// AnnotateOne annotates a relatable with the Sources in an Annotator.
// In most cases, no need to specify end (it should always be a single
// arugment indicting LEFT, RIGHT, or INTERVAL, used from AnnotateEnds
func (a *Annotator) AnnotateOne(r interfaces.Relatable, strict bool, end ...string) error {
if len(r.Related()) == 0 {
return nil
}
prefix := ""
if len(end) > 0 {
prefix = end[0]
if len(end) > 1 {
log.Fatalf("too many ends in AnnotateOne")
}
}
parted := a.partition(r)
var v interfaces.IVariant
v, ok := r.(interfaces.IVariant)
if !ok {
log.Fatal("can't annotate non-IVariant", r)
}
var src *Source
for i := range a.Sources {
src = a.Sources[i]
if len(parted) <= src.Index {
continue
}
related := parted[src.Index]
if len(related) == 0 {
continue
}
vals := collect(v, related, src, strict)
src.AnnotateOne(v, vals, prefix)
}
return nil
}
// partition separates the relateds for a relatable so it reduces running over the data multiple times for each file.
func (a *Annotator) partition(r interfaces.Relatable) [][]interfaces.Relatable {
parted := make([][]interfaces.Relatable, 0, 0)
for _, o := range r.Related() {
s := int(o.Source()) - 1
for len(parted) <= s {
parted = append(parted, make([]interfaces.Relatable, 0))
}
parted[s] = append(parted[s], o)
}
return parted
}
// AnnotateEnds makes a new 1-base interval for the left and one for the right end
// so that it can use the same machinery to annotate the ends and the entire interval.
// Output into the info field is prefixed with "left_" or "right_".
func (a *Annotator) AnnotateEnds(v interfaces.Relatable, ends string) error {
var err error
// if Both, call the interval, left, and right version to annotate.
if ends == BOTH {
if e := a.AnnotateOne(v, a.Strict); e != nil {
err = e
}
if e := a.PostAnnotate(v.Chrom(), int(v.Start()), int(v.End()), v.(interfaces.IVariant).Info(), ""); e != nil {
err = e
}
if e := a.AnnotateEnds(v, LEFT); e != nil {
err = e
}
if e := a.AnnotateEnds(v, RIGHT); e != nil {
err = e
}
}
if ends == INTERVAL {
err := a.AnnotateOne(v, a.Strict)
err2 := a.PostAnnotate(v.Chrom(), int(v.Start()), int(v.End()), v.(interfaces.IVariant).Info(), "")
if err != nil {
return err
}
return err2
}
// hack:
// modify the variant in-place to create a 1-base variant at the end of
// the interval. annotate that end and then change the position back to what it was.
if ends == LEFT || ends == RIGHT {
// the end is determined by the SVLEN, so we have to make sure it has length 1.
variant := v.(*parsers.Variant).IVariant
var l, r uint32
var ok bool
if ends == LEFT {
l, r, ok = variant.CIPos()
} else {
l, r, ok = variant.CIEnd()
}
// dont reannotate same interval
if !ok && (l == v.Start() && r == v.End()) {
return nil
}
m := vcfgo.NewInfoByte([]byte(fmt.Sprintf("SVLEN=%d;END=%d", r-l-1, r)), variant.(*vcfgo.Variant).Header)
v2 := parsers.NewVariant(&vcfgo.Variant{Chromosome: v.Chrom(), Pos: uint64(l + 1),
Reference: "A", Alternate: []string{"<DEL>"}, Info_: m}, v.Source(), v.Related())
err = a.AnnotateOne(v2, false, ends)
var val interface{}
for _, key := range v2.Info().Keys() {
if key == "SVLEN" || key == "END" {
continue
}
val, err = v2.Info().Get(key)
variant.Info().Set(key, val)
}
err2 := a.PostAnnotate(v.Chrom(), int(l), int(r), variant.Info(), ends)
if err2 != nil {
err = err2
}
}
return err
}