Avoid empty "ref" field in anno2vcf output.

[lightning.git] / slicenumpy.go

diff --git a/slicenumpy.go b/slicenumpy.go
index 5aa97ac5a7c44707b03720ac6631eaa03599ce54..fff70d7379f81aa90e50c2d917bbf5c268ffee7a 100644 (file)
--- a/slicenumpy.go
+++ b/slicenumpy.go
@@ -349,7 +349,7 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s
                                        diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
                                        for _, diff := range diffs {
                                                diff.Position += rt.pos
-                                               fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s,%s,%d,%s,%s\n", tag, outcol, remap[v], rt.seqname, diff.String(), rt.seqname, diff.Position, diff.Ref, diff.New)
+                                               fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s,%s,%d,%s,%s,%s\n", tag, outcol, remap[v], rt.seqname, diff.String(), rt.seqname, diff.Position, diff.Ref, diff.New, diff.Left)
                                        }
                                }
                        }