fix flipping allele strand bug for genes on -ve strand

jeremymcrae · Oct 28, 2021 · e094da8 · e094da8
1 parent 5aa9273
commit e094da8
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Showing 2 changed files with 5 additions and 2 deletions.
diff --git a/setup.py b/setup.py
@@ -59,7 +59,7 @@
     description='Package to examine de novo clustering',
     long_description=io.open('README.md', encoding='utf-8').read(),
     long_description_content_type='text/markdown',
-    version="0.9.7",
+    version="0.9.8",
     author="Jeremy McRae",
     author_email="jeremy.mcrae@gmail.com",
     license="MIT",

diff --git a/src/site_rates.cpp b/src/site_rates.cpp
@@ -135,6 +135,10 @@ void SitesChecks::check_position(int bp) {
         alts.erase(matches);
     }
 
+    if (_tx.get_strand() != fwd) {
+        ref = transdict[ref];
+    }
+
     char mutated_aa;
     std::string alt_seq = seq;
     std::string category;
@@ -153,7 +157,6 @@ void SitesChecks::check_position(int bp) {
         // figure out what the ref and alt alleles are, with respect to
         // the + strand.
         if (_tx.get_strand() != fwd) {
-            ref = transdict[ref];
             alt = transdict[alt];
         }