Mercurial > repos > sanbi-uwc > assess_poliovirus_alignment

diff assess_alignment.py @ 4:1897677e107c draft

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planemo upload for repository https://github.com/pvanheus/polio_report commit a99e10fec2fac5aae70974c977eb3b362a1a8429-dirty
author sanbi-uwc
date Fri, 22 Jul 2022 09:55:46 +0000
parents 31ca16290d4f
children 0e556a3f85d6
line wrap: on
line diff
--- a/assess_alignment.py	Fri Jul 22 09:13:45 2022 +0000
+++ b/assess_alignment.py	Fri Jul 22 09:55:46 2022 +0000
@@ -106,7 +106,7 @@
         if state == "M":
             # for mismatch store [pos_in_genome, pos_in_vp1, reference_base, sequenced_base]
             mismatch_list.append(
-                [i, i - offset + 1, reference["align"][i], mismatch_bases[i]]
+                [i + 1, i - offset + 1, reference["align"][i], mismatch_bases[i]]
             )
     return [conflicts, matches, mismatches, mismatch_list]