Add support for deduplicated files

bin/concatenate_read_counts.py

@@ -71,7 +71,14 @@ everything from "_to_" until the end.
     else:
         without_path = filename
 
-    without_prefix = without_path.replace("Mapped_read_counts-", "")
+    if "Mapped_read_counts" in without_path:
+        without_prefix = without_path.replace("Mapped_read_counts-", "")
+    elif "Deduplicated_read_counts" in without_path:
+        without_prefix = without_path.replace("Deduplicated_read_counts-", "")
+    else:
+        # This should never happen, but it will show in sample names otherwise.
+        pass
+
     sample = without_prefix[: without_prefix.index("_to_")]
     reference = without_prefix[without_prefix.index("_to_") + 4 : -4]
     # Assume the .tsv file extension; hence strip the last 4 characters