X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/fab96d7f0f6c1564b6ed376c0e253c59f343dc09..HEAD:/export.go

diff --git a/export.go b/export.go
deleted file mode 100644
index 5e0ecf43e1..0000000000
--- a/export.go
+++ /dev/null
@@ -1,626 +0,0 @@
-package lightning
-
-import (
-	"bufio"
-	"bytes"
-	"context"
-	"errors"
-	"flag"
-	"fmt"
-	"io"
-	"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"
-	log "github.com/sirupsen/logrus"
-)
-
-type tvVariant struct {
-	hgvs.Variant
-	librefs map[tileLibRef]bool
-}
-
-type outputFormat struct {
-	Filename string
-	Head     func(out io.Writer, cgs []CompactGenome)
-	Print    func(out io.Writer, seqname string, varslice []tvVariant)
-	PadLeft  bool
-}
-
-var (
-	outputFormats = map[string]outputFormat{
-		"hgvs-onehot": outputFormatHGVSOneHot,
-		"hgvs":        outputFormatHGVS,
-		"pvcf":        outputFormatPVCF,
-		"vcf":         outputFormatVCF,
-	}
-	outputFormatHGVS       = outputFormat{Filename: "out.tsv", Head: headNone, Print: printHGVS}
-	outputFormatHGVSOneHot = outputFormat{Filename: "out.tsv", Head: headNone, Print: printHGVSOneHot}
-	outputFormatPVCF       = outputFormat{Filename: "out.vcf", Head: headPVCF, Print: printPVCF, PadLeft: true}
-	outputFormatVCF        = outputFormat{Filename: "out.vcf", Head: headVCF, Print: printVCF, PadLeft: true}
-	headNone               = func(io.Writer, []CompactGenome) {}
-)
-
-type exporter struct {
-	outputFormat   outputFormat
-	outputPerChrom bool
-	compress       bool
-	maxTileSize    int
-}
-
-func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
-	var err error
-	defer func() {
-		if err != nil {
-			fmt.Fprintf(stderr, "%s\n", err)
-		}
-	}()
-	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`")
-	inputDir := flags.String("input-dir", ".", "input `directory`")
-	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`")
-	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`")
-	err = flags.Parse(args)
-	if err == flag.ErrHelp {
-		err = nil
-		return 0
-	} 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
-	}
-
-	if *pprof != "" {
-		go func() {
-			log.Println(http.ListenAndServe(*pprof, nil))
-		}()
-	}
-	if *pprofdir != "" {
-		go writeProfilesPeriodically(*pprofdir)
-	}
-
-	if !*runlocal {
-		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:         700000000000,
-			VCPUs:       96,
-			Priority:    *priority,
-			APIAccess:   true,
-		}
-		err = runner.TranslatePaths(inputDir)
-		if err != nil {
-			return 1
-		}
-		if *outputBed != "" {
-			if strings.Contains(*outputBed, "/") {
-				err = fmt.Errorf("cannot use -output-bed filename %q containing '/' char", *outputBed)
-				return 1
-			}
-			*outputBed = "/mnt/output/" + *outputBed
-		}
-		runner.Args = []string{"export", "-local=true",
-			"-pprof", ":6000",
-			"-pprof-dir", "/mnt/output",
-			"-ref", *refname,
-			"-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),
-		}
-		var output string
-		output, err = runner.Run()
-		if err != nil {
-			return 1
-		}
-		fmt.Fprintln(stdout, output)
-		return 0
-	}
-
-	var cgs []CompactGenome
-	tilelib := &tileLibrary{
-		retainNoCalls:       true,
-		retainTileSequences: true,
-		compactGenomes:      map[string][]tileVariantID{},
-	}
-	err = tilelib.LoadDir(context.Background(), *inputDir, nil)
-	if err != nil {
-		return 1
-	}
-
-	refseq, ok := tilelib.refseqs[*refname]
-	if !ok {
-		err = fmt.Errorf("reference name %q not found in input; have %v", *refname, func() (names []string) {
-			for name := range tilelib.refseqs {
-				names = append(names, name)
-			}
-			return
-		}())
-		return 1
-	}
-
-	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 bedout io.Writer
-	var bedfile *os.File
-	var bedbufw *bufio.Writer
-	if *outputBed != "" {
-		bedfile, err = os.OpenFile(*outputBed, os.O_CREATE|os.O_WRONLY, 0666)
-		if err != nil {
-			return 1
-		}
-		defer bedfile.Close()
-		bedbufw = bufio.NewWriterSize(bedfile, 16*1024*1024)
-		bedout = bedbufw
-	}
-
-	err = cmd.export(*outputDir, bedout, tilelib, refseq, cgs)
-	if err != nil {
-		return 1
-	}
-	if bedout != nil {
-		err = bedbufw.Flush()
-		if err != nil {
-			return 1
-		}
-		err = bedfile.Close()
-		if err != nil {
-			return 1
-		}
-	}
-	return 0
-}
-
-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 && tilelib.TileVariantSequence(libref) == nil {
-				missing = append(missing, libref)
-			}
-		}
-	}
-	sort.Strings(seqnames)
-
-	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))
-	}
-
-	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
-			}
-			cmd.outputFormat.Head(outw[i], cgs)
-		}
-	} 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)
-		merge(out, outw, "output")
-	}
-	if bedout != nil {
-		merge(bedout, bedw, "bed")
-	}
-
-	throttle := throttle{Max: runtime.NumCPU()}
-	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)
-			cmd.exportSeq(outwb, bedw, tilelib.taglib.keylen, seqname, refseq[seqname], tilelib, cgs)
-			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, write diffs to outw, and (if
-// bedw is not nil) write tile coverage to bedw.
-func (cmd *exporter) exportSeq(outw, bedw io.Writer, taglen int, seqname string, reftiles []tileLibRef, tilelib *tileLibrary, cgs []CompactGenome) {
-	t0 := time.Now()
-	progressbar := time.NewTicker(time.Minute)
-	defer progressbar.Stop()
-	var outmtx sync.Mutex
-	defer outmtx.Lock()
-	refpos := 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++ {
-				if len(cg.Variants) <= int(libref.Tag)*2+phase {
-					continue
-				}
-				variant := cg.Variants[int(libref.Tag)*2+phase]
-				if variant == 0 {
-					continue
-				}
-				tagcoverage++
-				if variant == libref.Variant {
-					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
-					}
-					if len(genomeseq) > cmd.maxTileSize {
-						continue
-					}
-					refSequence := refseq
-					// If needed, extend the
-					// reference sequence up to
-					// the tag at the end of the
-					// genomeseq sequence.
-					refstepend := refstep + 1
-					for refstepend < len(reftiles) && len(refSequence) >= taglen && !bytes.EqualFold(refSequence[len(refSequence)-taglen:], genomeseq[len(genomeseq)-taglen:]) && len(refSequence) <= cmd.maxTileSize {
-						if &refSequence[0] == &refseq[0] {
-							refSequence = append([]byte(nil), refSequence...)
-						}
-						refSequence = append(refSequence, tilelib.TileVariantSequence(reftiles[refstepend])...)
-						refstepend++
-					}
-					// (TODO: handle no-calls)
-					if len(refSequence) <= cmd.maxTileSize {
-						refstr := strings.ToUpper(string(refSequence))
-						genomestr := strings.ToUpper(string(genomeseq))
-						vars, _ = hgvs.Diff(refstr, genomestr, time.Second)
-					}
-					diffs[glibref] = vars
-				}
-				for _, v := range vars {
-					if cmd.outputFormat.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
-					}
-				}
-			}
-		}
-		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)
-			for i := range varslice {
-				if varslice[i].Position == 0 {
-					varslice[i].Position = pos
-				}
-			}
-			flushvariants[i] = varslice
-		}
-		outmtx.Lock()
-		go func() {
-			defer outmtx.Unlock()
-			for _, varslice := range flushvariants {
-				cmd.outputFormat.Print(outw, seqname, 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)
-		}
-	}
-}
-
-func bucketVarsliceByRef(varslice []tvVariant) map[string]map[string]int {
-	byref := map[string]map[string]int{}
-	for _, v := range varslice {
-		if v.Ref == "" && v.New == "" {
-			continue
-		}
-		alts := byref[v.Ref]
-		if alts == nil {
-			alts = map[string]int{}
-			byref[v.Ref] = alts
-		}
-		alts[v.New]++
-	}
-	return byref
-}
-
-func headVCF(out io.Writer, cgs []CompactGenome) {
-	fmt.Fprint(out, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n")
-}
-
-func printVCF(out io.Writer, seqname string, varslice []tvVariant) {
-	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])
-		}
-		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)
-	}
-}
-
-func headPVCF(out io.Writer, cgs []CompactGenome) {
-	fmt.Fprintln(out, `##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">`)
-	fmt.Fprintf(out, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT")
-	for _, cg := range cgs {
-		fmt.Fprintf(out, "\t%s", cg.Name)
-	}
-	fmt.Fprintf(out, "\n")
-}
-
-func printPVCF(out io.Writer, seqname string, varslice []tvVariant) {
-	for ref, alts := range bucketVarsliceByRef(varslice) {
-		altslice := make([]string, 0, len(alts))
-		for alt := range alts {
-			altslice = append(altslice, alt)
-		}
-		sort.Strings(altslice)
-		for i, a := range altslice {
-			alts[a] = i + 1
-		}
-		fmt.Fprintf(out, "%s\t%d\t.\t%s\t%s\t.\t.\t.\tGT", seqname, varslice[0].Position, ref, strings.Join(altslice, ","))
-		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)
-		}
-		out.Write([]byte{'\n'})
-	}
-}
-
-func printHGVS(out io.Writer, seqname string, varslice []tvVariant) {
-	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.Variant == var2.Variant {
-			if var1.Ref == var1.New {
-				out.Write([]byte{'.'})
-			} else {
-				fmt.Fprintf(out, "%s:g.%s", seqname, var1.String())
-			}
-		} else {
-			fmt.Fprintf(out, "%s:g.[%s];[%s]", seqname, var1.String(), var2.String())
-		}
-	}
-	out.Write([]byte{'\n'})
-}
-
-func printHGVSOneHot(out io.Writer, seqname string, varslice []tvVariant) {
-	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 {
-		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"))
-			}
-		}
-		out.Write([]byte{'\n'})
-	}
-}