From f34f78480318cf4ea74268baa8e0ce2c65298c55 Mon Sep 17 00:00:00 2001
From: Tom Clegg <tom@tomclegg.ca>
Date: Thu, 16 Jul 2020 13:47:42 -0400
Subject: [PATCH] Add "timed out?" column to diff output.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
---
 diff.go           |  4 ++--
 diff_test.go      |  6 +++---
 hgvs/diff.go      | 11 ++++++++---
 hgvs/diff_test.go |  3 ++-
 4 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/diff.go b/diff.go
index 2740104cf8..f1440cef19 100644
--- a/diff.go
+++ b/diff.go
@@ -64,14 +64,14 @@ func (cmd *diffFasta) RunCommand(prog string, args []string, stdin io.Reader, st
 		}
 	}
 
-	variants := hgvs.Diff(string(fasta[0]), string(fasta[1]), *timeout)
+	variants, timedOut := hgvs.Diff(string(fasta[0]), string(fasta[1]), *timeout)
 	if *offset != 0 {
 		for i := range variants {
 			variants[i].Position += *offset
 		}
 	}
 	for _, v := range variants {
-		fmt.Fprintf(stdout, "%s:g.%s\t%s\t%d\t%s\t%s\n", *sequence, v.String(), *sequence, v.Position, v.Ref, v.New)
+		fmt.Fprintf(stdout, "%s:g.%s\t%s\t%d\t%s\t%s\t%v\n", *sequence, v.String(), *sequence, v.Position, v.Ref, v.New, timedOut)
 	}
 	return 0
 }
diff --git a/diff_test.go b/diff_test.go
index 622d6c47ec..00c5f0c598 100644
--- a/diff_test.go
+++ b/diff_test.go
@@ -26,8 +26,8 @@ func (s *diffSuite) TestDiff(c *check.C) {
 	exited := (&diffFasta{}).RunCommand("diff-fasta", []string{"-sequence", "chr2", "-offset", "1000", tempdir + "/f1.fa", tempdir + "/f2.fa"}, nil, &output, os.Stderr)
 	c.Check(exited, check.Equals, 0)
 	c.Check("\n"+output.String(), check.Equals, `
-chr2:g.1008C>G	chr2	1008	C	G
-chr2:g.1028_1029delinsTT	chr2	1028	AA	TT
-chr2:g.1032_1033insA	chr2	1033		A
+chr2:g.1008C>G	chr2	1008	C	G	false
+chr2:g.1028_1029delinsTT	chr2	1028	AA	TT	false
+chr2:g.1032_1033insA	chr2	1033		A	false
 `)
 }
diff --git a/hgvs/diff.go b/hgvs/diff.go
index 7808259869..a6366eb36f 100644
--- a/hgvs/diff.go
+++ b/hgvs/diff.go
@@ -30,13 +30,18 @@ func (v *Variant) String() string {
 	}
 }
 
-func Diff(a, b string, timeout time.Duration) []Variant {
+func Diff(a, b string, timeout time.Duration) ([]Variant, bool) {
 	dmp := diffmatchpatch.New()
 	var deadline time.Time
 	if timeout > 0 {
 		deadline = time.Now().Add(timeout)
 	}
-	diffs := cleanup(dmp.DiffCleanupEfficiency(dmp.DiffBisect(a, b, deadline)))
+	diffs := dmp.DiffBisect(a, b, deadline)
+	timedOut := false
+	if timeout > 0 && time.Now().After(deadline) {
+		timedOut = true
+	}
+	diffs = cleanup(dmp.DiffCleanupEfficiency(diffs))
 	pos := 1
 	var variants []Variant
 	for i := 0; i < len(diffs); i++ {
@@ -64,7 +69,7 @@ func Diff(a, b string, timeout time.Duration) []Variant {
 			}
 		}
 	}
-	return variants
+	return variants, timedOut
 }
 
 func cleanup(in []diffmatchpatch.Diff) (out []diffmatchpatch.Diff) {
diff --git a/hgvs/diff_test.go b/hgvs/diff_test.go
index 9c04ea75b6..48360efd54 100644
--- a/hgvs/diff_test.go
+++ b/hgvs/diff_test.go
@@ -61,7 +61,8 @@ func (s *diffSuite) TestDiff(c *check.C) {
 	} {
 		c.Log(trial)
 		var vars []string
-		for _, v := range Diff(trial.a, trial.b, 0) {
+		diffs, _ := Diff(trial.a, trial.b, 0)
+		for _, v := range diffs {
 			vars = append(vars, v.String())
 		}
 		c.Check(vars, check.DeepEquals, trial.expect)
-- 
2.30.2