From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 9 Oct 2017 10:55:55 +0000 (+0100)
Subject: JAL-2738 ensure variant feature is in forward sense
X-Git-Tag: Release_2_11_0~198
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=82c158fd0d30fc1d1e46c164df7bf4932b522df5;p=jalview.git

JAL-2738 ensure variant feature is in forward sense
---

diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index 711b82a..3d269d8 100644
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -437,13 +437,16 @@ public class VCFLoader
 
       /*
        * convert chromosomal location to sequence coordinates
+       * - may be reverse strand (convert to forward for sequence feature)
        * - null if a partially overlapping feature
        */
       int[] seqLocation = mapping.locateInFrom(start, end);
       if (seqLocation != null)
       {
-        count += addAlleleFeatures(seq, variant, seqLocation[0],
-                seqLocation[1], forwardStrand);
+        int featureStart = Math.min(seqLocation[0], seqLocation[1]);
+        int featureEnd = Math.max(seqLocation[0], seqLocation[1]);
+        count += addAlleleFeatures(seq, variant, featureStart, featureEnd,
+                forwardStrand);
       }
     }