Switched to new small RNA classification.

This is not yet fully tested, and may have effects on other pipelines.

libhts/libhts.py

@@ -275,8 +275,11 @@ def aligner2min_mapq(aligner, wildcards):
     What minimal MAPQ value should a read have to be considered uniquely mapped?
     See <https://sequencing.qcfail.com/articles/mapq-values-are-really-useful-but-their-implementation-is-a-mess/>.
     """
-    mapped_type = wildcards.mapped_type
-    if mapped_type.startswith("unique_"):
+    try:
+        mapping_type = wildcards.mapping_type
+    except AttributeError:
+        mapping_type = wildcards.mapped_type
+    if mapping_type.startswith("unique_"):
         if aligner == "hisat2":
             return "-Q 60"
         elif aligner == "bowtie2":