"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 []hgvs.Variant)
+ Print func(out io.Writer, seqname string, varslice []tvVariant)
PadLeft bool
}
type exporter struct {
outputFormat outputFormat
outputPerChrom bool
+ compress bool
maxTileSize int
}
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|os.O_TRUNC, 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())
- cmd.outputFormat.Head(f, cgs)
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|os.O_TRUNC, 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 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
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:
refstepend++
}
// (TODO: handle no-calls)
- refstr := strings.ToUpper(string(refSequence))
- genomestr := strings.ToUpper(string(genomeseq))
- vars, _ = hgvs.Diff(refstr, genomestr, time.Second)
+ 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 {
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
+ }
}
}
}
}
}
sort.Slice(flushpos, func(i, j int) bool { return flushpos[i] < flushpos[j] })
- flushvariants := make([][]hgvs.Variant, len(flushpos))
+ flushvariants := make([][]tvVariant, len(flushpos))
for i, pos := range flushpos {
varslice := variantAt[pos]
delete(variantAt, pos)
}
}
-func bucketVarsliceByRef(varslice []hgvs.Variant) 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 == "" {
fmt.Fprint(out, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n")
}
-func printVCF(out io.Writer, seqname string, varslice []hgvs.Variant) {
+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 {
fmt.Fprintf(out, "\n")
}
-func printPVCF(out io.Writer, seqname string, varslice []hgvs.Variant) {
+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 {
}
}
-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