// PostAnnotate happens after everything is done.
func (a *Annotator) PostAnnotate(chrom string, start int, end int, info interfaces.Info, prefix string) error {
var e, err error
vals := make([]interface{}, 0, 2)
fields := make([]string, 0, 2)
missing := make([]string, 0, 2)
var val interface{}
for i := range a.PostAnnos {
post := a.PostAnnos[i]
vals = vals[:0]
fields = fields[:0]
missing = missing[:0]
// lua code
if post.code != "" {
for _, field := range post.Fields {
val, e = info.Get(field)
if val != nil {
vals = append(vals, val)
fields = append(fields, field)
} else {
missing = append(missing, field)
}
if e != nil {
err = e
}
}
// we need to try even if it didn't get all values.
if len(vals) == 0 && len(post.Fields) > 0 {
continue
}
k := 0
out:
// could also use fanIn where all channels send to a single
// channel and pull from that.
for {
select {
case k = <-post.mus[0]:
break out
case k = <-post.mus[1]:
break out
case k = <-post.mus[2]:
break out
case k = <-post.mus[3]:
break out
case k = <-post.mus[4]:
break out
case k = <-post.mus[5]:
break out
case k = <-post.mus[6]:
break out
case k = <-post.mus[7]:
break out
default:
}
}
for i, val := range vals {
post.Vms[k].SetGlobal(fields[i], val)
}
post.Vms[k].SetGlobal("chrom", chrom)
post.Vms[k].SetGlobal("start", start)
post.Vms[k].SetGlobal("stop", end)
// need to unset missing values so we don't use those
// from previous run.
for _, miss := range missing {
post.Vms[k].SetGlobal(miss, nil)
}
value, e := post.Vms[k].Run(post.code)
post.mus[k] <- k
if value == nil {
if e != nil {
code := post.code
if len(code) > 40 {
code = code[:37] + "..."
}
log.Printf("ERROR: in lua postannotation at %s:%d for %s.\n%s\nempty values were: %+v\nvalues were: %+v\ncode is: %s", chrom, start+1, post.Name, e, missing, vals, code)
}
continue
}
if e != nil {
err = e
}
val := fmt.Sprintf("%v", value)
if post.Type == "Flag" {
if !(strings.ToLower(val) == "false" || val == "0" || val == "") {
e := info.Set(post.Name, true)
if e != nil {
err = e
}
}
} else {
if e := info.Set(prefix+post.Name, val); e != nil {
err = e
}
}
} else {
// built in function.
// re-use vals
var e error
for _, field := range post.Fields {
// ignore error when field isnt found. we expect that to occur a lot.
val, e = info.Get(field)
if val != nil {
vals = append(vals, val)
} else {
if e != nil {
err = e
}
}
}
// run this as long as we found any of the values.
if len(vals) != 0 {
fn := Reducers[post.Op]
info.Set(prefix+post.Name, fn(vals))
}
}
}
return err
}
func (a *Annotator) PostAnnotate(info interfaces.Info) error {
var err error
vals := make([]interface{}, 0, 2)
for i := range a.PostAnnos {
post := a.PostAnnos[i]
// built in function
vals = vals[:0]
if post.code != "" {
for _, field := range post.Fields {
val, _ := info.Get(field)
// ignore the error as it means the field is not present.
if val != nil {
vals = append(vals, val)
}
}
if len(vals) != len(post.Fields) {
continue
}
post.mu.Lock()
for i, val := range vals {
post.Vm.SetGlobal(post.Fields[i], val)
}
value, e := post.Vm.Run(post.code)
post.mu.Unlock()
if e != nil {
err = e
}
val := fmt.Sprintf("%v", value)
if post.Type == "Flag" {
if !(strings.ToLower(val) == "false" || val == "0" || val == "") {
e := info.Set(post.Name, true)
if e != nil {
err = e
}
}
} else {
if e := info.Set(post.Name, val); e != nil {
err = e
}
}
} else {
// built in function.
// re-use vals
for _, field := range post.Fields {
// ignore error when field isnt found. we expect that to occur a lot.
val, _ := info.Get(field)
if val != nil {
vals = append(vals, val)
}
}
if len(vals) == len(post.Fields) {
fn := Reducers[post.Op]
info.Set(post.Name, fn(vals))
}
}
}
return err
}