X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/80c6ae7fcdf650d0cdc211aa3c12008aab4564f7..4ef1b78b8c8d118e2318376079b921aa5244aa1c:/diff.go

diff --git a/diff.go b/diff.go
index 43ed90ce3f..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"
@@ -8,7 +12,7 @@ import (
 	"io"
 	"os"
 
-	"github.com/curii/lightning/hgvs"
+	"github.com/arvados/lightning/hgvs"
 )
 
 type diffFasta struct{}
@@ -24,6 +28,7 @@ func (cmd *diffFasta) RunCommand(prog string, args []string, stdin io.Reader, st
 	flags.SetOutput(stderr)
 	offset := flags.Int("offset", 0, "coordinate offset")
 	sequence := flags.String("sequence", "chr1", "sequence label")
+	timeout := flags.Duration("timeout", 0, "timeout (examples: \"1s\", \"1ms\")")
 	err = flags.Parse(args)
 	if err == flag.ErrHelp {
 		err = nil
@@ -48,6 +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] != '>' {
@@ -63,14 +69,14 @@ func (cmd *diffFasta) RunCommand(prog string, args []string, stdin io.Reader, st
 		}
 	}
 
-	variants := hgvs.Diff(string(fasta[0]), string(fasta[1]))
+	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
 }