# HG changeset patch
# User mheinzl
# Date 1661334428 0
# Node ID d1cd4cd9f18d90ccebf45bd2d1e9dcc46bfbbc67
# Parent  e46d5e377760c700ce23d6a4757ae67ec4f2a441
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty

diff -r e46d5e377760 -r d1cd4cd9f18d read2mut.py
--- a/read2mut.py	Fri Aug 19 11:23:37 2022 +0000
+++ b/read2mut.py	Wed Aug 24 09:47:08 2022 +0000
@@ -477,9 +477,9 @@
                     continue
 
                 if (((key2[:-5] in tag_dict.keys()) and (key2[:-5] in pure_tags_dict_short[key1].keys()) and (key1 in tag_dict[key2[:-5]].keys()) and (key2[:-5] not in used_keys)) or ((key2[:-5] in tag_dict_ref.keys()) and (key2[:-5] in pure_tags_dict_ref[key1].keys()) and (key1 in tag_dict_ref[key2[:-5]].keys()) and (key2[:-5] not in used_keys))):
-                    if key2[:-5] in tag_dict.keys():
+                    if key2[:-5] in tag_dict.keys() and key1 in tag_dict[key2[:-5]].keys():
                         variant_type = "alt"
-                    elif key2[:-5] in tag_dict_ref.keys():
+                    elif key2[:-5] in tag_dict_ref.keys() and key1 in tag_dict_ref[key2[:-5]].keys():
                         variant_type = "ref"
 
                     if refalttiers is False and variant_type == "ref":  # if we only want information about alt tiers, skip all refs