-package main
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package lightning
import (
"bufio"
"io"
"os"
- "git.arvados.org/lightning/hgvs"
+ "github.com/arvados/lightning/hgvs"
)
type diffFasta struct{}
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
}
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]))
+ 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
}