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 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 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 main2() {
/*
f, err := os.Create("q.pprof")
if err != nil {
panic(err)
}
pprof.StartCPUProfile(f)
defer pprof.StopCPUProfile()
*/
t, err := cgotbx.New(os.Args[1])
if err != nil {
log.Fatal(err)
}
var rdr io.Reader
for i := 0; i < 1000; i++ {
tot := 0
f, err := xopen.Ropen(os.Args[1])
check(err)
vcf, err := vcfgo.NewReader(f, true)
check(err)
t0 := 0
for {
v := vcf.Read()
if v == nil {
break
}
ts := time.Now()
for k := 0; k < 100; k++ {
rdr, err = t.Get(v.Chrom(), int(v.Start()), int(v.Start())+1)
check(err)
brdr := bufio.NewReader(rdr)
//fmt.Fprintln(os.Stderr, v.Chrom(), v.Start(), v.Start()+1)
j := 0
for l, err := brdr.ReadString('\n'); err == nil; l, err = brdr.ReadString('\n') {
//fmt.Fprintln(os.Stderr, "...", l[:20])
_ = l
tot += 1
j += 1
}
if j == 0 {
log.Fatal("should have found something")
}
}
t0 += int(time.Since(ts).Nanoseconds())
}
log.Println(tot, float64(t0)*1e-9)
}
}
func ReadJs(js string) string {
var jsString string
if js != "" {
jsReader, err := xopen.Ropen(js)
if err != nil {
log.Fatal(err)
}
jsBytes, err := ioutil.ReadAll(jsReader)
if err != nil {
log.Fatal(err)
}
jsString = string(jsBytes)
} else {
jsString = ""
}
return jsString
}
func ReadLua(lua string) string {
var luaString string
if lua != "" {
luaReader, err := xopen.Ropen(lua)
if err != nil {
log.Fatal(err)
}
luaBytes, err := ioutil.ReadAll(luaReader)
if err != nil {
log.Fatal(err)
}
luaString = string(luaBytes)
} else {
luaString = ""
}
return luaString
}
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.")
lua := flag.String("lua", "", "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.")
flag.Parse()
inFiles := flag.Args()
if len(inFiles) != 2 {
fmt.Printf(`Usage:
%s config.toml input.vcf > annotated.vcf
`, os.Args[0])
flag.PrintDefaults()
return
}
queryFile := inFiles[1]
if !(xopen.Exists(queryFile) || queryFile == "") {
fmt.Fprintf(os.Stderr, "\nERROR: can't find query file: %s\n", queryFile)
os.Exit(2)
}
runtime.GOMAXPROCS(*procs)
var config Config
if _, err := toml.DecodeFile(inFiles[0], &config); err != nil {
if strings.Contains(err.Error(), "Expected value but found") {
fmt.Fprintln(os.Stderr, "\nNOTE: you must quote values in the conf file, e.g. fields=['AC', 'AN'] instead of fields=[AC, AN]")
}
panic(err)
}
config.Base = *base
for _, a := range config.Annotation {
err := CheckAnno(&a)
if err != nil {
log.Fatal("CheckAnno err:", err)
}
for _, op := range a.Ops {
if len(op) > 4 && op[:4] == "lua:" && *lua == "" {
log.Fatal("ERROR: requested lua op without specifying -lua flag")
}
}
}
for i := range config.PostAnnotation {
r := config.PostAnnotation[i]
err := CheckPostAnno(&r)
if err != nil {
log.Fatal(fmt.Sprintf("error in postannotaion section %s err: %s", r.Name, err))
}
if len(r.Op) > 4 && r.Op[:4] == "lua:" && *lua == "" {
log.Fatal("ERROR: requested lua op without specifying -lua flag")
}
}
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))
}()
*/
luaString := ReadLua(*lua)
strict := !*notstrict
var a = NewAnnotator(sources, luaString, *ends, strict, config.PostAnnotation)
var out io.Writer = os.Stdout
defer os.Stdout.Close()
var err error
qrdr, err := xopen.Ropen(queryFile)
if err != nil {
log.Fatal(fmt.Errorf("error opening query file %s: %s", queryFile, err))
}
qstream, query, err := parsers.VCFIterator(qrdr)
if err != nil {
log.Fatal(fmt.Errorf("error parsing VCF query file %s: %s", queryFile, err))
}
queryables, err := a.Setup(query)
if err != nil {
log.Fatal(err)
}
aends := INTERVAL
if *ends {
aends = BOTH
}
lastMsg := struct {
sync.RWMutex
s [10]string
i int
}{}
fn := func(v interfaces.Relatable) {
e := a.AnnotateEnds(v, aends)
if e != nil {
lastMsg.RLock()
em := e.Error()
found := false
for i := len(lastMsg.s) - 1; i >= 0; i-- {
if em == lastMsg.s[i] {
found = true
break
}
}
if !found {
log.Println(e, ">> this error/warning may occur many times. reporting once here...")
lastMsg.RUnlock()
lastMsg.Lock()
lastMsg.s[lastMsg.i] = em
if lastMsg.i == len(lastMsg.s)-1 {
lastMsg.i = -1
}
lastMsg.i++
lastMsg.Unlock()
} else {
lastMsg.RUnlock()
}
}
}
maxGap := envGet("IRELATE_MAX_GAP", 20000)
maxChunk := envGet("IRELATE_MAX_CHUNK", 8000)
// make a new writer from the string header.
out, err = vcfgo.NewWriter(out, query.Header)
stream := irelate.PIRelate(maxChunk, maxGap, qstream, *ends, fn, queryables...)
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 {
//log.Printf("%v\n", interval)
fmt.Fprintln(out, interval)
n++
}
printTime(start, n)
}
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.")
lua := flag.String("lua", "", "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
`, os.Args[0])
flag.PrintDefaults()
return
}
queryFile := inFiles[1]
if !(xopen.Exists(queryFile) || queryFile == "") {
fmt.Fprintf(os.Stderr, "\nERROR: can't find 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)
}
}
for i := range config.PostAnnotation {
r := config.PostAnnotation[i]
err := CheckPostAnno(&r)
if err != nil {
log.Fatal(fmt.Sprintf("error in postannotaion section %s err: %s", r.Name, 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))
}()
*/
luaString := ReadLua(*lua)
strict := !*notstrict
var a = NewAnnotator(sources, luaString, *ends, strict, config.PostAnnotation)
var out io.Writer = os.Stdout
defer os.Stdout.Close()
var err error
qrdr, err := xopen.Ropen(queryFile)
if err != nil {
log.Fatal(fmt.Errorf("error opening query file %s: %s", queryFile, err))
}
qstream, query, err := parsers.VCFIterator(qrdr)
if err != nil {
log.Fatal(fmt.Errorf("error parsing VCF query file %s: %s", queryFile, err))
}
queryables, err := a.Setup(query)
if err != nil {
log.Fatal(err)
}
aends := INTERVAL
if *ends {
aends = BOTH
}
fn := func(v interfaces.Relatable) {
e := a.AnnotateEnds(v, aends)
if e != nil {
log.Println(e)
}
}
smaxGap := os.Getenv("IRELATE_MAX_GAP")
maxGap := 20000
if smaxGap != "" {
maxGap, err = strconv.Atoi(smaxGap)
if err != nil {
log.Printf("couldn't parse %s using %d\n", smaxGap, maxGap)
} else {
log.Printf("using maxGap of %d\n", maxGap)
}
}
stream := irelate.PIRelate(8000, maxGap, qstream, *ends, fn, queryables...)
// make a new writer from the string header.
out, err = vcfgo.NewWriter(out, query.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 {
//log.Printf("%v\n", interval)
fmt.Fprintln(out, interval)
n++
}
printTime(start, n)
}