func New(path string, n ...int) (*Tbx, error) {
if !(xopen.Exists(path) && (xopen.Exists(path+".tbi") || xopen.Exists(path+".csi"))) {
return nil, fmt.Errorf("need gz file and .tbi for %s", path)
}
size := 20
if len(n) > 0 {
size = n[0]
}
t := &Tbx{path: path}
cs, mode := C.CString(t.path), C.char('r')
defer C.free(unsafe.Pointer(cs))
t.htfs = make(chan *C.htsFile, size)
for i := 0; i < cap(t.htfs); i++ {
t.htfs <- C.hts_open(cs, &mode)
}
t.kCache = make(chan C.kstring_t, size*2)
for i := 0; i < cap(t.kCache); i++ {
t.kCache <- C.kstring_t{}
}
t.chromCache = make(map[string]C.int)
if xopen.Exists(path + ".csi") {
csi := C.CString(path + ".csi")
defer C.free(unsafe.Pointer(csi))
t.tbx = C.tbx_index_load2(cs, csi)
} else {
t.tbx = C.tbx_index_load(cs)
}
runtime.SetFinalizer(t, _close)
return t, nil
}
// Flatten turns an annotation into a slice of Sources. Pass in the index of the file.
// having it as a Source makes the code cleaner, but it's simpler for the user to
// specify multiple ops per file in the toml config.
func (a *Annotation) Flatten(index int, basepath string) ([]*Source, error) {
if len(a.Ops) == 0 {
if !strings.HasSuffix(a.File, ".bam") {
return nil, fmt.Errorf("no ops specified for %s\n", a.File)
}
// auto-fill bam to count.
a.Ops = make([]string, len(a.Names))
for i := range a.Names {
a.Ops[i] = "count"
}
}
if len(a.Columns) == 0 && len(a.Fields) == 0 {
if !strings.HasSuffix(a.File, ".bam") {
return nil, fmt.Errorf("no columns or fields specified for %s\n", a.File)
}
// auto-fill bam to count.
if len(a.Fields) == 0 {
a.Columns = make([]int, len(a.Names))
for i := range a.Names {
a.Columns[i] = 1
}
}
}
if !(xopen.Exists(a.File) || a.File == "-") {
if basepath != "" {
a.File = basepath + "/" + a.File
}
if !(xopen.Exists(a.File) || a.File == "-") {
return nil, fmt.Errorf("[Flatten] unable to open file: %s in %s\n", a.File, basepath)
}
}
n := len(a.Ops)
sources := make([]*Source, n)
for i := 0; i < n; i++ {
isjs := strings.HasPrefix(a.Ops[i], "js:")
if !isjs {
if _, ok := Reducers[a.Ops[i]]; !ok {
return nil, fmt.Errorf("requested op not found: %s for %s\n", a.Ops[i], a.File)
}
}
op := a.Ops[i]
if len(a.Names) == 0 {
a.Names = a.Fields
}
sources[i] = &Source{File: a.File, Op: op, Name: a.Names[i], Index: index}
if nil != a.Fields {
sources[i].Field = a.Fields[i]
sources[i].Column = -1
} else {
sources[i].Column = a.Columns[i]
}
}
return sources, nil
}
// New takes a path to a bgziped (and tabixed file) and returns the tabix struct.
func New(path string) (*Tabix, error) {
if !(xopen.Exists(path) && xopen.Exists(path+".tbi")) {
return nil, fmt.Errorf("need gz file and .tbi for %s", path)
}
t := &Tabix{path: path}
cs := C.CString(t.path)
defer C.free(unsafe.Pointer(cs))
mode := C.char('r')
t.htf = C.hts_open(cs, &mode)
t.tbx = C.tbx_index_load(cs)
runtime.SetFinalizer(t, tabixCloser)
if strings.HasSuffix(path, ".bed.gz") {
t.typ = BED
} else if strings.HasSuffix(path, ".vcf.gz") {
t.hdr = C.bcf_hdr_read(t.htf)
t.typ = VCF
} else {
t.typ = OTHER
}
t.original_header = true
return t, nil
}
func (c Config) Sources() ([]*Source, error) {
annos := c.Annotation
for i, a := range annos {
if !xopen.Exists(a.File) && a.File != "-" {
a.File = c.Base + "/" + a.File
annos[i] = a
}
}
s := make([]*Source, 0)
for i, a := range annos {
flats, err := a.Flatten(i, c.Base)
if err != nil {
return nil, err
}
s = append(s, flats...)
}
return s, nil
}
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)
}
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)
}