X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/701b1d8a25780ae77f6a4d05ef25103b7ea2cbd8..ec86ad521dff7cb8529e7931f7756e41f03029ff:/diff.go

diff --git a/diff.go b/diff.go
index 2740104cf8..4a328ac756 100644
--- a/diff.go
+++ b/diff.go
@@ -1,4 +1,8 @@
-package main
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package lightning
 
 import (
 	"bufio"
@@ -49,6 +53,7 @@ func (cmd *diffFasta) RunCommand(prog string, args []string, stdin io.Reader, st
 			}
 			defer f.Close()
 			scanner := bufio.NewScanner(f)
+			scanner.Buffer(nil, 64*1024*1024)
 			for scanner.Scan() {
 				buf := scanner.Bytes()
 				if len(buf) > 0 && buf[0] != '>' {
@@ -64,14 +69,14 @@ 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
 }