Name: "lightning export",
Client: arvados.NewClientFromEnv(),
ProjectUUID: *projectUUID,
- RAM: 128000000000,
- VCPUs: 2,
+ RAM: 240000000000,
+ VCPUs: 32,
Priority: *priority,
}
err = runner.TranslatePaths(inputFilename)
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]
- 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 {
- 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]
+ 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 {
+ continue
+ }
+ genometile := tileVariant[tileLibRef{Tag: libref.Tag, Variant: variant}]
+ if variant == libref.Variant {
+ 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()
}
- // (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
+ 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
}
- coverage += int64(len(reftile.Sequence))
+ varslice[cgidx*2+phase] = v
}
+ coverage += int64(len(reftile.Sequence))
}
- 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)
}
- if bedout != 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 * 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)
+ 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 * coverage / int64(len(reftile.Sequence)) / int64(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) {
projects / lightning.git / blobdiff