Merge pull request #21 from xin-huang/recomb

Fix bugs in recombination maps
xin-huang · Jul 16, 2023 · b564075 · b564075
2 parents 9c26d58 + 938cac4
commit b564075
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/setup.py b/setup.py
@@ -11,7 +11,7 @@
 # This call to setup() does all the work
 setup(
     name="sstar",
-    version="1.1.2",
+    version="1.1.3",
     description="A Python package for detecting archaic introgression from population genetic data with S*",
     long_description=README,
     long_description_content_type="text/markdown",

diff --git a/sstar/cal_threshold.py b/sstar/cal_threshold.py
@@ -125,7 +125,7 @@ def _predict_res(gam, score_file, recomb_rate, recomb_map, quantile, fit_lr):
 
             line = "\t".join(meta_data[s][i])
             line += "\t" + str(null_score)
-            line += "\t" + str(10**data[s]['lr'][i])
+            line += "\t" + str(data[s]['lr'][i])
             line += "\t" + str(data[s]['q'][i])
             line += "\t" + sig
 
@@ -168,10 +168,10 @@ def _read_score_file(score_file, recomb_rate, recomb_map, quantile, fit_lr):
                 if fit_lr:
                     if recomb_map != None: 
                         key = chr_name+":"+win_start+"-"+win_end
-                        if key in recomb_map.keys(): local_recomb_rate = np.log10(recomb_map[key])
+                        if key in recomb_map.keys(): local_recomb_rate = recomb_map[key]
                         else: continue
                     else:
-                        local_recomb_rate = np.log10(recomb_rate)
+                        local_recomb_rate = recomb_rate
                 else: local_recomb_rate = np.nan
 
                 if sample not in data.keys():