Fix coordinates in hgvs annotations.

refs #18438

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

diff --git a/slicenumpy.go b/slicenumpy.go
index 8696aa53f33e3386d3e8430b25e9635eecb23fac..82cfff75ce9edc9f3ca3e1357956ac0b3ea3b635 100644 (file)
--- a/slicenumpy.go
+++ b/slicenumpy.go
@@ -454,8 +454,10 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s
                                                continue
                                        }
                                        diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
+                                       for i := range diffs {
+                                               diffs[i].Position += rt.pos
+                                       }
                                        for _, diff := range diffs {
-                                               diff.Position += rt.pos
                                                fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s,%s,%d,%s,%s,%s\n", tag, outcol, v, rt.seqname, diff.String(), rt.seqname, diff.Position, diff.Ref, diff.New, diff.Left)
                                        }
                                        if *hgvsChunked {