Escape case when three FastQ files per sample exist

By default, we evaluate whether there are more than two FastQ files
available in the column download_links by checking the presence of a
semicolon. If there is a semicolon, the first entry is used as R1 and
the second entry as R2.

However, in the case that a third FastQ file is uploaded, such as the
merged reads or singletons, the first FastQ file does not contain the
paired reads but the second and third do.

This implements the check whether there are three FastQ files to pick
the correct paired FastQ files for the assembly.

Author: alexhbnr

amdirt/core/__init__.py

@@ -233,8 +233,12 @@ def get_filename(path_string: str, orientation: str) -> Tuple[str, str]:
     """
 
     if ";" in path_string:
-        fwd = Path(path_string.split(";")[0]).name
-        rev = Path(path_string.split(";")[1]).name
+        if path_string.count(";") == 1:
+            fwd = Path(path_string.split(";")[0]).name
+            rev = Path(path_string.split(";")[1]).name
+        else:  # three files per sample
+            fwd = Path(path_string.split(";")[1]).name
+            rev = Path(path_string.split(";")[2]).name
     else:
         fwd = Path(path_string).name
         rev = "NA"