+ if !*runlocal {
+ if *outputFilename != "" {
+ err = errors.New("cannot specify output file in container mode: not implemented")
+ return 1
+ }
+ runner := arvadosContainerRunner{
+ Name: "lightning filter",
+ Client: arvados.NewClientFromEnv(),
+ ProjectUUID: *projectUUID,
+ RAM: 64000000000,
+ VCPUs: 2,
+ }
+ err = runner.TranslatePaths(inputFilename)
+ if err != nil {
+ return 1
+ }
+ runner.Args = []string{"filter", "-local=true",
+ "-i", *inputFilename,
+ "-o", "/mnt/output/library.gob",
+ "-max-variants", fmt.Sprintf("%d", *maxvariants),
+ "-min-coverage", fmt.Sprintf("%f", *mincoverage),
+ "-max-tag", fmt.Sprintf("%d", *maxtag),
+ }
+ err = runner.Run()
+ if err != nil {
+ return 1
+ }
+ return 0
+ }
+
+ var infile io.ReadCloser
+ if *inputFilename == "" {
+ infile = ioutil.NopCloser(stdin)
+ } else {
+ infile, err = os.Open(*inputFilename)
+ if err != nil {
+ return 1
+ }
+ defer infile.Close()
+ }