func _main_gvcf_to_rotini(c *cli.Context) {
var e error
infn_slice := c.StringSlice("input")
if len(infn_slice) < 1 {
infn_slice = append(infn_slice, "-")
}
ain, err := autoio.OpenReadScanner(infn_slice[0])
if err != nil {
fmt.Fprintf(os.Stderr, "%v", err)
os.Stderr.Sync()
os.Exit(1)
}
defer ain.Close()
fp := os.Stdin
if c.String("refstream") != "-" {
fp, e = os.Open(c.String("refstream"))
if e != nil {
fmt.Fprintf(os.Stderr, "%v", e)
os.Stderr.Sync()
os.Exit(1)
}
defer fp.Close()
}
ref_stream := bufio.NewReader(fp)
out := bufio.NewWriter(os.Stdout)
g := gvcf.GVCFRefVar{}
g.Init()
line_no := 0
g.PastaBegin(out)
for ain.ReadScan() {
gvcf_line := ain.ReadText()
line_no++
if len(gvcf_line) == 0 || gvcf_line == "" {
continue
}
e := g.Pasta(gvcf_line, ref_stream, out)
if e != nil {
fmt.Fprintf(os.Stderr, "ERROR: %v at line %v\n", e, line_no)
return
}
}
g.PastaEnd(out)
out.Flush()
}
