This fixes milaboratory#560

hkmoon · Dec 6, 2019 · 82c35be · 82c35be
1 parent 3baa3df
commit 82c35be
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAligner.java b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAligner.java
@@ -120,7 +120,7 @@ protected VDJCAlignmentResult<VDJCMultiRead> process0(VDJCMultiRead input) {
                         if (g == 0) // V
                             lastVTarget = targetId;
 
-                        if (g == 1) // J
+                        if (g == 1 && firstJTarget == -1) // J
                             firstJTarget = targetId;
 
                         alignmentHits[targetId] = als.getHits().toArray(new AlignmentHit[als.getHits().size()]);