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package main
import (
"bufio"
"fmt"
"io/ioutil"
"log"
"testing"
"github.com/BurntSushi/toml"
"github.com/brentp/irelate"
"github.com/brentp/irelate/interfaces"
"github.com/brentp/irelate/parsers"
"github.com/brentp/vcfanno/api"
"github.com/brentp/vcfanno/shared"
"github.com/shenwei356/xopen"
)
func benchmarkAnno(b *testing.B) {
var configs shared.Config
if _, err := toml.DecodeFile("example/conf.toml", &configs); err != nil {
panic(err)
}
out := bufio.NewWriter(ioutil.Discard)
Lua, _ := xopen.Ropen("example/custom.lua")
lbytes, _ := ioutil.ReadAll(Lua)
l_string := string(lbytes)
srcs, err := configs.Sources()
if err != nil {
log.Fatal(err)
}
empty := make([]api.PostAnnotation, 0)
for n := 0; n < b.N; n++ {
if err != nil {
log.Fatal(err)
}
a := api.NewAnnotator(srcs, l_string, false, true, empty)
qrdr, err := xopen.Ropen("example/query.vcf.gz")
if err != nil {
log.Fatal(err)
}
qstream, query, err := parsers.VCFIterator(qrdr)
queryables, err := a.Setup(query)
if err != nil {
log.Fatal(err)
}
//files := []string{"example/cadd.sub.txt.gz", "example/query.vcf.gz", "example/fitcons.bed.gz"}
//files := []string{"example/query.vcf.gz", "example/fitcons.bed.gz"}
fn := func(v interfaces.Relatable) {
a.AnnotateEnds(v, api.INTERVAL)
}
stream := irelate.PIRelate(6000, 20000, qstream, false, fn, queryables...)
for interval := range stream {
fmt.Fprintf(out, "%s\n", interval)
}
out.Flush()
}
}
func BenchmarkNormal(b *testing.B) { benchmarkAnno(b) }
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