diff --git a/QUILT.R b/QUILT.R index 405af96..e73ad31 100755 --- a/QUILT.R +++ b/QUILT.R @@ -385,6 +385,12 @@ option_list <- list( type = "logical", help = "Plot per sample likelihoods i.e. the likelihood as the method progresses through the Gibbs sampling iterations [default FALSE] ", default = FALSE + ), + make_option( + "--use_small_eHapsCurrent_tc", + type = "integer", + help = "For testing purposes only [default TRUE] ", + default = TRUE ) ) opt <- suppressWarnings(parse_args(OptionParser(option_list = option_list))) @@ -454,5 +460,6 @@ QUILT( print_extra_timing_information = opt$print_extra_timing_information, block_gibbs_iterations = eval(parse(text=opt$block_gibbs_iterations)), n_gibbs_burn_in_its = opt$n_gibbs_burn_in_its, - plot_per_sample_likelihoods = opt$plot_per_sample_likelihoods + plot_per_sample_likelihoods = opt$plot_per_sample_likelihoods, + use_small_eHapsCurrent_tc = opt$use_small_eHapsCurrent_tc ) diff --git a/scripts/test-cli.R b/scripts/test-cli.R index 19a034a..1cc8148 100755 --- a/scripts/test-cli.R +++ b/scripts/test-cli.R @@ -37,7 +37,7 @@ STITCH::make_STITCH_cli( integer_vectors = c("block_gibbs_iterations"), character_vectors = c("RData_objects_to_save"), other_logical_params = c("make_plots", "verbose", "record_read_label_usage", "record_interim_dosages", "use_bx_tag", "addOptimalHapsToVCF", "estimate_bq_using_truth_read_labels", "make_plots_block_gibbs", "override_default_params_for_small_ref_panel", "hla_run", "make_fake_vcf_with_sites_list", "print_extra_timing_information", "plot_per_sample_likelihoods", "save_prepared_reference"), - other_integer_params = c("nGibbsSamples", "n_seek_its", "Ksubset", "Knew", "K_top_matches", "panel_size", "bxTagUpperLimit", "seed", "gamma_physically_closest_to", "nMaxDH", "minimum_number_of_sample_reads", "n_gibbs_burn_in_its"), + other_integer_params = c("nGibbsSamples", "n_seek_its", "Ksubset", "Knew", "K_top_matches", "panel_size", "bxTagUpperLimit", "seed", "gamma_physically_closest_to", "nMaxDH", "minimum_number_of_sample_reads", "n_gibbs_burn_in_its", "use_small_eHapsCurrent_tc"), other_double_params = c("heuristic_match_thin", "minGLValue"), function_name = "QUILT", library_name = "QUILT"