"runtime"
"sort"
"strings"
+ "sync"
+ "sync/atomic"
"git.arvados.org/arvados.git/sdk/go/arvados"
"github.com/arvados/lightning/hgvs"
RAM: 250000000000,
VCPUs: 32,
Priority: *priority,
- KeepCache: 1,
+ KeepCache: 2,
APIAccess: true,
}
err = runner.TranslatePaths(inputDir, regionsFilename)
log.Info("building list of reference tiles to load") // TODO: more efficient if we had saved all ref tiles in slice0
type reftileinfo struct {
+ variant tileVariantID
seqname string // chr1
pos int // distance from start of chr1 to start of tile
tiledata []byte // acgtggcaa...
reftile := map[tagID]*reftileinfo{}
for seqname, cseq := range refseq {
for _, libref := range cseq {
- reftile[libref.Tag] = &reftileinfo{seqname: seqname}
+ reftile[libref.Tag] = &reftileinfo{seqname: seqname, variant: libref.Variant}
}
}
log.Info("loading reference tiles from all slices")
- throttle := throttle{Max: runtime.NumCPU()}
+ throttle := throttle{Max: runtime.GOMAXPROCS(0)}
for _, infile := range infiles {
infile := infile
throttle.Go(func() error {
defer f.Close()
return DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
for _, tv := range ent.TileVariants {
- if dst, ok := reftile[tv.Tag]; ok {
+ if dst, ok := reftile[tv.Tag]; ok && dst.variant == tv.Variant {
dst.tiledata = tv.Sequence
}
}
log.Info("TODO: determining which tiles intersect given regions")
log.Info("generating annotations and numpy matrix for each slice")
+ var done int64
for infileIdx, infile := range infiles {
infileIdx, infile := infileIdx, infile
throttle.Go(func() error {
- defer log.Infof("%s: done", infile)
- seq := map[tagID][][]byte{}
+ seq := make(map[tagID][]TileVariant, 50000)
cgs := make(map[string]CompactGenome, len(cgnames))
f, err := open(infile)
if err != nil {
return err
}
defer f.Close()
+ log.Infof("reading %s", infile)
err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
for _, tv := range ent.TileVariants {
variants := seq[tv.Tag]
for len(variants) <= int(tv.Variant) {
- variants = append(variants, nil)
+ variants = append(variants, TileVariant{})
}
- variants[int(tv.Variant)] = tv.Sequence
+ variants[int(tv.Variant)] = tv
seq[tv.Tag] = variants
}
for _, cg := range ent.CompactGenomes {
tagstart := cgs[cgnames[0]].StartTag
tagend := cgs[cgnames[0]].EndTag
- log.Infof("TODO: %s: filtering", infile)
- log.Infof("TODO: %s: tidying", infile)
- log.Infof("TODO: %s: lowqual to -1", infile)
+ // TODO: filters
+
+ log.Infof("renumbering variants for tags %d-%d", tagstart, tagend)
+ variantRemap := make([][]tileVariantID, tagend-tagstart)
+ var wg sync.WaitGroup
+ for tag, variants := range seq {
+ tag, variants := tag, variants
+ wg.Add(1)
+ go func() {
+ defer wg.Done()
+ count := make([]tileVariantID, len(variants))
+ for _, cg := range cgs {
+ idx := (tag - tagstart) * 2
+ count[cg.Variants[idx]]++
+ count[cg.Variants[idx+1]]++
+ }
+ ranked := make([]tileVariantID, len(variants))
+ for i := range ranked {
+ ranked[i] = tileVariantID(i)
+ }
+ sort.Slice(ranked, func(i, j int) bool {
+ if i == 0 {
+ return true // leave ranked[0] at position 0, unused
+ } else if j == 0 {
+ return false // ditto
+ }
+ if cri, crj := count[ranked[i]], count[ranked[j]]; cri != crj {
+ return cri > crj
+ } else {
+ return bytes.Compare(variants[ranked[i]].Blake2b[:], variants[ranked[j]].Blake2b[:]) < 0
+ }
+ })
+ remap := make([]tileVariantID, len(ranked))
+ for i, r := range ranked {
+ remap[r] = tileVariantID(i)
+ }
+ variantRemap[tag-tagstart] = remap
+ }()
+ }
+ wg.Wait()
annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
- log.Infof("%s: writing annotations to %s", infile, annotationsFilename)
+ log.Infof("writing %s", annotationsFilename)
annof, err := os.Create(annotationsFilename)
if err != nil {
return err
}
outcol := tag - tagID(tagstart)
reftilestr := strings.ToUpper(string(rt.tiledata))
- for v, seq := range variants {
- if len(seq) == 0 || !bytes.HasSuffix(rt.tiledata, seq[len(seq)-taglen:]) {
+ remap := variantRemap[tag-tagstart]
+ for v, tv := range variants {
+ if len(tv.Sequence) < taglen || !bytes.HasSuffix(rt.tiledata, tv.Sequence[len(tv.Sequence)-taglen:]) {
continue
}
- if lendiff := len(rt.tiledata) - len(seq); lendiff < -1000 || lendiff > 1000 {
+ if lendiff := len(rt.tiledata) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
continue
}
- diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(seq)), 0)
+ diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
for _, diff := range diffs {
diff.Position += rt.pos
- fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s\n", tag, outcol, v, rt.seqname, diff.String())
+ fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s\n", tag, outcol, remap[v], rt.seqname, diff.String())
}
}
}
for row, name := range cgnames {
out := out[row*cols:]
for col, v := range cgs[name].Variants {
- if variants, ok := seq[tagstart+tagID(col/2)]; ok && len(variants) > int(v) && len(variants[v]) > 0 {
- out[col] = int16(v)
+ if variants, ok := seq[tagstart+tagID(col/2)]; ok && len(variants) > int(v) && len(variants[v].Sequence) > 0 {
+ out[col] = int16(variantRemap[col/2][v])
} else {
out[col] = -1
}
return err
}
defer output.Close()
- bufw := bufio.NewWriter(output)
+ bufw := bufio.NewWriterSize(output, 1<<26)
npw, err := gonpy.NewWriter(nopCloser{bufw})
if err != nil {
return err
if err != nil {
return err
}
+ log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
return nil
})
}
}
return 0
}
-
-func (*sliceNumpy) writeLibRefs(fnm string, tilelib *tileLibrary, librefs []tileLibRef) error {
- f, err := os.OpenFile(fnm, os.O_CREATE|os.O_WRONLY, 0666)
- if err != nil {
- return err
- }
- defer f.Close()
- for i, libref := range librefs {
- _, err = fmt.Fprintf(f, "%d,%d,%d\n", i, libref.Tag, libref.Variant)
- if err != nil {
- return err
- }
- }
- return f.Close()
-}
projects / lightning.git / blobdiff