From 99bea95b726805c44392c60da888f6b67b9ed3a1 Mon Sep 17 00:00:00 2001
From: Tom Clegg <tom@curii.com>
Date: Fri, 18 Feb 2022 15:11:19 -0500
Subject: [PATCH] Fix left-most diff cases.

refs #18721

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
---
 hgvs/diff.go      | 21 +++++++++++++++++++++
 hgvs/diff_test.go | 22 ++++++++++++++++++++++
 2 files changed, 43 insertions(+)

diff --git a/hgvs/diff.go b/hgvs/diff.go
index 206cf7e56c..780cfacf10 100644
--- a/hgvs/diff.go
+++ b/hgvs/diff.go
@@ -144,6 +144,27 @@ func cleanup(in []diffmatchpatch.Diff) (out []diffmatchpatch.Diff) {
 			in[i+1] = ins
 			in[i+2] = eq
 		}
+		// when diffmatchpatch says [=yyyyXXXX, delX, =zzz],
+		// we really want [=yyyy, delX, =XXXXzzz] (ditto for
+		// ins instead of del)
+		if i < len(in)-2 &&
+			d.Type == diffmatchpatch.DiffEqual &&
+			in[i+1].Type != diffmatchpatch.DiffEqual &&
+			in[i+2].Type == diffmatchpatch.DiffEqual &&
+			len(in[i+1].Text) <= len(d.Text) {
+			for cut := 0; cut < len(d.Text); cut++ {
+				skip := strings.Index(d.Text[cut:], in[i+1].Text)
+				if skip < 0 {
+					break
+				}
+				cut += skip
+				if d.Text[cut:]+in[i+1].Text == in[i+1].Text+d.Text[cut:] {
+					in[i+2].Text = d.Text[cut:] + in[i+2].Text
+					d.Text = d.Text[:cut]
+					break
+				}
+			}
+		}
 		// diffmatchpatch solves diff("AXX","XXX") with
 		// [delA,=XX,insX] but we prefer to spell it
 		// [delA,insX,=XX].
diff --git a/hgvs/diff_test.go b/hgvs/diff_test.go
index a5e861e35a..10acdb772c 100644
--- a/hgvs/diff_test.go
+++ b/hgvs/diff_test.go
@@ -148,6 +148,28 @@ func (s *diffSuite) TestDiff(c *check.C) {
 			b:      "tcGCcggac",
 			expect: []string{"3A>G", "4T>C", "7del"},
 		},
+		{
+			// should delete leftmost
+			a:      "acgacaTTtttacac",
+			b:      "acgacatttacac",
+			expect: []string{"7_8del"},
+		},
+		{
+			// should insert leftmost
+			a:      "acgacatttacac",
+			b:      "acgacaTTtttacac",
+			expect: []string{"6_7insTT"},
+		},
+		{
+			a:      "ccccaGATAtat",
+			b:      "ccccatat",
+			expect: []string{"6_9del"},
+		},
+		{
+			a:      "aGATAtat",
+			b:      "atat",
+			expect: []string{"2_5del"},
+		},
 	} {
 		c.Log(trial)
 		var vars []string
-- 
2.30.2