From 519577af0a389a3d6dc4af8da8a3332b9504e9fb Mon Sep 17 00:00:00 2001
From: Tom Clegg <tom@curii.com>
Date: Tue, 26 Jul 2022 13:16:15 -0400
Subject: [PATCH] Fix diff case

refs #19236 #note-15.1

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
---
 hgvs/diff.go      | 13 +++++++++++++
 hgvs/diff_test.go |  5 +++++
 2 files changed, 18 insertions(+)

diff --git a/hgvs/diff.go b/hgvs/diff.go
index e2b73439bf..c217949ee4 100644
--- a/hgvs/diff.go
+++ b/hgvs/diff.go
@@ -219,6 +219,19 @@ func cleanup(in []diffmatchpatch.Diff) (out []diffmatchpatch.Diff) {
 			i++
 			continue
 		}
+		// when diffmatchpatch says [delA, =X, delBX], we
+		// prefer [delAB, =X].
+		if i < len(in)-2 &&
+			d.Type == diffmatchpatch.DiffDelete &&
+			in[i+1].Type == diffmatchpatch.DiffEqual &&
+			in[i+2].Type == diffmatchpatch.DiffDelete &&
+			strings.HasSuffix(in[i+2].Text, in[i+1].Text) {
+			out = append(out,
+				diffmatchpatch.Diff{diffmatchpatch.DiffDelete, d.Text + in[i+2].Text[:len(in[i+2].Text)-len(in[i+1].Text)]},
+				in[i+1])
+			i += 2
+			continue
+		}
 		out = append(out, d)
 	}
 	in, out = out, make([]diffmatchpatch.Diff, 0, len(in))
diff --git a/hgvs/diff_test.go b/hgvs/diff_test.go
index 2778dc8f55..3cac5db020 100644
--- a/hgvs/diff_test.go
+++ b/hgvs/diff_test.go
@@ -192,6 +192,11 @@ func (s *diffSuite) TestDiff(c *check.C) {
 			b:      "acGTTTTTatcc",
 			expect: []string{"2_3insGT"},
 		},
+		{
+			a:      "aGACGGACAGGGCCCgg",
+			b:      "agg",
+			expect: []string{"3_15del"},
+		},
 	} {
 		c.Log(trial)
 		var vars []string
-- 
2.30.2