From: Tom Clegg <tom@curii.com>
Date: Thu, 30 Dec 2021 16:24:44 +0000 (-0500)
Subject: Fix coordinates in hgvs annotations.
X-Git-Url: https://git.arvados.org/lightning.git/commitdiff_plain/cc97887069d26dd79ab1a28e3040ee7beb0a6f6d

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 8696aa53f3..82cfff75ce 100644
--- 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 {