"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
- Print func(out io.Writer, seqname string, varslice []hgvs.Variant)
+ Head func(out io.Writer, cgs []CompactGenome)
+ Print func(out io.Writer, seqname string, varslice []tvVariant)
PadLeft bool
}
outputFormats = map[string]outputFormat{
"hgvs-onehot": outputFormatHGVSOneHot,
"hgvs": outputFormatHGVS,
+ "pvcf": outputFormatPVCF,
"vcf": outputFormatVCF,
}
- outputFormatHGVS = outputFormat{Filename: "out.csv", Print: printHGVS}
- outputFormatHGVSOneHot = outputFormat{Filename: "out.csv", Print: printHGVSOneHot}
- outputFormatVCF = outputFormat{Filename: "out.vcf", Print: printVCF, PadLeft: true}
+ 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
}
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 or vcf")
+ 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)
"-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 cmd.outputPerChrom {
for i, seqname := range seqnames {
- f, err := os.OpenFile(filepath.Join(outdir, strings.Replace(cmd.outputFormat.Filename, ".", "."+seqname+".", 1)), os.O_CREATE|os.O_WRONLY, 0666)
+ 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)
- log.Infof("writing %q", fnm)
- out, err := os.OpenFile(fnm, os.O_CREATE|os.O_WRONLY, 0666)
+ 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 out.Close()
+ 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 {
if bedw != nil {
defer bedw.Close()
}
- defer outw.Close()
outwb := bufio.NewWriterSize(outw, 8*1024*1024)
- defer outwb.Flush()
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 nil
+ 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][]hgvs.Variant{} // variantAt[chromOffset][genomeIndex*2+phase]
+ 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 {
if variant == libref.Variant {
continue
}
- genomeseq := tilelib.TileVariantSequence(tileLibRef{Tag: libref.Tag, Variant: variant})
- 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...)
+ 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
}
- refSequence = append(refSequence, tilelib.TileVariantSequence(reftiles[refstepend])...)
- refstepend++
+ 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
}
- // (TODO: handle no-calls)
- vars, _ := hgvs.Diff(strings.ToUpper(string(refSequence)), strings.ToUpper(string(genomeseq)), time.Second)
for _, v := range vars {
if cmd.outputFormat.PadLeft {
v = v.PadLeft()
v.Position += refpos
varslice := variantAt[v.Position]
if varslice == nil {
- varslice = make([]hgvs.Variant, len(cgs)*2)
+ varslice = make([]tvVariant, len(cgs)*2)
variantAt[v.Position] = varslice
}
- varslice[cgidx*2+phase] = v
+ 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
+ }
}
}
}
// Flush entries from variantAt that are behind
// refpos. Flush all entries if this is the last
// reftile of the path/chromosome.
- var flushpos []int
+ flushpos := make([]int, 0, len(variantAt))
lastrefstep := refstep == len(reftiles)-1
for pos := range variantAt {
if lastrefstep || pos <= refpos {
}
}
sort.Slice(flushpos, func(i, j int) bool { return flushpos[i] < flushpos[j] })
- for _, pos := range flushpos {
+ flushvariants := make([][]tvVariant, len(flushpos))
+ for i, pos := range flushpos {
varslice := variantAt[pos]
delete(variantAt, pos)
for i := range varslice {
varslice[i].Position = pos
}
}
- cmd.outputFormat.Print(outw, seqname, varslice)
+ 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
}
}
-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 == "" {
continue
}
- alts := refs[v.Ref]
+ alts := byref[v.Ref]
if alts == nil {
alts = map[string]int{}
- refs[v.Ref] = alts
+ 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)
}
- alts[v.New] = 0
+ 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)
}
- for ref, alts := range refs {
- var altslice []string
+}
+
+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)
}
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, ","))
+ 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 {
}
}
-func printHGVS(out io.Writer, seqname string, varslice []hgvs.Variant) {
+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 == var2 {
+ if var1.Variant == var2.Variant {
if var1.Ref == var1.New {
out.Write([]byte{'.'})
} else {
out.Write([]byte{'\n'})
}
-func printHGVSOneHot(out io.Writer, seqname string, varslice []hgvs.Variant) {
+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] = true
+ vars[v.Variant] = true
}
}
for _, v := range sorted {
fmt.Fprintf(out, "%s.%s", seqname, v.String())
for i := 0; i < len(varslice); i += 2 {
- if varslice[i] == v || varslice[i+1] == v {
+ if varslice[i].Variant == v || varslice[i+1].Variant == v {
out.Write([]byte("\t1"))
} else {
out.Write([]byte("\t0"))
projects / lightning.git / blobdiff