From: Tom Clegg <tom@tomclegg.ca>
Date: Thu, 3 Jun 2021 20:27:44 +0000 (-0400)
Subject: Fix another category of misspelled hgvs diff.
X-Git-Url: https://git.arvados.org/lightning.git/commitdiff_plain/2382e6c62ced70780d4b56bf0569ce849fa3d9f0?ds=sidebyside

Fix another category of misspelled hgvs diff.

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

diff --git a/hgvs/diff.go b/hgvs/diff.go
index e04ccff587..47deab7246 100644
--- a/hgvs/diff.go
+++ b/hgvs/diff.go
@@ -125,6 +125,20 @@ func cleanup(in []diffmatchpatch.Diff) (out []diffmatchpatch.Diff) {
 			in[i+1] = ins
 			in[i+2] = eq
 		}
+		// diffmatchpatch solves diff("AXX","XXX") with
+		// [delA,=XX,insX] but we prefer to spell it
+		// [delA,insX,=XX].
+		//
+		// So, when we see a [del,=,ins] sequence that has the
+		// same effect after swapping the "=" and "ins" parts,
+		// we swap them.
+		if i < len(in)-2 &&
+			d.Type == diffmatchpatch.DiffDelete &&
+			in[i+1].Type == diffmatchpatch.DiffEqual &&
+			in[i+2].Type == diffmatchpatch.DiffInsert &&
+			in[i+1].Text+in[i+2].Text == in[i+2].Text+in[i+1].Text {
+			in[i+2], in[i+1] = in[i+1], in[i+2]
+		}
 		out = append(out, d)
 	}
 	return
diff --git a/hgvs/diff_test.go b/hgvs/diff_test.go
index 20043ca31a..9a4e35531c 100644
--- a/hgvs/diff_test.go
+++ b/hgvs/diff_test.go
@@ -104,6 +104,11 @@ func (s *diffSuite) TestDiff(c *check.C) {
 			b:      "acTtgaa",
 			expect: []string{"3G>T"},
 		},
+		{
+			a:      "tcagaagac",
+			b:      "tcaAaagac",
+			expect: []string{"4G>A"},
+		},
 	} {
 		c.Log(trial)
 		var vars []string