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|
package vcfgo
import (
"fmt"
"strconv"
)
func SplitAlts(v *Variant) []*Variant {
vars := make([]*Variant, len(v.Alt()))
for i := range v.Alt() {
vars[i] = &Variant{Chromosome: v.Chromosome, Pos: v.Pos, Id_: v.Id_,
Reference: v.Ref(), Alternate: []string{v.Alt()[i]}, Quality: v.Quality, Filter: v.Filter,
Info_: v.Info_, Samples: v.Samples, sampleString: v.sampleString,
Header: v.Header, LineNumber: v.LineNumber}
split(vars[i], i, len(v.Alt()))
}
return vars
}
func split(v *Variant, i int, nAlts int) error {
// extract the appropriate
var err error
for _, k := range v.Info_.Keys() {
h := v.Header.Infos[k]
switch h.Number {
case "A":
var s interface{}
s, err = splitA(v, i, nAlts)
v.Info_.Set(k, s)
case "G":
var s []interface{}
var val interface{}
val, err = v.Info_.Get(k)
s, err = splitG(val, i, nAlts)
v.Info_.Set(k, s)
case "R":
var s []interface{}
var val interface{}
val, err = v.Info_.Get(k)
s, err = splitR(val, i, nAlts)
v.Info_.Set(k, s)
}
}
v.Header.ParseSamples(v)
for _, h := range v.Header.SampleFormats {
if h.Number != "A" && h.Number != "G" && h.Number != "R" {
continue
}
/*
for j, samp := range v.Samples {
switch h.Number {
case "A":
// TODO: should this still be a list?
var s interface{}
s, err = splitA(samp.Fields[k], i, nAlts)
//samp.Fields[k] = s
case "G":
case "R":
}
}
*/
}
// TODO: v.Samples
return err
}
func splitG(m interface{}, i int, nAlts int) ([]interface{}, error) {
pairs := [][]int{{0, 0}, {0, i}, {i, i}}
G := make([]interface{}, 3)
for o, jk := range pairs {
order := (jk[1] * (jk[1] + 1) / 2) + jk[0]
G[o] = m.([]interface{})[order]
}
return G, nil
}
func splitGT(m interface{}, i int) ([]interface{}, error) {
ml := m.([]interface{})
out := make([]interface{}, len(ml))
ai := strconv.Itoa(i)
for i, allelei := range ml {
allele := allelei.(string)
if allele == "0" {
out[i] = "0"
}
if ai == allele {
out[i] = "1"
} else {
out[i] = "."
}
}
return out, nil
}
func splitR(m interface{}, i int, nAlts int) ([]interface{}, error) {
ml := m.([]interface{})
if len(ml) != nAlts+1 {
return nil, fmt.Errorf("incorrect number of alts in splitR: %v", m)
}
if i+1 >= len(ml) {
return nil, fmt.Errorf("requested bad alt in splitR: %v", m)
}
out := make([]interface{}, 2)
out[0] = ml[0]
out[1] = ml[i+1]
return out, nil
}
// when we split on alt, it returns a single int since we are decomposing.
func splitA(m interface{}, i int, nAlts int) (interface{}, error) {
ml := m.([]interface{})
if len(ml) != nAlts {
return nil, fmt.Errorf("incorrect number of alts in splitA: %v", m)
}
return ml[i], nil
}
|
