inputFilename := flags.String("i", "-", "input `file` (library)")
outputFilename := flags.String("o", "-", "output `file`")
outputFormatStr := flags.String("output-format", "hgvs", "output `format`: hgvs or vcf")
+ outputBed := flags.String("output-bed", "", "also output bed `file`")
pick := flags.String("pick", "", "`name` of single genome to export")
err = flags.Parse(args)
if err == flag.ErrHelp {
Name: "lightning export",
Client: arvados.NewClientFromEnv(),
ProjectUUID: *projectUUID,
- RAM: 128000000000,
- VCPUs: 2,
+ RAM: 240000000000,
+ VCPUs: 32,
Priority: *priority,
}
err = runner.TranslatePaths(inputFilename)
if err != nil {
return 1
}
- runner.Args = []string{"export", "-local=true", "-pick", *pick, "-ref", *refname, "-output-format", *outputFormatStr, "-i", *inputFilename, "-o", "/mnt/output/export.csv"}
+ 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", "-pick", *pick, "-ref", *refname, "-output-format", *outputFormatStr, "-output-bed", *outputBed, "-i", *inputFilename, "-o", "/mnt/output/export.csv"}
var output string
output, err = runner.Run()
if err != nil {
var mtx sync.Mutex
var cgs []CompactGenome
- var tilelib tileLibrary
- err = tilelib.LoadGob(context.Background(), input, func(cg CompactGenome) {
+ tilelib := tileLibrary{
+ retainNoCalls: true,
+ }
+ err = tilelib.LoadGob(context.Background(), input, strings.HasSuffix(*inputFilename, ".gz"), func(cg CompactGenome) {
if *pick != "" && *pick != cg.Name {
return
}
if *outputFilename == "-" {
output = nopCloser{stdout}
} else {
- output, err = os.OpenFile(*outputFilename, os.O_CREATE|os.O_WRONLY, 0777)
+ output, err = os.OpenFile(*outputFilename, os.O_CREATE|os.O_WRONLY, 0666)
if err != nil {
return 1
}
defer output.Close()
}
bufw := bufio.NewWriter(output)
- err = cmd.export(bufw, input, tilelib.taglib.keylen, refseq, cgs)
+
+ var bedout *os.File
+ var bedbufw *bufio.Writer
+ if *outputBed != "" {
+ bedout, err = os.OpenFile(*outputBed, os.O_CREATE|os.O_WRONLY, 0666)
+ if err != nil {
+ return 1
+ }
+ defer bedout.Close()
+ bedbufw = bufio.NewWriter(bedout)
+ }
+
+ err = cmd.export(bufw, bedout, input, strings.HasSuffix(*inputFilename, ".gz"), tilelib.taglib.keylen, refseq, cgs)
if err != nil {
return 1
}
if err != nil {
return 1
}
+ if bedout != nil {
+ err = bedbufw.Flush()
+ if err != nil {
+ return 1
+ }
+ err = bedout.Close()
+ if err != nil {
+ return 1
+ }
+ }
err = input.Close()
if err != nil {
return 1
return 0
}
-func (cmd *exporter) export(out io.Writer, librdr io.Reader, taglen int, refseq map[string][]tileLibRef, cgs []CompactGenome) error {
+func (cmd *exporter) export(out, bedout io.Writer, librdr io.Reader, gz bool, taglen int, refseq map[string][]tileLibRef, cgs []CompactGenome) error {
need := map[tileLibRef]bool{}
var seqnames []string
for seqname, librefs := range refseq {
log.Infof("export: loading %d tile variants", len(need))
tileVariant := map[tileLibRef]TileVariant{}
- err := DecodeLibrary(librdr, func(ent *LibraryEntry) error {
+ err := DecodeLibrary(librdr, gz, func(ent *LibraryEntry) error {
for _, tv := range ent.TileVariants {
libref := tileLibRef{Tag: tv.Tag, Variant: tv.Variant}
if need[libref] {
return fmt.Errorf("%d needed tiles are missing from library", len(missing))
}
+ log.Infof("assembling %d sequences concurrently", len(seqnames))
+ var wg sync.WaitGroup
+ outbuf := make([]bytes.Buffer, len(seqnames))
+ bedbuf := make([]bytes.Buffer, len(seqnames))
+ for seqidx, seqname := range seqnames {
+ seqname := seqname
+ outbuf := &outbuf[seqidx]
+ bedbuf := &bedbuf[seqidx]
+ if bedout == nil {
+ bedbuf = nil
+ }
+ // TODO: limit number of goroutines and unflushed bufs to ncpus
+ wg.Add(1)
+ go func() {
+ defer wg.Done()
+ cmd.exportSeq(outbuf, bedbuf, taglen, seqname, refseq[seqname], tileVariant, cgs)
+ log.Infof("assembled %q to outbuf %d bedbuf %d", seqname, outbuf.Len(), bedbuf.Len())
+ }()
+ }
+ wg.Wait()
+
+ wg.Add(1)
+ go func() {
+ defer wg.Done()
+ for i, seqname := range seqnames {
+ log.Infof("writing outbuf %s", seqname)
+ io.Copy(out, &outbuf[i])
+ }
+ }()
+ if bedout != nil {
+ wg.Add(1)
+ go func() {
+ defer wg.Done()
+ for i, seqname := range seqnames {
+ log.Infof("writing bedbuf %s", seqname)
+ io.Copy(bedout, &bedbuf[i])
+ }
+ }()
+ }
+ wg.Wait()
+ return nil
+}
+
+// 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, tileVariant map[tileLibRef]TileVariant, cgs []CompactGenome) {
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]
- 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
- }
- genometile := tileVariant[tileLibRef{Tag: libref.Tag, Variant: variant}]
- if variant == libref.Variant {
- continue
+ variantAt := map[int][]hgvs.Variant{} // variantAt[chromOffset][genomeIndex*2+phase]
+ for refstep, libref := range reftiles {
+ reftile := tileVariant[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
+ }
+ genometile := tileVariant[tileLibRef{Tag: libref.Tag, Variant: variant}]
+ if len(genometile.Sequence) == 0 {
+ // Hash is known but sequence
+ // is not, e.g., retainNoCalls
+ // was false during import
+ continue
+ }
+ refSequence := reftile.Sequence
+ // If needed, extend the reference
+ // sequence up to the tag at the end
+ // of the genometile sequence.
+ refstepend := refstep + 1
+ for refstepend < len(reftiles) && len(refSequence) >= taglen && !bytes.EqualFold(refSequence[len(refSequence)-taglen:], genometile.Sequence[len(genometile.Sequence)-taglen:]) {
+ if &refSequence[0] == &reftile.Sequence[0] {
+ refSequence = append([]byte(nil), refSequence...)
}
- refSequence := reftile.Sequence
- // If needed, extend the
- // reference sequence up to
- // the tag at the end of the
- // genometile 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] {
- refSequence = append([]byte(nil), refSequence...)
- }
- refSequence = append(refSequence, tileVariant[refseq[seqname][refstepend]].Sequence...)
- refstepend++
+ refSequence = append(refSequence, tileVariant[reftiles[refstepend]].Sequence...)
+ 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()
}
- 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
+ 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
}
}
- refpos += len(reftile.Sequence) - taglen
+ }
+ 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)
- }
+ // 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(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] })
- for _, pos := range flushpos {
- varslice := variantAt[pos]
- delete(variantAt, pos)
- for i := range varslice {
- if varslice[i].Position == 0 {
- varslice[i].Position = pos
- }
+ }
+ 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
}
- cmd.outputFormat.Print(out, seqname, varslice)
}
+ cmd.outputFormat.Print(outw, seqname, varslice)
+ }
+ if bedw != nil && len(reftile.Sequence) > 0 {
+ tilestart := refpos - len(reftile.Sequence) + taglen
+ tileend := refpos
+ if !lastrefstep {
+ tileend += taglen
+ }
+ thickstart := tilestart + taglen
+ if refstep == 0 {
+ thickstart = 0
+ }
+ thickend := refpos
+ // coverage score, 0 to 1000
+ 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) {
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]
+ 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 {
a1 = 0
projects / lightning.git / blobdiff