func _main(c *cli.Context) { if c.String("input") == "" { fmt.Fprintf(os.Stderr, "Input required, exiting\n") cli.ShowAppHelp(c) os.Exit(1) } gff_ain, err := autoio.OpenReadScannerSimple(c.String("input")) _ = gff_ain if err != nil { fmt.Fprintf(os.Stderr, "%v", err) os.Exit(1) } defer gff_ain.Close() ref_ain := simplestream.SimpleStream{} ref_fp := os.Stdin if c.String("ref-input") != "-" { var e error ref_fp, e = os.Open(c.String("ref-input")) if e != nil { fmt.Fprintf(os.Stderr, "%v", err) os.Exit(1) } defer ref_fp.Close() } ref_ain.Init(ref_fp) var ref_start int64 ref_start = 0 ss := c.Int("ref-start") if ss > 0 { ref_start = int64(ss) } var seq_start int64 seq_start = 0 _ = seq_start ss = c.Int("seq-start") if ss > 0 { seq_start = int64(ss) } aout := os.Stdout if c.String("output") != "-" { aout, err = os.Open(c.String("output")) if err != nil { fmt.Fprintf(os.Stderr, "%v", err) os.Exit(1) } defer aout.Close() } if c.Bool("pprof") { gProfileFlag = true gProfileFile = c.String("pprof-file") } if c.Bool("mprof") { gMemProfileFlag = true gMemProfileFile = c.String("mprof-file") } gVerboseFlag = c.Bool("Verbose") if c.Int("max-procs") > 0 { runtime.GOMAXPROCS(c.Int("max-procs")) } allele := c.Int("allele") if gProfileFlag { prof_f, err := os.Create(gProfileFile) if err != nil { fmt.Fprintf(os.Stderr, "Could not open profile file %s: %v\n", gProfileFile, err) os.Exit(2) } pprof.StartCPUProfile(prof_f) defer pprof.StopCPUProfile() } e := convert(&gff_ain, &ref_ain, aout, ref_start, allele) if e != nil && e != io.EOF { panic(e) } aout.Sync() }
func _main(c *cli.Context) { var err error if c.String("input") == "" { fmt.Fprintf(os.Stderr, "Input required, exiting\n") cli.ShowAppHelp(c) os.Exit(1) } pasta_ain := simplestream.SimpleStream{} pasta_fp := os.Stdin if len(c.String("input")) > 0 && c.String("input") != "-" { var e error pasta_fp, e = os.Open(c.String("input")) if e != nil { fmt.Fprintf(os.Stderr, "%v", e) os.Exit(1) } defer pasta_fp.Close() } pasta_ain.Init(pasta_fp) aout := os.Stdout if c.String("output") != "-" { aout, err = os.Open(c.String("output")) if err != nil { fmt.Fprintf(os.Stderr, "%v", err) os.Exit(1) } defer aout.Close() } /* aout := os.Stdout if err!=nil { fmt.Fprintf(os.Stderr, "%v", err) os.Exit(1) } */ if c.Bool("pprof") { gProfileFlag = true gProfileFile = c.String("pprof-file") } if c.Bool("mprof") { gMemProfileFlag = true gMemProfileFile = c.String("mprof-file") } gVerboseFlag = c.Bool("Verbose") if c.Int("max-procs") > 0 { runtime.GOMAXPROCS(c.Int("max-procs")) } if gProfileFlag { prof_f, err := os.Create(gProfileFile) if err != nil { fmt.Fprintf(os.Stderr, "Could not open profile file %s: %v\n", gProfileFile, err) os.Exit(2) } pprof.StartCPUProfile(prof_f) defer pprof.StopCPUProfile() } convert(&pasta_ain, aout) }