From: Tom Clegg <tom@tomclegg.ca>
Date: Mon, 1 Nov 2021 14:27:04 +0000 (-0400)
Subject: Fix duplicate entries in slice-numpy annotations.
X-Git-Url: https://git.arvados.org/lightning.git/commitdiff_plain/f77ce7f130e5668cbb347ef086e80c30a4955e55

Fix duplicate entries in slice-numpy annotations.

refs #17763

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

diff --git a/slicenumpy.go b/slicenumpy.go
index fff70d7379..5c55b35af0 100644
--- a/slicenumpy.go
+++ b/slicenumpy.go
@@ -339,7 +339,14 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s
 				outcol := tag - tagID(tagstart)
 				reftilestr := strings.ToUpper(string(rt.tiledata))
 				remap := variantRemap[tag-tagstart]
+				done := make([]bool, len(variants))
 				for v, tv := range variants {
+					v := remap[v]
+					if done[v] {
+						continue
+					} else {
+						done[v] = true
+					}
 					if len(tv.Sequence) < taglen || !bytes.HasSuffix(rt.tiledata, tv.Sequence[len(tv.Sequence)-taglen:]) {
 						continue
 					}
@@ -349,7 +356,7 @@ 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,%s\n", tag, outcol, remap[v], rt.seqname, diff.String(), rt.seqname, diff.Position, diff.Ref, diff.New, diff.Left)
+						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)
 					}
 				}
 			}