update CLI for temp var

rwdavies · Apr 22, 2021 · cd684f0 · cd684f0
1 parent c3555f7
commit cd684f0
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Showing 2 changed files with 9 additions and 2 deletions.
diff --git 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
@@ -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"