fix unbounderror

README.md

@@ -18,9 +18,9 @@
 1. [`count`](https://pinellolab.github.io/crispr-bean/count.html), [`count-samples`](https://pinellolab.github.io/crispr-bean/count_samples.html): Base-editing-aware **mapping** of guide, optionally with reporter from `.fastq` files.
     *   [`create-screen`](https://pinellolab.github.io/crispr-bean/create_screen.html) creates minimal ReporterScreen object from flat gRNA count file. Note that this way, allele counts are not included and many functionalities involving allele and edit counts are not supported.
 2. [`profile`](https://pinellolab.github.io/crispr-bean/profile.html): Profile editing preferences of your editor.  
-3. [`qc`](#bean-qc-qc-of-reporter-screen-data): Quality control report and filtering out / masking of aberrant sample and guides  
-4. [`filter`](#bean-filter-filtering-and-optionally-translating-alleles): Filter reporter alleles; essential for `tiling` mode that allows for all alleles generated from gRNA.
-5. [`run`](#bean-run-quantify-variant-effects): Quantify targeted variants' effect sizes from screen data.  
+3. [`qc`](https://pinellolab.github.io/crispr-bean/qc.html): Quality control report and filtering out / masking of aberrant sample and guides  
+4. [`filter`](https://pinellolab.github.io/crispr-bean/filter.html): Filter reporter alleles; essential for `tiling` mode that allows for all alleles generated from gRNA.
+5. [`run`](https://pinellolab.github.io/crispr-bean/run.html): Quantify targeted variants' effect sizes from screen data.  
 * Screen data is saved as *ReporterScreen* object in the pipeline.
 BEAN stores mapped gRNA and allele counts in `ReporterScreen` object which is compatible with [AnnData](https://anndata.readthedocs.io/en/latest/index.html). See [Data Structure](#data-structure) section for more information.
 ## Installation 

bean/cli/run.py

@@ -172,6 +172,8 @@ def main(args):
                     negctrl_model, negctrl_guide, ndata_negctrl, num_steps=args.n_iter
                 )
             )
+        else:
+            param_history_dict_negctrl = None
 
     outfile_path = (
         f"{prefix}/bean_element[sgRNA]_result.{model_label}{args.result_suffix}.csv"

bean/model/readwrite.py

@@ -103,9 +103,9 @@ def write_result_table(
     fit_df = pd.DataFrame(param_dict)
     if negctrl_params is not None:
         print("Normalizing with common negative control distribution")
-        mu0 = negctrl_params["params"]["mu_loc"].detach().cpu().numpy()
+        mu0 = negctrl_params["mu_loc"].detach().cpu().numpy()
         if sd_is_fitted:
-            sd0 = negctrl_params["params"]["sd_loc"].detach().exp().cpu().numpy()
+            sd0 = negctrl_params["sd_loc"].detach().exp().cpu().numpy()
         else:
             sd0 = 1.0
         print(f"Fitted mu0={mu0}" + (f", sd0={sd0}." if sd_is_fitted else ""))