repertoire_metrics_by_chain_name
convergent_clonotype_merged_dataframe
                        a dataframe where convergent clonotypes are
                        merged
format_clonotype_to_immunarch_style
                        Convert clonotype dataframe to immunarch format
get_item_name_x_sample_name_for_each_metric
                        get_item_name_x_sample_name_for_each_metric
immunarch_style_dataframe
                        An converted dataframe to immunarch format
merge_convergent_clonotype
                        Merge convergent clonotype
nonproductive_CDR3aa_removed_dataframe
                        a dataframe with nonproductive CDR3aa removed
parse_mixcr             Parse mixcr format
parse_trust4            Parse trust4 format
raw_input_clonotype_dataframe
                        Raw clonotype output from trust4
remove_nonproductive_CDR3aa
                        Clean the clonotype dataframe
summarize_convergence_function
                        summarize_convergence_function
summarize_repertoire_metrics
                        summarize_repertoire_metrics
the global variables    Make variable names global to avoid CHECK notes
the_divergent_clonotype_dataframe_list
                        a list of dataframe where convergent clonotypes
                        are merged
