projects
/
lightning.git
/ blobdiff
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Use native client to read annotations.csv.
[lightning.git]
/
cmd.go
diff --git
a/cmd.go
b/cmd.go
index 1fff7b4b7e312ca09655ce1ba5c08e6dc6bd055b..b10b1caa3fc4a65531de88e6818013a628380494 100644
(file)
--- a/
cmd.go
+++ b/
cmd.go
@@
-1,3
+1,7
@@
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
package lightning
import (
package lightning
import (
@@
-6,6
+10,8
@@
import (
"io/ioutil"
"os"
"os/exec"
"io/ioutil"
"os"
"os/exec"
+ "runtime/debug"
+ "strings"
"git.arvados.org/arvados.git/lib/cmd"
"github.com/mattn/go-isatty"
"git.arvados.org/arvados.git/lib/cmd"
"github.com/mattn/go-isatty"
@@
-24,6
+30,10
@@
var (
"annotate": &annotatecmd{},
"export": &exporter{},
"export-numpy": &exportNumpy{},
"annotate": &annotatecmd{},
"export": &exporter{},
"export-numpy": &exportNumpy{},
+ "flake": &flakecmd{},
+ "slice": &slicecmd{},
+ "slice-numpy": &sliceNumpy{},
+ "anno2vcf": &anno2vcf{},
"numpy-comvar": &numpyComVar{},
"filter": &filtercmd{},
"build-docker-image": &buildDockerImage{},
"numpy-comvar": &numpyComVar{},
"filter": &filtercmd{},
"build-docker-image": &buildDockerImage{},
@@
-37,10
+47,19
@@
var (
})
)
})
)
+func init() {
+ if os.Getenv("GOGC") == "" {
+ debug.SetGCPercent(30)
+ }
+}
+
func Main() {
if !isatty.IsTerminal(os.Stderr.Fd()) {
logrus.StandardLogger().Formatter = &logrus.TextFormatter{DisableTimestamp: true}
}
func Main() {
if !isatty.IsTerminal(os.Stderr.Fd()) {
logrus.StandardLogger().Formatter = &logrus.TextFormatter{DisableTimestamp: true}
}
+ if len(os.Args) >= 2 && !strings.HasSuffix(os.Args[1], "version") {
+ cmd.Version.RunCommand("lightning", nil, nil, os.Stderr, os.Stderr)
+ }
os.Exit(handler.RunCommand(os.Args[0], os.Args[1:], os.Stdin, os.Stdout, os.Stderr))
}
os.Exit(handler.RunCommand(os.Args[0], os.Args[1:], os.Stdin, os.Stdout, os.Stderr))
}
@@
-53,7
+72,7
@@
func (cmd *buildDockerImage) RunCommand(prog string, args []string, stdin io.Rea
return 1
}
defer os.RemoveAll(tmpdir)
return 1
}
defer os.RemoveAll(tmpdir)
- err = ioutil.WriteFile(tmpdir+"/Dockerfile", []byte(`FROM debian:
10
+ err = ioutil.WriteFile(tmpdir+"/Dockerfile", []byte(`FROM debian:
bullseye
RUN DEBIAN_FRONTEND=noninteractive \
apt-get update && \
apt-get dist-upgrade -y && \
RUN DEBIAN_FRONTEND=noninteractive \
apt-get update && \
apt-get dist-upgrade -y && \