func main() {
f, err := os.Create("irelate.cpu.pprof")
if err != nil {
panic(err)
}
pprof.StartCPUProfile(f)
defer pprof.StopCPUProfile()
files := os.Args[1:]
buf := bufio.NewWriter(os.Stdout)
b, err := bix.New(files[0], 1)
check(err)
bx, err := b.Query(nil)
check(err)
queryables := make([]I.Queryable, len(files)-1)
for i, f := range files[1:] {
q, err := bix.New(f, 1)
if err != nil {
log.Fatal(err)
}
queryables[i] = q
}
for interval := range irelate.PIRelate(80000, 25000, bx, false, func(a I.Relatable) {}, queryables...) {
fmt.Fprintf(buf, "%s\t%d\t%d\t%d\n", interval.Chrom(), interval.Start(), interval.End(), len(interval.Related()))
}
buf.Flush()
}
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)
Js, _ := xopen.Ropen("example/custom.js")
jbytes, _ := ioutil.ReadAll(Js)
js_string := string(jbytes)
srcs, err := configs.Sources()
if err != nil {
log.Fatal(err)
}
a := api.NewAnnotator(srcs, js_string, false, true)
files, err := a.SetupStreams()
if err != nil {
log.Fatal(err)
}
for n := 0; n < b.N; n++ {
q, err := bix.New("example/query.vcf.gz", 1)
if err != nil {
log.Fatal(err)
}
bx, err := q.Query(nil)
if err != nil {
log.Fatal(err)
}
a.UpdateHeader(q)
//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"}
queryables := make([]interfaces.Queryable, len(files))
for i, f := range files {
q, err := bix.New(f, 1)
if err != nil {
log.Fatal(err)
}
queryables[i] = q
}
fn := func(v interfaces.Relatable) {
a.AnnotateEnds(v, api.INTERVAL)
}
stream := irelate.PIRelate(4000, 20000, bx, false, fn, queryables...)
for interval := range stream {
fmt.Fprintf(out, "%s\n", interval)
}
out.Flush()
}
}
func main() {
f := os.Args[1]
tbx, err := bix.New(f)
check(err)
chrom := os.Args[2]
s, err := strconv.Atoi(os.Args[3])
check(err)
e, err := strconv.Atoi(os.Args[4])
check(err)
vals, _ := tbx.Query(loc{chrom, s, e})
i := 0
for {
v, err := vals.Next()
if err != nil {
break
}
fmt.Println(v.(interfaces.IVariant).String()[:40])
i++
}
tbx.Close()
}
func main() {
f, err := xopen.Ropen(os.Args[1])
check(err)
vcf, err := vcfgo.NewReader(f, true)
check(err)
tbx, err := bix.New(os.Args[1])
check(err)
var rdr io.Reader
tot := 0
t0 := time.Now()
for {
v := vcf.Read()
if v == nil {
break
}
rdr, err = tbx.ChunkedReader(location{v.Chrom(), int(v.Start()), int(v.Start()) + 1})
check(err)
brdr := bufio.NewReader(rdr)
for _, err := brdr.ReadString('\n'); err == nil; _, err = brdr.ReadString('\n') {
tot += 1
}
}
log.Println(tot, time.Since(t0).Seconds())
main2()
}
func benchmarkStreams(nStreams int, b *testing.B) {
for n := 0; n < b.N; n++ {
streams := make([]interfaces.RelatableIterator, 0)
f := "data/test.bed.gz"
for i := 0; i < nStreams; i++ {
s, e := bix.New(f)
if e != nil {
panic(e)
}
q, e := s.Query(nil)
streams = append(streams, q)
}
//for a := range IRelate(CheckRelatedByOverlap, 0, Less, streams...) {
iter := IRelate(CheckOverlapPrefix, 0, LessPrefix, streams...)
for {
a, err := iter.Next()
if err != nil {
break
a.Start()
}
}
}
}
// Setup reads all the tabix indexes and setups up the Queryables
func (a *Annotator) Setup(query HeaderUpdater) ([]interfaces.Queryable, error) {
files, fmap, err := a.setupStreams()
if err != nil {
return nil, err
}
var wg sync.WaitGroup
wg.Add(len(files))
queryables := make([]interfaces.Queryable, len(files))
for i, file := range files {
go func(idx int, file string) {
var q interfaces.Queryable
var err error
if strings.HasSuffix(file, ".bam") {
q, err = parsers.NewBamQueryable(file, 2)
} else {
q, err = bix.New(file, 1)
}
if err != nil {
log.Fatal(err)
}
queryables[idx] = q
wg.Done()
}(i, file)
}
wg.Wait()
for i, file := range files {
if q, ok := queryables[i].(*bix.Bix); ok {
for _, src := range fmap[file] {
src.UpdateHeader(query, a.Ends, q.GetHeaderType(src.Field), q.GetHeaderNumber(src.Field))
}
} else if _, ok := queryables[i].(*parsers.BamQueryable); ok {
for _, src := range fmap[file] {
htype := "String"
if src.IsNumber() {
htype = "Float"
}
src.UpdateHeader(query, a.Ends, htype, "1")
}
} else {
log.Printf("type not known: %T\n", queryables[i])
}
}
for _, post := range a.PostAnnos {
query.AddInfoToHeader(post.Name, ".", post.Type, fmt.Sprintf("calculated field: %s", post.Name))
}
return queryables, nil
}
func (a *Annotator) Setup(query HeaderUpdater) ([]interfaces.Queryable, error) {
queryables := make([]interfaces.Queryable, 0)
files, fmap, err := a.setupStreams()
if err != nil {
return nil, err
}
for _, file := range files {
q, err := bix.New(file, 1)
if err != nil {
return nil, err
}
queryables = append(queryables, q)
for _, src := range fmap[file] {
src.UpdateHeader(query, a.Ends, q.GetHeaderType(src.Field))
}
}
for _, post := range a.PostAnnos {
query.AddInfoToHeader(post.Name, ".", post.Type, fmt.Sprintf("calculated field: %s", post.Name))
}
return queryables, nil
}
func AsQueryable(f string) (interfaces.Queryable, error) {
return bix.New(f, 1)
}
func main() {
fmt.Fprintf(os.Stderr, `
=============================================
vcfanno version %s [built with %s]
see: https://github.com/brentp/vcfanno
=============================================
`, VERSION, runtime.Version())
ends := flag.Bool("ends", false, "annotate the start and end as well as the interval itself.")
notstrict := flag.Bool("permissive-overlap", false, "annotate with an overlapping variant even it doesn't"+
" share the same ref and alt alleles. Default is to require exact match between variants.")
js := flag.String("js", "", "optional path to a file containing custom javascript functions to be used as ops")
base := flag.String("base-path", "", "optional base-path to prepend to annotation files in the config")
procs := flag.Int("p", 2, "number of processes to use. default is 2")
flag.Parse()
inFiles := flag.Args()
if len(inFiles) != 2 {
fmt.Printf(`Usage:
%s config.toml intput.vcf > annotated.vcf
To run a server:
%s server
`, os.Args[0], os.Args[0])
flag.PrintDefaults()
return
}
queryFile := inFiles[1]
if !(xopen.Exists(queryFile)) {
fmt.Fprintf(os.Stderr, "\nERROR: can't find query file: %s\n", queryFile)
os.Exit(2)
}
if !(xopen.Exists(queryFile + ".tbi")) {
fmt.Fprintf(os.Stderr, "\nERROR: can't find index for query file: %s\n", queryFile)
os.Exit(2)
}
runtime.GOMAXPROCS(*procs)
var config Config
if _, err := toml.DecodeFile(inFiles[0], &config); err != nil {
panic(err)
}
config.Base = *base
for _, a := range config.Annotation {
err := CheckAnno(&a)
if err != nil {
log.Fatal("CheckAnno err:", err)
}
}
sources, e := config.Sources()
if e != nil {
log.Fatal(e)
}
log.Printf("found %d sources from %d files\n", len(sources), len(config.Annotation))
go func() {
log.Println(http.ListenAndServe("localhost:6060", nil))
}()
jsString := ReadJs(*js)
strict := !*notstrict
var a = NewAnnotator(sources, jsString, *ends, strict)
var out io.Writer = os.Stdout
defer os.Stdout.Close()
var err error
var bx interfaces.RelatableIterator
b, err := bix.New(queryFile, 1)
if err != nil {
log.Fatal(fmt.Errorf("error opening query file and/or index: %s ... %s", queryFile, err))
}
a.UpdateHeader(b)
if err != nil {
log.Fatal(err)
}
bx, err = b.Query(nil)
if err != nil {
log.Fatal(err)
}
files, err := a.SetupStreams()
if err != nil {
log.Fatal(err)
}
aends := INTERVAL
if *ends {
aends = BOTH
}
fn := func(v interfaces.Relatable) {
a.AnnotateEnds(v, aends)
}
queryables := make([]interfaces.Queryable, len(files))
for i, f := range files {
q, err := bix.New(f, 1)
if err != nil {
log.Fatal(err)
}
queryables[i] = q
}
stream := irelate.PIRelate(4000, 20000, bx, *ends, fn, queryables...)
// make a new writer from the string header.
out, err = vcfgo.NewWriter(out, b.VReader.Header)
if err != nil {
log.Fatal(err)
}
start := time.Now()
n := 0
if os.Getenv("IRELATE_PROFILE") == "TRUE" {
log.Println("profiling to: irelate.pprof")
f, err := os.Create("irelate.pprof")
if err != nil {
panic(err)
}
pprof.StartCPUProfile(f)
defer pprof.StopCPUProfile()
}
for interval := range stream {
fmt.Fprintf(out, "%s\n", interval)
n++
}
printTime(start, n)
}
