added N as a possible base in pileup

jts · Feb 13, 2024 · 3028cc6 · 3028cc6
1 parent 3c9acec
commit 3028cc6
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/workflow/scripts/format_pileup.py b/workflow/scripts/format_pileup.py
@@ -12,7 +12,7 @@
 
 print("\t".join(["contig", "position", "depth", "ref_base", "count_A", "count_C", "count_G", "count_T", "count_del", "alt_frequency"]))
 for pc in samfile.pileup(ignore_orphans=False):
-    freqs = {'A': 0, 'T': 0, 'G': 0, 'C': 0, '-': 0, 'R': 0 }
+    freqs = {'A': 0, 'T': 0, 'G': 0, 'C': 0, '-': 0, 'R': 0, 'N': 0 }
     for pr in pc.pileups:
         if pr.is_del:
             freqs['-'] += 1