return 0
} else if err != nil {
return 2
- }
- if flag.NArg() > 0 {
- err = fmt.Errorf("extra unparsed command line arguments: %q", flag.Args())
+ } else if flags.NArg() > 0 {
+ err = fmt.Errorf("errant command line arguments after parsed flags: %v", flags.Args())
return 2
}
Priority: *priority,
APIAccess: true,
}
- err = runner.TranslatePaths(inputDir)
+ err = runner.TranslatePaths(inputDir, cases)
if err != nil {
return 1
}
retainTileSequences: true,
compactGenomes: map[string][]tileVariantID{},
}
- err = tilelib.LoadDir(context.Background(), *inputDir, nil)
+ err = tilelib.LoadDir(context.Background(), *inputDir)
if err != nil {
return 1
}
cmd.cases = make([]bool, len(names))
if *cases != "" {
log.Infof("reading cases file: %s", *cases)
- f, err := open(*cases)
+ var f io.ReadCloser
+ f, err = open(*cases)
if err != nil {
return 1
}
- buf, err := io.ReadAll(f)
+ defer f.Close()
+ var buf []byte
+ buf, err = io.ReadAll(f)
if err != nil {
return 1
}