Пример #1
0
// LuaOp uses go-lua to run a lua snippet on a list of values and return a single value.
// It makes the chrom, start, end, and values available to the lua interpreter.
func (s *Source) LuaOp(v interfaces.IVariant, code string, vals []interface{}) string {
	value, err := s.Vm.Run(code, map[string]interface{}{
		"chrom": v.Chrom(),
		"start": v.Start(),
		"stop":  v.End(),
		"vals":  vals})
	if err != nil {
		return fmt.Sprintf("lua-error: %s", err)
	}
	return fmt.Sprintf("%v", value)
}
Пример #2
0
// AnnotateOne annotates a single variant with the vals
func (s *Source) AnnotateOne(v interfaces.IVariant, vals []interface{}, prefix string) {
	if len(vals) == 0 {
		return
	}
	if s.code != "" {
		luaval := s.LuaOp(v, s.code, vals)
		if luaval == "true" || luaval == "false" && strings.Contains(s.Op, "_flag(") {
			if luaval == "true" {
				v.Info().Set(prefix+s.Name, true)
			}
		} else {
			v.Info().Set(prefix+s.Name, luaval)
		}
	} else {
		val := Reducers[s.Op](vals)
		v.Info().Set(prefix+s.Name, val)
	}
}
Пример #3
0
func (src *Source) AnnotateOne(v interfaces.IVariant, vals []interface{}, prefix string) {
	if len(vals) == 0 {
		return
	}
	if src.Js != nil {
		jsval := src.JsOp(v, src.Js, vals)
		if jsval == "true" || jsval == "false" && strings.Contains(src.Op, "_flag(") {
			if jsval == "true" {
				v.Info().Set(prefix+src.Name, true)
			}
		} else {
			v.Info().Set(prefix+src.Name, jsval)
		}
	} else {
		val := Reducers[src.Op](vals)
		v.Info().Set(prefix+src.Name, val)
	}
}
Пример #4
0
// JsOp uses Otto to run a javascript snippet on a list of values and return a single value.
// It makes the chrom, start, end, and values available to the js interpreter.
func (s *Source) JsOp(v interfaces.IVariant, js *otto.Script, vals []interface{}) string {
	s.mu.Lock()
	s.Vm.Set("chrom", v.Chrom())
	s.Vm.Set("start", v.Start())
	s.Vm.Set("end", v.End())
	s.Vm.Set("vals", vals)
	//s.Vm.Set("info", v.Info.String())
	value, err := s.Vm.Run(js)
	if err != nil {
		return fmt.Sprintf("js-error: %s", err)
	}
	val, err := value.ToString()
	s.mu.Unlock()
	if err != nil {
		log.Println("js-error:", err)
		val = fmt.Sprintf("error:%s", err)
	}
	return val
}
Пример #5
0
// LuaOp uses go-lua to run a lua snippet on a list of values and return a single value.
// It makes the chrom, start, end, and values available to the lua interpreter.
func (s *Source) LuaOp(v interfaces.IVariant, code string, vals []interface{}) string {
	value, err := s.Vm.Run(code, map[string]interface{}{
		"chrom": v.Chrom(),
		"start": v.Start(),
		"stop":  v.End(),
		"ref":   v.Ref(),
		"alt":   v.Alt(),
		"vals":  vals})
	if err != nil {
		log.Printf("ERROR in at %s:%d. %s\nvals:%+v", v.Chrom(), v.Start()+1, err, vals)
		return fmt.Sprintf("err:%v", value)
	}
	return fmt.Sprintf("%v", value)
}