Add support for deduplicated files

bin/concatenate_depth_tables.py

@@ -71,7 +71,15 @@ everything from "_to_" until the end.
     else:
         without_path = filename
 
-    without_prefix = without_path.replace("Depth_of_coverage-", "")
+    if "Depth_of_coverage" in without_path:
+        without_prefix = without_path.replace("Depth_of_coverage-", "")
+    elif "Deduplicated_depth_of_coverge" in without_path:
+        without_prefix = without_path.replace("Deduplicated_depth_of_coverage-", "")
+    else:
+        # This should never happen, but the result will show in the sample names
+        # of the output files
+        pass
+
     sample = without_prefix[: without_prefix.index("_to_")]
 
     return sample