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vcfanno.go
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// vcfanno is a command-line application and an api for annotating intervals (bed or vcf).
package main
import (
"flag"
"fmt"
"io"
"log"
//_ "net/http/pprof"
"os"
"runtime"
"strconv"
"strings"
"sync"
"time"
"github.com/BurntSushi/toml"
"github.com/biogo/hts/bgzf"
"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/brentp/vcfgo"
"github.com/brentp/xopen"
)
const VERSION = "0.3.5"
func envGet(name string, vdefault int) int {
sval := os.Getenv(name)
var err error
if sval != "" {
vdefault, err = strconv.Atoi(sval)
if err != nil {
log.Printf("couldn't parse %s using %d\n", name, vdefault)
} else {
log.Printf("using %s of %d\n", name, vdefault)
}
}
return vdefault
}
func init() {
log.SetFlags(log.Lshortfile)
}
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 lua 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()
os.Exit(2)
}
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 postannotation 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
var qrdr io.Reader
// try to parallelize reading if we have plenty of CPUs and it's (possibly)
// a bgzf file.
if len(config.Annotation) < runtime.GOMAXPROCS(0) && strings.HasSuffix(queryFile, ".gz") || strings.HasSuffix(queryFile, ".bgz") {
if rdr, err := os.Open(queryFile); err == nil {
if st, err := rdr.Stat(); err == nil && st.Size() > 2320303098 {
qrdr, err = bgzf.NewReader(rdr, 4)
if err == nil {
log.Printf("using 4 worker threads to decompress bgzip file")
} else {
qrdr = nil
}
} else {
qrdr, err = bgzf.NewReader(rdr, 2)
if err == nil {
log.Printf("using 2 worker threads to decompress bgzip file")
} else {
qrdr = nil
}
}
} else {
log.Fatal(err)
}
}
if qrdr == nil {
qrdr, err = xopen.Ropen(queryFile)
log.Printf("falling back to non-bgzip")
}
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.
query.Header.Extras = append(query.Header.Extras, fmt.Sprintf("##vcfanno=%s", VERSION))
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 printTime(start time.Time, n int) {
dur := time.Since(start)
duri, duru := dur.Seconds(), "second"
log.Printf("annotated %d variants in %.2f %ss (%.1f / %s)", n, duri, duru, float64(n)/duri, duru)
}