22 "git.arvados.org/arvados.git/sdk/go/arvados"
23 "github.com/arvados/lightning/hgvs"
24 "github.com/klauspost/pgzip"
25 log "github.com/sirupsen/logrus"
28 type outputFormat struct {
30 Head func(out io.Writer, cgs []CompactGenome)
31 Print func(out io.Writer, seqname string, varslice []hgvs.Variant)
36 outputFormats = map[string]outputFormat{
37 "hgvs-onehot": outputFormatHGVSOneHot,
38 "hgvs": outputFormatHGVS,
39 "pvcf": outputFormatPVCF,
40 "vcf": outputFormatVCF,
42 outputFormatHGVS = outputFormat{Filename: "out.csv", Head: headNone, Print: printHGVS}
43 outputFormatHGVSOneHot = outputFormat{Filename: "out.csv", Head: headNone, Print: printHGVSOneHot}
44 outputFormatPVCF = outputFormat{Filename: "out.vcf", Head: headPVCF, Print: printPVCF, PadLeft: true}
45 outputFormatVCF = outputFormat{Filename: "out.vcf", Head: headVCF, Print: printVCF, PadLeft: true}
46 headNone = func(io.Writer, []CompactGenome) {}
49 type exporter struct {
50 outputFormat outputFormat
56 func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
60 fmt.Fprintf(stderr, "%s\n", err)
63 flags := flag.NewFlagSet("", flag.ContinueOnError)
64 flags.SetOutput(stderr)
65 pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
66 pprofdir := flags.String("pprof-dir", "", "write Go profile data to `directory` periodically")
67 runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
68 projectUUID := flags.String("project", "", "project `UUID` for output data")
69 priority := flags.Int("priority", 500, "container request priority")
70 refname := flags.String("ref", "", "reference genome `name`")
71 inputDir := flags.String("input-dir", ".", "input `directory`")
72 outputDir := flags.String("output-dir", ".", "output `directory`")
73 outputFormatStr := flags.String("output-format", "hgvs", "output `format`: hgvs, pvcf, or vcf")
74 outputBed := flags.String("output-bed", "", "also output bed `file`")
75 flags.BoolVar(&cmd.outputPerChrom, "output-per-chromosome", true, "output one file per chromosome")
76 flags.BoolVar(&cmd.compress, "z", false, "write gzip-compressed output files")
77 labelsFilename := flags.String("output-labels", "", "also output genome labels csv `file`")
78 flags.IntVar(&cmd.maxTileSize, "max-tile-size", 50000, "don't try to make annotations for tiles bigger than given `size`")
79 err = flags.Parse(args)
80 if err == flag.ErrHelp {
83 } else if err != nil {
87 err = fmt.Errorf("extra unparsed command line arguments: %q", flag.Args())
91 if f, ok := outputFormats[*outputFormatStr]; !ok {
92 err = fmt.Errorf("invalid output format %q", *outputFormatStr)
100 log.Println(http.ListenAndServe(*pprof, nil))
104 go writeProfilesPeriodically(*pprofdir)
108 if *outputDir != "." {
109 err = errors.New("cannot specify output directory in container mode: not implemented")
112 runner := arvadosContainerRunner{
113 Name: "lightning export",
114 Client: arvados.NewClientFromEnv(),
115 ProjectUUID: *projectUUID,
121 err = runner.TranslatePaths(inputDir)
125 if *outputBed != "" {
126 if strings.Contains(*outputBed, "/") {
127 err = fmt.Errorf("cannot use -output-bed filename %q containing '/' char", *outputBed)
130 *outputBed = "/mnt/output/" + *outputBed
132 runner.Args = []string{"export", "-local=true",
134 "-pprof-dir", "/mnt/output",
136 "-output-format", *outputFormatStr,
137 "-output-bed", *outputBed,
138 "-output-labels", "/mnt/output/labels.csv",
139 "-output-per-chromosome=" + fmt.Sprintf("%v", cmd.outputPerChrom),
140 "-max-tile-size", fmt.Sprintf("%d", cmd.maxTileSize),
141 "-input-dir", *inputDir,
142 "-output-dir", "/mnt/output",
143 "-z=" + fmt.Sprintf("%v", cmd.compress),
146 output, err = runner.Run()
150 fmt.Fprintln(stdout, output)
154 var cgs []CompactGenome
155 tilelib := &tileLibrary{
157 retainTileSequences: true,
158 compactGenomes: map[string][]tileVariantID{},
160 err = tilelib.LoadDir(context.Background(), *inputDir, nil)
165 refseq, ok := tilelib.refseqs[*refname]
167 err = fmt.Errorf("reference name %q not found in input; have %v", *refname, func() (names []string) {
168 for name := range tilelib.refseqs {
169 names = append(names, name)
176 names := cgnames(tilelib)
177 for _, name := range names {
178 cgs = append(cgs, CompactGenome{Name: name, Variants: tilelib.compactGenomes[name]})
180 if *labelsFilename != "" {
181 log.Infof("writing labels to %s", *labelsFilename)
183 f, err = os.OpenFile(*labelsFilename, os.O_CREATE|os.O_WRONLY, 0777)
188 for i, name := range names {
189 _, err = fmt.Fprintf(f, "%d,%q,%q\n", i, trimFilenameForLabel(name), cmd.outputFormat.Filename)
191 err = fmt.Errorf("write %s: %w", *labelsFilename, err)
197 err = fmt.Errorf("close %s: %w", *labelsFilename, err)
204 var bedbufw *bufio.Writer
205 if *outputBed != "" {
206 bedfile, err = os.OpenFile(*outputBed, os.O_CREATE|os.O_WRONLY, 0666)
210 defer bedfile.Close()
211 bedbufw = bufio.NewWriterSize(bedfile, 16*1024*1024)
215 err = cmd.export(*outputDir, bedout, tilelib, refseq, cgs)
220 err = bedbufw.Flush()
224 err = bedfile.Close()
232 func (cmd *exporter) export(outdir string, bedout io.Writer, tilelib *tileLibrary, refseq map[string][]tileLibRef, cgs []CompactGenome) error {
233 var seqnames []string
234 var missing []tileLibRef
235 for seqname, librefs := range refseq {
236 seqnames = append(seqnames, seqname)
237 for _, libref := range librefs {
238 if libref.Variant != 0 && tilelib.TileVariantSequence(libref) == nil {
239 missing = append(missing, libref)
243 sort.Strings(seqnames)
245 if len(missing) > 0 {
246 if limit := 100; len(missing) > limit {
247 log.Warnf("first %d missing tiles: %v", limit, missing[:limit])
249 log.Warnf("missing tiles: %v", missing)
251 return fmt.Errorf("%d needed tiles are missing from library", len(missing))
254 outw := make([]io.WriteCloser, len(seqnames))
255 bedw := make([]io.WriteCloser, len(seqnames))
257 var merges sync.WaitGroup
258 merge := func(dst io.Writer, src []io.WriteCloser, label string) {
260 for i, seqname := range seqnames {
267 log.Infof("writing %s %s", seqname, label)
268 scanner := bufio.NewScanner(pr)
271 dst.Write(scanner.Bytes())
272 dst.Write([]byte{'\n'})
275 log.Infof("writing %s %s done", seqname, label)
279 if cmd.outputPerChrom {
280 for i, seqname := range seqnames {
281 fnm := filepath.Join(outdir, strings.Replace(cmd.outputFormat.Filename, ".", "."+seqname+".", 1))
285 f, err := os.OpenFile(fnm, os.O_CREATE|os.O_WRONLY|os.O_TRUNC, 0666)
290 log.Infof("writing %q", f.Name())
293 z := pgzip.NewWriter(f)
297 cmd.outputFormat.Head(outw[i], cgs)
300 fnm := filepath.Join(outdir, cmd.outputFormat.Filename)
304 f, err := os.OpenFile(fnm, os.O_CREATE|os.O_WRONLY|os.O_TRUNC, 0666)
309 log.Infof("writing %q", fnm)
310 var out io.Writer = f
312 z := pgzip.NewWriter(out)
316 cmd.outputFormat.Head(out, cgs)
317 merge(out, outw, "output")
320 merge(bedout, bedw, "bed")
323 throttle := throttle{Max: runtime.NumCPU()}
324 log.Infof("assembling %d sequences in %d goroutines", len(seqnames), throttle.Max)
325 for seqidx, seqname := range seqnames {
326 seqidx, seqname := seqidx, seqname
331 defer throttle.Release()
335 outwb := bufio.NewWriterSize(outw, 8*1024*1024)
336 cmd.exportSeq(outwb, bedw, tilelib.taglib.keylen, seqname, refseq[seqname], tilelib, cgs)
346 return throttle.Err()
349 // Align genome tiles to reference tiles, write diffs to outw, and (if
350 // bedw is not nil) write tile coverage to bedw.
351 func (cmd *exporter) exportSeq(outw, bedw io.Writer, taglen int, seqname string, reftiles []tileLibRef, tilelib *tileLibrary, cgs []CompactGenome) {
353 progressbar := time.NewTicker(time.Minute)
354 defer progressbar.Stop()
355 var outmtx sync.Mutex
358 variantAt := map[int][]hgvs.Variant{} // variantAt[chromOffset][genomeIndex*2+phase]
359 for refstep, libref := range reftiles {
361 case <-progressbar.C:
364 fin := t0.Add(time.Duration(float64(time.Now().Sub(t0)) * float64(len(reftiles)) / float64(refstep)))
365 eta = fmt.Sprintf("%v (%v)", fin.Format(time.RFC3339), fin.Sub(time.Now()))
369 log.Printf("exportSeq: %s: refstep %d of %d, %.0f/s, ETA %v", seqname, refstep, len(reftiles), float64(refstep)/time.Now().Sub(t0).Seconds(), eta)
372 diffs := map[tileLibRef][]hgvs.Variant{}
373 refseq := tilelib.TileVariantSequence(libref)
374 tagcoverage := 0 // number of times the start tag was found in genomes -- max is len(cgs)*2
375 for cgidx, cg := range cgs {
376 for phase := 0; phase < 2; phase++ {
377 if len(cg.Variants) <= int(libref.Tag)*2+phase {
380 variant := cg.Variants[int(libref.Tag)*2+phase]
385 if variant == libref.Variant {
388 glibref := tileLibRef{Tag: libref.Tag, Variant: variant}
389 vars, ok := diffs[glibref]
391 genomeseq := tilelib.TileVariantSequence(glibref)
392 if len(genomeseq) == 0 {
393 // Hash is known but sequence
394 // is not, e.g., retainNoCalls
395 // was false during import
398 if len(genomeseq) > cmd.maxTileSize {
401 refSequence := refseq
402 // If needed, extend the
403 // reference sequence up to
404 // the tag at the end of the
405 // genomeseq sequence.
406 refstepend := refstep + 1
407 for refstepend < len(reftiles) && len(refSequence) >= taglen && !bytes.EqualFold(refSequence[len(refSequence)-taglen:], genomeseq[len(genomeseq)-taglen:]) && len(refSequence) <= cmd.maxTileSize {
408 if &refSequence[0] == &refseq[0] {
409 refSequence = append([]byte(nil), refSequence...)
411 refSequence = append(refSequence, tilelib.TileVariantSequence(reftiles[refstepend])...)
414 // (TODO: handle no-calls)
415 refstr := strings.ToUpper(string(refSequence))
416 genomestr := strings.ToUpper(string(genomeseq))
417 vars, _ = hgvs.Diff(refstr, genomestr, time.Second)
418 diffs[glibref] = vars
420 for _, v := range vars {
421 if cmd.outputFormat.PadLeft {
425 varslice := variantAt[v.Position]
427 varslice = make([]hgvs.Variant, len(cgs)*2)
428 variantAt[v.Position] = varslice
430 varslice[cgidx*2+phase] = v
434 refpos += len(refseq) - taglen
436 // Flush entries from variantAt that are behind
437 // refpos. Flush all entries if this is the last
438 // reftile of the path/chromosome.
439 flushpos := make([]int, 0, len(variantAt))
440 lastrefstep := refstep == len(reftiles)-1
441 for pos := range variantAt {
442 if lastrefstep || pos <= refpos {
443 flushpos = append(flushpos, pos)
446 sort.Slice(flushpos, func(i, j int) bool { return flushpos[i] < flushpos[j] })
447 flushvariants := make([][]hgvs.Variant, len(flushpos))
448 for i, pos := range flushpos {
449 varslice := variantAt[pos]
450 delete(variantAt, pos)
451 for i := range varslice {
452 if varslice[i].Position == 0 {
453 varslice[i].Position = pos
456 flushvariants[i] = varslice
460 defer outmtx.Unlock()
461 for _, varslice := range flushvariants {
462 cmd.outputFormat.Print(outw, seqname, varslice)
465 if bedw != nil && len(refseq) > 0 {
466 tilestart := refpos - len(refseq) + taglen
471 thickstart := tilestart + taglen
477 // coverage score, 0 to 1000
480 score = 1000 * tagcoverage / len(cgs) / 2
483 fmt.Fprintf(bedw, "%s %d %d %d %d . %d %d\n",
484 seqname, tilestart, tileend,
487 thickstart, thickend)
492 func bucketVarsliceByRef(varslice []hgvs.Variant) map[string]map[string]int {
493 byref := map[string]map[string]int{}
494 for _, v := range varslice {
495 if v.Ref == "" && v.New == "" {
500 alts = map[string]int{}
508 func headVCF(out io.Writer, cgs []CompactGenome) {
509 fmt.Fprint(out, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n")
512 func printVCF(out io.Writer, seqname string, varslice []hgvs.Variant) {
513 for ref, alts := range bucketVarsliceByRef(varslice) {
514 altslice := make([]string, 0, len(alts))
515 for alt := range alts {
516 altslice = append(altslice, alt)
518 sort.Strings(altslice)
521 for i, a := range altslice {
525 info += strconv.Itoa(alts[a])
527 fmt.Fprintf(out, "%s\t%d\t.\t%s\t%s\t.\t.\t%s\n", seqname, varslice[0].Position, ref, strings.Join(altslice, ","), info)
531 func headPVCF(out io.Writer, cgs []CompactGenome) {
532 fmt.Fprintln(out, `##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">`)
533 fmt.Fprintf(out, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT")
534 for _, cg := range cgs {
535 fmt.Fprintf(out, "\t%s", cg.Name)
537 fmt.Fprintf(out, "\n")
540 func printPVCF(out io.Writer, seqname string, varslice []hgvs.Variant) {
541 for ref, alts := range bucketVarsliceByRef(varslice) {
542 altslice := make([]string, 0, len(alts))
543 for alt := range alts {
544 altslice = append(altslice, alt)
546 sort.Strings(altslice)
547 for i, a := range altslice {
550 fmt.Fprintf(out, "%s\t%d\t.\t%s\t%s\t.\t.\t.\tGT", seqname, varslice[0].Position, ref, strings.Join(altslice, ","))
551 for i := 0; i < len(varslice); i += 2 {
552 v1, v2 := varslice[i], varslice[i+1]
553 a1, a2 := alts[v1.New], alts[v2.New]
555 // variant on allele 0 belongs on a
556 // different output line -- same
557 // chr,pos but different "ref" length
563 fmt.Fprintf(out, "\t%d/%d", a1, a2)
565 out.Write([]byte{'\n'})
569 func printHGVS(out io.Writer, seqname string, varslice []hgvs.Variant) {
570 for i := 0; i < len(varslice)/2; i++ {
572 out.Write([]byte{'\t'})
574 var1, var2 := varslice[i*2], varslice[i*2+1]
576 if var1.Ref == var1.New {
577 out.Write([]byte{'.'})
579 fmt.Fprintf(out, "%s:g.%s", seqname, var1.String())
582 fmt.Fprintf(out, "%s:g.[%s];[%s]", seqname, var1.String(), var2.String())
585 out.Write([]byte{'\n'})
588 func printHGVSOneHot(out io.Writer, seqname string, varslice []hgvs.Variant) {
589 vars := map[hgvs.Variant]bool{}
590 for _, v := range varslice {
596 // sort variants to ensure output is deterministic
597 sorted := make([]hgvs.Variant, 0, len(vars))
598 for v := range vars {
599 sorted = append(sorted, v)
601 sort.Slice(sorted, func(a, b int) bool { return hgvs.Less(sorted[a], sorted[b]) })
603 for _, v := range sorted {
604 fmt.Fprintf(out, "%s.%s", seqname, v.String())
605 for i := 0; i < len(varslice); i += 2 {
606 if varslice[i] == v || varslice[i+1] == v {
607 out.Write([]byte("\t1"))
609 out.Write([]byte("\t0"))
612 out.Write([]byte{'\n'})