-package main
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package lightning
import (
"bufio"
return 0
} else if err != nil {
return 2
- }
- if len(flags.Args()) != 2 {
+ } else if len(flags.Args()) != 2 {
err = fmt.Errorf("usage: %s [options] a.fasta b.fasta", prog)
return 2
}
}
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] != '>' {
}
}
- 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
}