X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/cda874b19e13a70453c1ef9cf6e37e3703706fac..7cc2d4585f54e1121e295b07a12a52748bbe0792:/export.go diff --git a/export.go b/export.go index 256af21296..1ea08fe757 100644 --- a/export.go +++ b/export.go @@ -1,4 +1,8 @@ -package main +// Copyright (C) The Lightning Authors. All rights reserved. +// +// SPDX-License-Identifier: AGPL-3.0 + +package lightning import ( "bufio" @@ -11,32 +15,54 @@ import ( "net/http" _ "net/http/pprof" "os" + "path/filepath" + "runtime" "sort" + "strconv" "strings" "sync" "time" "git.arvados.org/arvados.git/sdk/go/arvados" "github.com/arvados/lightning/hgvs" + "github.com/klauspost/pgzip" + "github.com/kshedden/gonpy" + "github.com/sirupsen/logrus" log "github.com/sirupsen/logrus" ) -type outputFormat struct { - Print func(out io.Writer, seqname string, varslice []hgvs.Variant) - PadLeft bool +type tvVariant struct { + hgvs.Variant + librefs map[tileLibRef]bool } -var ( - outputFormats = map[string]outputFormat{ - "hgvs": outputFormatHGVS, - "vcf": outputFormatVCF, - } - outputFormatHGVS = outputFormat{Print: printHGVS} - outputFormatVCF = outputFormat{Print: printVCF, PadLeft: true} -) +type outputFormat interface { + Filename() string + PadLeft() bool + Head(out io.Writer, cgs []CompactGenome, cases []bool, p float64) error + Print(out io.Writer, seqname string, varslice []tvVariant) error + Finish(outdir string, out io.Writer, seqname string) error + MaxGoroutines() int +} + +var outputFormats = map[string]func() outputFormat{ + "hgvs-numpy": func() outputFormat { + return &formatHGVSNumpy{alleles: map[string][][]int8{}} + }, + "hgvs-onehot": func() outputFormat { return formatHGVSOneHot{} }, + "hgvs": func() outputFormat { return formatHGVS{} }, + "pvcf": func() outputFormat { return formatPVCF{} }, + "vcf": func() outputFormat { return formatVCF{} }, +} type exporter struct { - outputFormat outputFormat + outputFormat outputFormat + outputPerChrom bool + compress bool + maxTileSize int + filter filter + maxPValue float64 + cases []bool } func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int { @@ -49,15 +75,22 @@ func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, std flags := flag.NewFlagSet("", flag.ContinueOnError) flags.SetOutput(stderr) pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`") + pprofdir := flags.String("pprof-dir", "", "write Go profile data to `directory` periodically") runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)") projectUUID := flags.String("project", "", "project `UUID` for output data") priority := flags.Int("priority", 500, "container request priority") refname := flags.String("ref", "", "reference genome `name`") - inputFilename := flags.String("i", "-", "input `file` (library)") - outputFilename := flags.String("o", "-", "output `file`") - outputFormatStr := flags.String("output-format", "hgvs", "output `format`: hgvs or vcf") + inputDir := flags.String("input-dir", ".", "input `directory`") + cases := flags.String("cases", "", "file indicating which genomes are positive cases (for computing p-values)") + flags.Float64Var(&cmd.maxPValue, "p-value", 1, "do chi square test and omit columns with p-value above this threshold") + outputDir := flags.String("output-dir", ".", "output `directory`") + outputFormatStr := flags.String("output-format", "hgvs", "output `format`: hgvs, pvcf, or vcf") outputBed := flags.String("output-bed", "", "also output bed `file`") - pick := flags.String("pick", "", "`name` of single genome to export") + flags.BoolVar(&cmd.outputPerChrom, "output-per-chromosome", true, "output one file per chromosome") + flags.BoolVar(&cmd.compress, "z", false, "write gzip-compressed output files") + labelsFilename := flags.String("output-labels", "", "also output genome labels csv `file`") + flags.IntVar(&cmd.maxTileSize, "max-tile-size", 50000, "don't try to make annotations for tiles bigger than given `size`") + cmd.filter.Flags(flags) err = flags.Parse(args) if err == flag.ErrHelp { err = nil @@ -65,12 +98,16 @@ func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, std } else if err != nil { return 2 } + if flag.NArg() > 0 { + err = fmt.Errorf("extra unparsed command line arguments: %q", flag.Args()) + return 2 + } if f, ok := outputFormats[*outputFormatStr]; !ok { err = fmt.Errorf("invalid output format %q", *outputFormatStr) return 2 } else { - cmd.outputFormat = f + cmd.outputFormat = f() } if *pprof != "" { @@ -78,21 +115,25 @@ func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, std log.Println(http.ListenAndServe(*pprof, nil)) }() } + if *pprofdir != "" { + go writeProfilesPeriodically(*pprofdir) + } if !*runlocal { - if *outputFilename != "-" { - err = errors.New("cannot specify output file in container mode: not implemented") + if *outputDir != "." { + err = errors.New("cannot specify output directory in container mode: not implemented") return 1 } runner := arvadosContainerRunner{ Name: "lightning export", Client: arvados.NewClientFromEnv(), ProjectUUID: *projectUUID, - RAM: 128000000000, - VCPUs: 2, + RAM: 750000000000, + VCPUs: 96, Priority: *priority, + APIAccess: true, } - err = runner.TranslatePaths(inputFilename) + err = runner.TranslatePaths(inputDir, cases) if err != nil { return 1 } @@ -103,49 +144,41 @@ func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, std } *outputBed = "/mnt/output/" + *outputBed } - runner.Args = []string{"export", "-local=true", "-pick", *pick, "-ref", *refname, "-output-format", *outputFormatStr, "-output-bed", *outputBed, "-i", *inputFilename, "-o", "/mnt/output/export.csv"} + runner.Args = []string{"export", "-local=true", + "-pprof", ":6000", + "-pprof-dir", "/mnt/output", + "-ref", *refname, + "-cases", *cases, + "-p-value", fmt.Sprintf("%f", cmd.maxPValue), + "-output-format", *outputFormatStr, + "-output-bed", *outputBed, + "-output-labels", "/mnt/output/labels.csv", + "-output-per-chromosome=" + fmt.Sprintf("%v", cmd.outputPerChrom), + "-max-tile-size", fmt.Sprintf("%d", cmd.maxTileSize), + "-input-dir", *inputDir, + "-output-dir", "/mnt/output", + "-z=" + fmt.Sprintf("%v", cmd.compress), + } + runner.Args = append(runner.Args, cmd.filter.Args()...) var output string output, err = runner.Run() if err != nil { return 1 } - fmt.Fprintln(stdout, output+"/export.csv") + fmt.Fprintln(stdout, output) return 0 } - input, err := os.Open(*inputFilename) - if err != nil { - return 1 - } - defer input.Close() - - // Error out early if seeking doesn't work on the input file. - _, err = input.Seek(0, io.SeekEnd) - if err != nil { - return 1 - } - _, err = input.Seek(0, io.SeekStart) - if err != nil { - return 1 - } - - var mtx sync.Mutex var cgs []CompactGenome - var tilelib tileLibrary - err = tilelib.LoadGob(context.Background(), input, func(cg CompactGenome) { - if *pick != "" && *pick != cg.Name { - return - } - log.Debugf("export: pick %q", cg.Name) - mtx.Lock() - defer mtx.Unlock() - cgs = append(cgs, cg) - }) + tilelib := &tileLibrary{ + retainNoCalls: true, + retainTileSequences: true, + compactGenomes: map[string][]tileVariantID{}, + } + err = tilelib.LoadDir(context.Background(), *inputDir) if err != nil { return 1 } - sort.Slice(cgs, func(i, j int) bool { return cgs[i].Name < cgs[j].Name }) - log.Printf("export: pick %q => %d genomes", *pick, len(cgs)) refseq, ok := tilelib.refseqs[*refname] if !ok { @@ -158,43 +191,87 @@ func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, std return 1 } - _, err = input.Seek(0, io.SeekStart) - if err != nil { - return 1 + log.Infof("filtering: %+v", cmd.filter) + cmd.filter.Apply(tilelib) + + names := cgnames(tilelib) + for _, name := range names { + cgs = append(cgs, CompactGenome{Name: name, Variants: tilelib.compactGenomes[name]}) + } + if *labelsFilename != "" { + log.Infof("writing labels to %s", *labelsFilename) + var f *os.File + f, err = os.OpenFile(*labelsFilename, os.O_CREATE|os.O_WRONLY, 0777) + if err != nil { + return 1 + } + defer f.Close() + for i, name := range names { + _, err = fmt.Fprintf(f, "%d,%q,%q\n", i, trimFilenameForLabel(name), cmd.outputFormat.Filename()) + if err != nil { + err = fmt.Errorf("write %s: %w", *labelsFilename, err) + return 1 + } + } + err = f.Close() + if err != nil { + err = fmt.Errorf("close %s: %w", *labelsFilename, err) + return 1 + } } - var output io.WriteCloser - if *outputFilename == "-" { - output = nopCloser{stdout} - } else { - output, err = os.OpenFile(*outputFilename, os.O_CREATE|os.O_WRONLY, 0666) + cmd.cases = make([]bool, len(names)) + if *cases != "" { + log.Infof("reading cases file: %s", *cases) + var f io.ReadCloser + f, err = open(*cases) + if err != nil { + return 1 + } + defer f.Close() + var buf []byte + buf, err = io.ReadAll(f) if err != nil { return 1 } - defer output.Close() + for _, pattern := range bytes.Split(buf, []byte("\n")) { + if len(pattern) == 0 { + continue + } + pattern := string(pattern) + idx := -1 + for i, name := range names { + if !strings.Contains(name, pattern) { + continue + } else if idx >= 0 { + err = fmt.Errorf("pattern %q in cases file matches multiple genome IDs: %q, %q", pattern, names[idx], name) + return 1 + } else { + idx = i + } + } + if idx < 0 { + log.Warnf("pattern %q in cases file does not match any genome IDs", pattern) + continue + } + cmd.cases[idx] = true + } } - bufw := bufio.NewWriter(output) - var bedout *os.File + var bedout io.Writer + var bedfile *os.File var bedbufw *bufio.Writer if *outputBed != "" { - bedout, err = os.OpenFile(*outputBed, os.O_CREATE|os.O_WRONLY, 0666) + bedfile, err = os.OpenFile(*outputBed, os.O_CREATE|os.O_WRONLY, 0666) if err != nil { return 1 } - defer bedout.Close() - bedbufw = bufio.NewWriter(bedout) + defer bedfile.Close() + bedbufw = bufio.NewWriterSize(bedfile, 16*1024*1024) + bedout = bedbufw } - err = cmd.export(bufw, bedout, input, tilelib.taglib.keylen, refseq, cgs) - if err != nil { - return 1 - } - err = bufw.Flush() - if err != nil { - return 1 - } - err = output.Close() + err = cmd.export(*outputDir, bedout, tilelib, refseq, cgs) if err != nil { return 1 } @@ -203,184 +280,384 @@ func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, std if err != nil { return 1 } - err = bedout.Close() + err = bedfile.Close() if err != nil { return 1 } } - err = input.Close() - if err != nil { - return 1 - } return 0 } -func (cmd *exporter) export(out, bedout io.Writer, librdr io.Reader, taglen int, refseq map[string][]tileLibRef, cgs []CompactGenome) error { - need := map[tileLibRef]bool{} +func (cmd *exporter) export(outdir string, bedout io.Writer, tilelib *tileLibrary, refseq map[string][]tileLibRef, cgs []CompactGenome) error { var seqnames []string + var missing []tileLibRef for seqname, librefs := range refseq { seqnames = append(seqnames, seqname) for _, libref := range librefs { - if libref.Variant != 0 { - need[libref] = true + if libref.Variant != 0 && tilelib.TileVariantSequence(libref) == nil { + missing = append(missing, libref) } } } sort.Strings(seqnames) - for _, cg := range cgs { - for i, variant := range cg.Variants { - if variant == 0 { - continue - } - libref := tileLibRef{Tag: tagID(i / 2), Variant: variant} - need[libref] = true + if len(missing) > 0 { + if limit := 100; len(missing) > limit { + log.Warnf("first %d missing tiles: %v", limit, missing[:limit]) + } else { + log.Warnf("missing tiles: %v", missing) } + return fmt.Errorf("%d needed tiles are missing from library", len(missing)) } - log.Infof("export: loading %d tile variants", len(need)) - tileVariant := map[tileLibRef]TileVariant{} - err := DecodeLibrary(librdr, func(ent *LibraryEntry) error { - for _, tv := range ent.TileVariants { - libref := tileLibRef{Tag: tv.Tag, Variant: tv.Variant} - if need[libref] { - tileVariant[libref] = tv + outw := make([]io.WriteCloser, len(seqnames)) + bedw := make([]io.WriteCloser, len(seqnames)) + + var merges sync.WaitGroup + merge := func(dst io.Writer, src []io.WriteCloser, label string) { + var mtx sync.Mutex + for i, seqname := range seqnames { + pr, pw := io.Pipe() + src[i] = pw + merges.Add(1) + seqname := seqname + go func() { + defer merges.Done() + log.Infof("writing %s %s", seqname, label) + scanner := bufio.NewScanner(pr) + for scanner.Scan() { + mtx.Lock() + dst.Write(scanner.Bytes()) + dst.Write([]byte{'\n'}) + mtx.Unlock() + } + log.Infof("writing %s %s done", seqname, label) + }() + } + } + if cmd.outputPerChrom { + for i, seqname := range seqnames { + fnm := filepath.Join(outdir, strings.Replace(cmd.outputFormat.Filename(), ".", "."+seqname+".", 1)) + if cmd.compress { + fnm += ".gz" + } + f, err := os.OpenFile(fnm, os.O_CREATE|os.O_WRONLY|os.O_TRUNC, 0666) + if err != nil { + return err + } + defer f.Close() + log.Infof("writing %q", f.Name()) + outw[i] = f + if cmd.compress { + z := pgzip.NewWriter(f) + defer z.Close() + outw[i] = z + } + err = cmd.outputFormat.Head(outw[i], cgs, cmd.cases, cmd.maxPValue) + if err != nil { + return err } } - return nil - }) - if err != nil { - return err + } else { + fnm := filepath.Join(outdir, cmd.outputFormat.Filename()) + if cmd.compress { + fnm += ".gz" + } + f, err := os.OpenFile(fnm, os.O_CREATE|os.O_WRONLY|os.O_TRUNC, 0666) + if err != nil { + return err + } + defer f.Close() + log.Infof("writing %q", fnm) + var out io.Writer = f + if cmd.compress { + z := pgzip.NewWriter(out) + defer z.Close() + out = z + } + cmd.outputFormat.Head(out, cgs, cmd.cases, cmd.maxPValue) + merge(out, outw, "output") + } + if bedout != nil { + merge(bedout, bedw, "bed") } - log.Infof("export: loaded %d tile variants", len(tileVariant)) - var missing []tileLibRef - for libref := range need { - if _, ok := tileVariant[libref]; !ok { - missing = append(missing, libref) - } + throttle := throttle{Max: runtime.NumCPU()} + if max := cmd.outputFormat.MaxGoroutines(); max > 0 { + throttle.Max = max } - if len(missing) > 0 { - if limit := 100; len(missing) > limit { - log.Warnf("first %d missing tiles: %v", limit, missing[:limit]) - } else { - log.Warnf("missing tiles: %v", missing) - } - return fmt.Errorf("%d needed tiles are missing from library", len(missing)) + log.Infof("assembling %d sequences in %d goroutines", len(seqnames), throttle.Max) + for seqidx, seqname := range seqnames { + seqidx, seqname := seqidx, seqname + outw := outw[seqidx] + bedw := bedw[seqidx] + throttle.Acquire() + go func() { + defer throttle.Release() + if bedw != nil { + defer bedw.Close() + } + outwb := bufio.NewWriterSize(outw, 8*1024*1024) + eachVariant(bedw, tilelib.taglib.keylen, seqname, refseq[seqname], tilelib, cgs, cmd.outputFormat.PadLeft(), cmd.maxTileSize, func(varslice []tvVariant) { + err := cmd.outputFormat.Print(outwb, seqname, varslice) + throttle.Report(err) + }) + err := cmd.outputFormat.Finish(outdir, outwb, seqname) + throttle.Report(err) + err = outwb.Flush() + throttle.Report(err) + err = outw.Close() + throttle.Report(err) + }() } + merges.Wait() + throttle.Wait() + return throttle.Err() +} + +// Align genome tiles to reference tiles, call callback func on each +// variant, and (if bedw is not nil) write tile coverage to bedw. +func eachVariant(bedw io.Writer, taglen int, seqname string, reftiles []tileLibRef, tilelib *tileLibrary, cgs []CompactGenome, padLeft bool, maxTileSize int, callback func(varslice []tvVariant)) { + t0 := time.Now() + progressbar := time.NewTicker(time.Minute) + defer progressbar.Stop() + var outmtx sync.Mutex + defer outmtx.Lock() refpos := 0 - for _, seqname := range seqnames { - variantAt := map[int][]hgvs.Variant{} // variantAt[chromOffset][genomeIndex*2+phase] - for refstep, libref := range refseq[seqname] { - reftile := tileVariant[libref] - coverage := int64(0) // number of ref bases that are called in genomes -- max is len(reftile.Sequence)*len(cgs)*2 - for cgidx, cg := range cgs { - for phase := 0; phase < 2; phase++ { - if len(cg.Variants) <= int(libref.Tag)*2+phase { - continue - } - variant := cg.Variants[int(libref.Tag)*2+phase] - if variant == 0 { + variantAt := map[int][]tvVariant{} // variantAt[chromOffset][genomeIndex*2+phase] + for refstep, libref := range reftiles { + select { + case <-progressbar.C: + var eta interface{} + if refstep > 0 { + fin := t0.Add(time.Duration(float64(time.Now().Sub(t0)) * float64(len(reftiles)) / float64(refstep))) + eta = fmt.Sprintf("%v (%v)", fin.Format(time.RFC3339), fin.Sub(time.Now())) + } else { + eta = "N/A" + } + log.Printf("exportSeq: %s: refstep %d of %d, %.0f/s, ETA %v", seqname, refstep, len(reftiles), float64(refstep)/time.Now().Sub(t0).Seconds(), eta) + default: + } + diffs := map[tileLibRef][]hgvs.Variant{} + refseq := tilelib.TileVariantSequence(libref) + tagcoverage := 0 // number of times the start tag was found in genomes -- max is len(cgs)*2 + for cgidx, cg := range cgs { + for phase := 0; phase < 2; phase++ { + var variant tileVariantID + if i := int(libref.Tag)*2 + phase; len(cg.Variants) > i { + variant = cg.Variants[i] + } + if variant > 0 { + tagcoverage++ + } + if variant == libref.Variant || variant == 0 { + continue + } + glibref := tileLibRef{Tag: libref.Tag, Variant: variant} + vars, ok := diffs[glibref] + if !ok { + genomeseq := tilelib.TileVariantSequence(glibref) + if len(genomeseq) == 0 { + // Hash is known but sequence + // is not, e.g., retainNoCalls + // was false during import continue } - genometile := tileVariant[tileLibRef{Tag: libref.Tag, Variant: variant}] - if variant == libref.Variant { + if len(genomeseq) > maxTileSize { continue } - refSequence := reftile.Sequence + refSequence := refseq // If needed, extend the // reference sequence up to // the tag at the end of the - // genometile sequence. + // genomeseq sequence. refstepend := refstep + 1 - for refstepend < len(refseq[seqname]) && len(refSequence) >= taglen && !bytes.EqualFold(refSequence[len(refSequence)-taglen:], genometile.Sequence[len(genometile.Sequence)-taglen:]) { - if &refSequence[0] == &reftile.Sequence[0] { + for refstepend < len(reftiles) && len(refSequence) >= taglen && !bytes.EqualFold(refSequence[len(refSequence)-taglen:], genomeseq[len(genomeseq)-taglen:]) && len(refSequence) <= maxTileSize { + if &refSequence[0] == &refseq[0] { refSequence = append([]byte(nil), refSequence...) } - refSequence = append(refSequence, tileVariant[refseq[seqname][refstepend]].Sequence...) + refSequence = append(refSequence, tilelib.TileVariantSequence(reftiles[refstepend])...) refstepend++ } // (TODO: handle no-calls) - vars, _ := hgvs.Diff(strings.ToUpper(string(refSequence)), strings.ToUpper(string(genometile.Sequence)), time.Second) - for _, v := range vars { - if cmd.outputFormat.PadLeft { - v = v.PadLeft() - } - v.Position += refpos - log.Debugf("%s seq %s phase %d tag %d tile diff %s\n", cg.Name, seqname, phase, libref.Tag, v.String()) - varslice := variantAt[v.Position] - if varslice == nil { - varslice = make([]hgvs.Variant, len(cgs)*2) - variantAt[v.Position] = varslice - } - varslice[cgidx*2+phase] = v + if len(refSequence) <= maxTileSize { + refstr := strings.ToUpper(string(refSequence)) + genomestr := strings.ToUpper(string(genomeseq)) + vars, _ = hgvs.Diff(refstr, genomestr, time.Second) } - coverage += int64(len(reftile.Sequence)) - } - } - refpos += len(reftile.Sequence) - taglen - - // Flush entries from variantAt that are - // behind refpos. Flush all entries if this is - // the last reftile of the path/chromosome. - var flushpos []int - lastrefstep := refstep == len(refseq[seqname])-1 - for pos := range variantAt { - if lastrefstep || pos <= refpos { - flushpos = append(flushpos, pos) + diffs[glibref] = vars } - } - sort.Slice(flushpos, func(i, j int) bool { return flushpos[i] < flushpos[j] }) - for _, pos := range flushpos { - varslice := variantAt[pos] - delete(variantAt, pos) - for i := range varslice { - if varslice[i].Position == 0 { - varslice[i].Position = pos + for _, v := range vars { + if padLeft { + v = v.PadLeft() + } + v.Position += refpos + varslice := variantAt[v.Position] + if varslice == nil { + varslice = make([]tvVariant, len(cgs)*2) + variantAt[v.Position] = varslice + } + varslice[cgidx*2+phase].Variant = v + if varslice[cgidx*2+phase].librefs == nil { + varslice[cgidx*2+phase].librefs = map[tileLibRef]bool{glibref: true} + } else { + varslice[cgidx*2+phase].librefs[glibref] = true } } - cmd.outputFormat.Print(out, seqname, varslice) } - if bedout != nil && len(reftile.Sequence) > 0 { - tilestart := refpos - len(reftile.Sequence) + taglen - tileend := refpos - if !lastrefstep { - tileend += taglen + } + refpos += len(refseq) - taglen + + // Flush entries from variantAt that are behind + // refpos. Flush all entries if this is the last + // reftile of the path/chromosome. + flushpos := make([]int, 0, len(variantAt)) + lastrefstep := refstep == len(reftiles)-1 + for pos := range variantAt { + if lastrefstep || pos <= refpos { + flushpos = append(flushpos, pos) + } + } + sort.Slice(flushpos, func(i, j int) bool { return flushpos[i] < flushpos[j] }) + flushvariants := make([][]tvVariant, len(flushpos)) + for i, pos := range flushpos { + varslice := variantAt[pos] + delete(variantAt, pos) + // Check for uninitialized (zero-value) + // elements in varslice + for i := range varslice { + if varslice[i].Position != 0 { + // Not a zero-value element + continue + } + // Set the position so + // varslice[*].Position are all equal + varslice[i].Position = pos + // This could be either =ref or a + // missing/low-quality tile. Figure + // out which. + vidx := int(libref.Tag)*2 + i%2 + if vidx >= len(cgs[i/2].Variants) { + // Missing tile. + varslice[i].New = "-" + continue } - thickstart := tilestart + taglen - if refstep == 0 { - thickstart = 0 + v := cgs[i/2].Variants[vidx] + if v < 1 || len(tilelib.TileVariantSequence(tileLibRef{Tag: libref.Tag, Variant: v})) == 0 { + // Missing/low-quality tile. + varslice[i].New = "-" // fasta "gap of indeterminate length" } - thickend := refpos - // coverage score, 0 to 1000 - score := 1000 * coverage / int64(len(reftile.Sequence)) / int64(len(cgs)) / 2 - fmt.Fprintf(bedout, "%s %d %d %d %d . %d %d\n", - seqname, tilestart, tileend, - libref.Tag, - score, - thickstart, thickend) } + flushvariants[i] = varslice + } + outmtx.Lock() + go func() { + defer outmtx.Unlock() + for _, varslice := range flushvariants { + callback(varslice) + } + }() + if bedw != nil && len(refseq) > 0 { + tilestart := refpos - len(refseq) + taglen + tileend := refpos + if !lastrefstep { + tileend += taglen + } + thickstart := tilestart + taglen + if refstep == 0 { + thickstart = 0 + } + thickend := refpos + + // coverage score, 0 to 1000 + score := 1000 + if len(cgs) > 0 { + score = 1000 * tagcoverage / len(cgs) / 2 + } + + fmt.Fprintf(bedw, "%s %d %d %d %d . %d %d\n", + seqname, tilestart, tileend, + libref.Tag, + score, + thickstart, thickend) } } - return nil } -func printVCF(out io.Writer, seqname string, varslice []hgvs.Variant) { - refs := map[string]map[string]int{} +func bucketVarsliceByRef(varslice []tvVariant) map[string]map[string]int { + byref := map[string]map[string]int{} for _, v := range varslice { if v.Ref == "" && v.New == "" { + // =ref continue } - alts := refs[v.Ref] + if v.New == "-" { + // no-call + continue + } + alts := byref[v.Ref] if alts == nil { alts = map[string]int{} - refs[v.Ref] = alts + byref[v.Ref] = alts + } + alts[v.New]++ + } + return byref +} + +type formatVCF struct{} + +func (formatVCF) MaxGoroutines() int { return 0 } +func (formatVCF) Filename() string { return "out.vcf" } +func (formatVCF) PadLeft() bool { return true } +func (formatVCF) Finish(string, io.Writer, string) error { return nil } +func (formatVCF) Head(out io.Writer, cgs []CompactGenome, cases []bool, p float64) error { + _, err := fmt.Fprint(out, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n") + return err +} +func (formatVCF) Print(out io.Writer, seqname string, varslice []tvVariant) error { + for ref, alts := range bucketVarsliceByRef(varslice) { + altslice := make([]string, 0, len(alts)) + for alt := range alts { + altslice = append(altslice, alt) + } + sort.Strings(altslice) + + info := "AC=" + for i, a := range altslice { + if i > 0 { + info += "," + } + info += strconv.Itoa(alts[a]) } - alts[v.New] = 0 + _, err := 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) + if err != nil { + return err + } + } + return nil +} + +type formatPVCF struct{} + +func (formatPVCF) MaxGoroutines() int { return 0 } +func (formatPVCF) Filename() string { return "out.vcf" } +func (formatPVCF) PadLeft() bool { return true } +func (formatPVCF) Finish(string, io.Writer, string) error { return nil } +func (formatPVCF) Head(out io.Writer, cgs []CompactGenome, cases []bool, p float64) error { + fmt.Fprintln(out, `##FORMAT=`) + fmt.Fprintf(out, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT") + for _, cg := range cgs { + fmt.Fprintf(out, "\t%s", cg.Name) } - for ref, alts := range refs { - var altslice []string + _, err := fmt.Fprintf(out, "\n") + return err +} + +func (formatPVCF) Print(out io.Writer, seqname string, varslice []tvVariant) error { + for ref, alts := range bucketVarsliceByRef(varslice) { + altslice := make([]string, 0, len(alts)) for alt := range alts { altslice = append(altslice, alt) } @@ -388,37 +665,247 @@ func printVCF(out io.Writer, seqname string, varslice []hgvs.Variant) { for i, a := range altslice { alts[a] = i + 1 } - fmt.Fprintf(out, "%s\t%d\t%s\t%s", seqname, varslice[0].Position, ref, strings.Join(altslice, ",")) - for i := 0; i < len(varslice)/2; i++ { - v1, v2 := varslice[i*2], varslice[i*2+1] + _, err := fmt.Fprintf(out, "%s\t%d\t.\t%s\t%s\t.\t.\t.\tGT", seqname, varslice[0].Position, ref, strings.Join(altslice, ",")) + if err != nil { + return err + } + for i := 0; i < len(varslice); i += 2 { + v1, v2 := varslice[i], varslice[i+1] a1, a2 := alts[v1.New], alts[v2.New] if v1.Ref != ref { + // variant on allele 0 belongs on a + // different output line -- same + // chr,pos but different "ref" length a1 = 0 } if v2.Ref != ref { a2 = 0 } - fmt.Fprintf(out, "\t%d/%d", a1, a2) + _, err := fmt.Fprintf(out, "\t%d/%d", a1, a2) + if err != nil { + return err + } + } + _, err = out.Write([]byte{'\n'}) + if err != nil { + return err } - out.Write([]byte{'\n'}) } + return nil } -func printHGVS(out io.Writer, seqname string, varslice []hgvs.Variant) { +type formatHGVS struct{} + +func (formatHGVS) MaxGoroutines() int { return 0 } +func (formatHGVS) Filename() string { return "out.tsv" } +func (formatHGVS) PadLeft() bool { return false } +func (formatHGVS) Head(out io.Writer, cgs []CompactGenome, cases []bool, p float64) error { return nil } +func (formatHGVS) Finish(string, io.Writer, string) error { return nil } +func (formatHGVS) Print(out io.Writer, seqname string, varslice []tvVariant) error { for i := 0; i < len(varslice)/2; i++ { if i > 0 { out.Write([]byte{'\t'}) } var1, var2 := varslice[i*2], varslice[i*2+1] - if var1 == var2 { + if var1.New == "-" || var2.New == "-" { + _, err := out.Write([]byte{'N'}) + if err != nil { + return err + } + continue + } + if var1.Variant == var2.Variant { if var1.Ref == var1.New { - out.Write([]byte{'.'}) + _, err := out.Write([]byte{'.'}) + if err != nil { + return err + } } else { - fmt.Fprintf(out, "%s:g.%s", seqname, var1.String()) + _, err := fmt.Fprintf(out, "%s:g.%s", seqname, var1.String()) + if err != nil { + return err + } } } else { - fmt.Fprintf(out, "%s:g.[%s];[%s]", seqname, var1.String(), var2.String()) + _, err := fmt.Fprintf(out, "%s:g.[%s];[%s]", seqname, var1.String(), var2.String()) + if err != nil { + return err + } } } - out.Write([]byte{'\n'}) + _, err := out.Write([]byte{'\n'}) + return err +} + +type formatHGVSOneHot struct{} + +func (formatHGVSOneHot) MaxGoroutines() int { return 0 } +func (formatHGVSOneHot) Filename() string { return "out.tsv" } +func (formatHGVSOneHot) PadLeft() bool { return false } +func (formatHGVSOneHot) Head(out io.Writer, cgs []CompactGenome, cases []bool, p float64) error { + return nil +} +func (formatHGVSOneHot) Finish(string, io.Writer, string) error { return nil } +func (formatHGVSOneHot) Print(out io.Writer, seqname string, varslice []tvVariant) error { + vars := map[hgvs.Variant]bool{} + for _, v := range varslice { + if v.Ref != v.New { + vars[v.Variant] = true + } + } + + // sort variants to ensure output is deterministic + sorted := make([]hgvs.Variant, 0, len(vars)) + for v := range vars { + sorted = append(sorted, v) + } + sort.Slice(sorted, func(a, b int) bool { return hgvs.Less(sorted[a], sorted[b]) }) + + for _, v := range sorted { + if v.New == "-" { + continue + } + fmt.Fprintf(out, "%s.%s", seqname, v.String()) + for i := 0; i < len(varslice); i += 2 { + if varslice[i].Variant == v || varslice[i+1].Variant == v { + out.Write([]byte("\t1")) + } else { + out.Write([]byte("\t0")) + } + } + _, err := out.Write([]byte{'\n'}) + if err != nil { + return err + } + } + return nil +} + +type formatHGVSNumpy struct { + sync.Mutex + writelock sync.Mutex + alleles map[string][][]int8 // alleles[seqname][variantidx][genomeidx*2+phase] + cases []bool + maxPValue float64 +} + +func (*formatHGVSNumpy) MaxGoroutines() int { return 4 } +func (*formatHGVSNumpy) Filename() string { return "annotations.csv" } +func (*formatHGVSNumpy) PadLeft() bool { return false } +func (f *formatHGVSNumpy) Head(out io.Writer, cgs []CompactGenome, cases []bool, p float64) error { + f.cases = cases + f.maxPValue = p + return nil +} +func (f *formatHGVSNumpy) Print(outw io.Writer, seqname string, varslice []tvVariant) error { + // sort variants to ensure output is deterministic + sorted := make([]hgvs.Variant, 0, len(varslice)) + for _, v := range varslice { + sorted = append(sorted, v.Variant) + } + sort.Slice(sorted, func(a, b int) bool { return hgvs.Less(sorted[a], sorted[b]) }) + + f.Lock() + seqalleles := f.alleles[seqname] + f.Unlock() + + chi2x := make([]bool, 0, len(varslice)) + chi2y := make([]bool, 0, len(varslice)) + + // append a row to seqalleles for each unique non-ref variant + // in varslice. + var previous hgvs.Variant + for _, v := range sorted { + if previous == v || v.Ref == v.New || v.New == "-" { + continue + } + previous = v + chi2x, chi2y := chi2x, chi2y + newrow := make([]int8, len(varslice)) + for i, allele := range varslice { + if allele.Variant == v { + newrow[i] = 1 + chi2x = append(chi2x, true) + chi2y = append(chi2y, f.cases[i/2]) + } else if allele.Variant.New == "-" { + newrow[i] = -1 + } else { + chi2x = append(chi2x, false) + chi2y = append(chi2y, f.cases[i/2]) + } + } + if f.maxPValue < 1 && pvalue(chi2x, chi2y) > f.maxPValue { + continue + } + seqalleles = append(seqalleles, newrow) + _, err := fmt.Fprintf(outw, "%d,%q\n", len(seqalleles)-1, seqname+"."+v.String()) + if err != nil { + return err + } + } + + f.Lock() + f.alleles[seqname] = seqalleles + f.Unlock() + return nil +} +func (f *formatHGVSNumpy) Finish(outdir string, _ io.Writer, seqname string) error { + // Write seqname's data to a .npy matrix with one row per + // genome and 2 columns per variant. + f.Lock() + seqalleles := f.alleles[seqname] + delete(f.alleles, seqname) + f.Unlock() + if len(seqalleles) == 0 { + return nil + } + out := make([]int8, len(seqalleles)*len(seqalleles[0])) + rows := len(seqalleles[0]) / 2 + cols := len(seqalleles) * 2 + // copy seqalleles[varidx][genome*2+phase] to + // out[genome*nvars*2 + varidx*2 + phase] + for varidx, alleles := range seqalleles { + for g := 0; g < len(alleles)/2; g++ { + aa, ab := alleles[g*2], alleles[g*2+1] + if aa < 0 || ab < 0 { + // no-call + out[g*cols+varidx*2] = -1 + out[g*cols+varidx*2+1] = -1 + } else if aa > 0 && ab > 0 { + // hom + out[g*cols+varidx*2] = 1 + } else if aa > 0 || ab > 0 { + // het + out[g*cols+varidx*2+1] = 1 + } + } + } + outf, err := os.OpenFile(outdir+"/matrix."+seqname+".npy", os.O_CREATE|os.O_EXCL|os.O_WRONLY, 0777) + if err != nil { + return err + } + defer outf.Close() + bufw := bufio.NewWriter(outf) + npw, err := gonpy.NewWriter(nopCloser{bufw}) + if err != nil { + return err + } + log.WithFields(logrus.Fields{ + "seqname": seqname, + "rows": rows, + "cols": cols, + }).Info("writing numpy") + npw.Shape = []int{rows, cols} + f.writelock.Lock() // serialize because WriteInt8 uses lots of memory + npw.WriteInt8(out) + f.writelock.Unlock() + err = bufw.Flush() + if err != nil { + return err + } + err = outf.Close() + if err != nil { + return err + } + return nil }