fix: Allow mismatch_to_mapDamage to work with forward-only data

src/metaDMG/cli/cli.py

@@ -549,7 +549,7 @@ def mismatch_to_mapDamage(
     filename: Path = typer.Argument(
         ...,
         file_okay=True,
-        help="Path to the config-file.",
+        help="Path to the mismatch-file to convert.",
     ),
     csv_out: Path = typer.Option(
         "misincorporation.txt",

src/metaDMG/fit/bayesian.py

@@ -322,6 +322,7 @@ def make_fits(fit_result, data, mcmc_PMD, mcmc_null):
     fit_mcmc(mcmc_null, data)
     add_Bayesian_fit_result(fit_result, data, mcmc_PMD, mcmc_null)
     # mcmc_PMD.print_summary(prob=0.68)
+    # mcmc_null.print_summary(prob=0.68)
 
     # if False:
     #     use_last_state_as_warmup_state(mcmc_PMD)

src/metaDMG/fit/mismatch_to_mapDamage.py

@@ -1,12 +1,26 @@
+#%%
+
 import numpy as np
 import pandas as pd
 
 from metaDMG import __version__ as version
 from metaDMG.fit import mismatches
 
 
+#%%
+
+
 def df_mismatch_to_mapDamage(df_mismatch):
 
+    df_mapDamage = df_mismatch.copy()
+
+    bases = ["A", "C", "G", "T"]
+    for base in bases:
+        if base not in df_mapDamage.columns:
+            mismatches.add_reference_count(df_mapDamage, ref=base)
+
+    df_mapDamage["Total"] = df_mapDamage[bases].sum(axis=1)
+
     # fmt: off
     columns = [
         "Chr", "End", "Std", "Pos",
@@ -28,12 +42,6 @@ def df_mismatch_to_mapDamage(df_mismatch):
     for sub in columns[idx_start:idx_end]:
         d_rename[sub[0] + sub[-1]] = sub
 
-    df_mapDamage = df_mismatch.copy()
-
-    mismatches.add_reference_count(df_mapDamage, ref="A")
-    mismatches.add_reference_count(df_mapDamage, ref="T")
-    df_mapDamage["Total"] = df_mapDamage[["A", "C", "G", "T"]].sum(axis=1)
-
     df_mapDamage = df_mapDamage.rename(columns=d_rename)
     df_mapDamage["End"] = np.where(df_mapDamage["Pos"] > 0, "5p", "3p")
     df_mapDamage["Std"] = "+"
@@ -65,3 +73,6 @@ def convert(filename, csv_out):
 
     with open(csv_out, "w", encoding="utf-8") as file:
         file.write(out)
+
+
+# %%