func phaseInferCommand(c *cli.Context) {
if len(c.String("links")) == 0 {
glog.Errorf("error: must provide a path to a links file with --links.")
return
}
if _, err := os.Stat(c.String("links")); os.IsNotExist(err) {
glog.Errorf("error: the specified links file does not exist: %s\n", c.String("links"))
return
}
links, e2 := util.LoadLinks(c.String("links"))
if e2 != nil {
glog.Errorf("Error loading links: %s\n", e2)
}
Phase(&links)
}
func scaffoldInferCommand(c *cli.Context) {
if len(c.String("links")) == 0 {
fmt.Printf("error: must provide a path to a links file with --links\n")
return
}
if _, err := os.Stat(c.String("links")); os.IsNotExist(err) {
fmt.Printf("error: the specified links file does not exist: %s\n", c.String("links"))
return
}
/*
if (len(c.String("assembly")) == 0) {
fmt.Printf("error: must provide a path to a assembly file with --assembly\n")
return
}
if _, err := os.Stat(c.String("assembly")); os.IsNotExist(err) {
fmt.Printf("error: the specified assembly file does not exist: %s\n", c.String("assembly"))
return
}*/
links, _ := util.LoadLinks(c.String("links"))
//fmt.Println(links)
if len(c.String("subset")) > 0 {
links.Subset(c.String("subset"))
}
//fmt.Println(links.IntIDs())
//fmt.Println(links.StringIDs())
//fmt.Println(links.Decode(links.IntIDs()))
scaffolding := Scaffold(&links, c.String("output"))
/*scaffolding := ScaffoldNew(&links)
scaffolding, _ := links.Decode(scaffolding)
err := WriteScaffolding(scaffolding, c.String("output"))
if err != nil {
fmt.Printf("Error writing scaffolding: ", err)
}*/
//fmt.Println(scaffolding)
//fmt.Println(scaffDecoded)
if len(c.String("key")) > 0 {
key := ReadScaffolding(c.String("key"))
//fmt.Println(key)
score, nscore, _ := EvalScaffolding(scaffolding, key)
fmt.Printf("Evaluated scaffolding with score %f and neighbor score %f\n", score, nscore)
if len(c.String("viz")) > 0 {
VisualizeScaffolding(c.String("output"), c.String("key"), c.String("viz"))
}
}
/*if len(c.String("key")) > 0 {
key := ReadScaffolding(c.String("key"))
//fmt.Println(key)
score, nscore, _ := EvalScaffolding(scaffolding, key)
fmt.Printf("Evaluated scaffolding with score %f and neighbor score %f\n", score, nscore)
if len(c.String("viz")) > 0 {
VisualizeScaffolding(c.String("output"), c.String("key"), c.String("viz"))
}
}*/
}