1 // Copyright (C) The Lightning Authors. All rights reserved.
3 // SPDX-License-Identifier: AGPL-3.0
29 "git.arvados.org/arvados.git/sdk/go/arvados"
30 "github.com/arvados/lightning/hgvs"
31 "github.com/kshedden/gonpy"
32 "github.com/sirupsen/logrus"
33 log "github.com/sirupsen/logrus"
34 "golang.org/x/crypto/blake2b"
37 const annotationMaxTileSpan = 100
39 type sliceNumpy struct {
42 chi2CaseControlColumn string
43 chi2CaseControlFile string
52 func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
56 fmt.Fprintf(stderr, "%s\n", err)
59 flags := flag.NewFlagSet("", flag.ContinueOnError)
60 flags.SetOutput(stderr)
61 pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
62 runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
63 projectUUID := flags.String("project", "", "project `UUID` for output data")
64 priority := flags.Int("priority", 500, "container request priority")
65 inputDir := flags.String("input-dir", "./in", "input `directory`")
66 outputDir := flags.String("output-dir", "./out", "output `directory`")
67 ref := flags.String("ref", "", "reference name (if blank, choose last one that appears in input)")
68 regionsFilename := flags.String("regions", "", "only output columns/annotations that intersect regions in specified bed `file`")
69 expandRegions := flags.Int("expand-regions", 0, "expand specified regions by `N` base pairs on each side`")
70 mergeOutput := flags.Bool("merge-output", false, "merge output into one matrix.npy and one matrix.annotations.csv")
71 hgvsSingle := flags.Bool("single-hgvs-matrix", false, "also generate hgvs-based matrix")
72 hgvsChunked := flags.Bool("chunked-hgvs-matrix", false, "also generate hgvs-based matrix per chromosome")
73 onehotSingle := flags.Bool("single-onehot", false, "generate one-hot tile-based matrix")
74 onehotChunked := flags.Bool("chunked-onehot", false, "generate one-hot tile-based matrix per input chunk")
75 debugTag := flags.Int("debug-tag", -1, "log debugging details about specified tag")
76 flags.IntVar(&cmd.threads, "threads", 16, "number of memory-hungry assembly threads")
77 flags.StringVar(&cmd.chi2CaseControlFile, "chi2-case-control-file", "", "tsv file or directory indicating cases and controls for Χ² test (if directory, all .tsv files will be read)")
78 flags.StringVar(&cmd.chi2CaseControlColumn, "chi2-case-control-column", "", "name of case/control column in case-control files for Χ² test (value must be 0 for control, 1 for case)")
79 flags.Float64Var(&cmd.chi2PValue, "chi2-p-value", 1, "do Χ² test and omit columns with p-value above this threshold")
80 flags.BoolVar(&cmd.includeVariant1, "include-variant-1", false, "include most common variant when building one-hot matrix")
81 cmd.filter.Flags(flags)
82 err = flags.Parse(args)
83 if err == flag.ErrHelp {
86 } else if err != nil {
92 log.Println(http.ListenAndServe(*pprof, nil))
96 if cmd.chi2PValue != 1 && (cmd.chi2CaseControlFile == "" || cmd.chi2CaseControlColumn == "") {
97 log.Errorf("cannot use provided -chi2-p-value=%f because -chi2-case-control-file= or -chi2-case-control-column= value is empty", cmd.chi2PValue)
101 cmd.debugTag = tagID(*debugTag)
104 runner := arvadosContainerRunner{
105 Name: "lightning slice-numpy",
106 Client: arvados.NewClientFromEnv(),
107 ProjectUUID: *projectUUID,
114 err = runner.TranslatePaths(inputDir, regionsFilename, &cmd.chi2CaseControlFile)
118 runner.Args = []string{"slice-numpy", "-local=true",
120 "-input-dir=" + *inputDir,
121 "-output-dir=/mnt/output",
122 "-threads=" + fmt.Sprintf("%d", cmd.threads),
123 "-regions=" + *regionsFilename,
124 "-expand-regions=" + fmt.Sprintf("%d", *expandRegions),
125 "-merge-output=" + fmt.Sprintf("%v", *mergeOutput),
126 "-single-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsSingle),
127 "-chunked-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsChunked),
128 "-single-onehot=" + fmt.Sprintf("%v", *onehotSingle),
129 "-chunked-onehot=" + fmt.Sprintf("%v", *onehotChunked),
130 "-chi2-case-control-file=" + cmd.chi2CaseControlFile,
131 "-chi2-case-control-column=" + cmd.chi2CaseControlColumn,
132 "-chi2-p-value=" + fmt.Sprintf("%f", cmd.chi2PValue),
133 "-include-variant-1=" + fmt.Sprintf("%v", cmd.includeVariant1),
134 "-debug-tag=" + fmt.Sprintf("%d", cmd.debugTag),
136 runner.Args = append(runner.Args, cmd.filter.Args()...)
138 output, err = runner.Run()
142 fmt.Fprintln(stdout, output)
146 infiles, err := allFiles(*inputDir, matchGobFile)
150 if len(infiles) == 0 {
151 err = fmt.Errorf("no input files found in %s", *inputDir)
154 sort.Strings(infiles)
156 var refseq map[string][]tileLibRef
157 var reftiledata = make(map[tileLibRef][]byte, 11000000)
158 in0, err := open(infiles[0])
163 matchGenome, err := regexp.Compile(cmd.filter.MatchGenome)
165 err = fmt.Errorf("-match-genome: invalid regexp: %q", cmd.filter.MatchGenome)
171 err = DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
172 if len(ent.TagSet) > 0 {
175 for _, cseq := range ent.CompactSequences {
176 if cseq.Name == *ref || *ref == "" {
177 refseq = cseq.TileSequences
180 for _, cg := range ent.CompactGenomes {
181 if matchGenome.MatchString(cg.Name) {
182 cmd.cgnames = append(cmd.cgnames, cg.Name)
185 for _, tv := range ent.TileVariants {
187 reftiledata[tileLibRef{tv.Tag, tv.Variant}] = tv.Sequence
197 err = fmt.Errorf("%s: reference sequence not found", infiles[0])
200 if len(tagset) == 0 {
201 err = fmt.Errorf("tagset not found")
205 taglib := &tagLibrary{}
206 err = taglib.setTags(tagset)
210 taglen := taglib.TagLen()
212 if len(cmd.cgnames) == 0 {
213 err = fmt.Errorf("no genomes found matching regexp %q", cmd.filter.MatchGenome)
216 sort.Strings(cmd.cgnames)
217 err = cmd.useCaseControlFiles()
221 if len(cmd.cgnames) == 0 {
222 err = fmt.Errorf("fatal: 0 cases, 0 controls, nothing to do")
225 cmd.minCoverage = int(math.Ceil(cmd.filter.MinCoverage * float64(len(cmd.cgnames))))
228 labelsFilename := *outputDir + "/samples.csv"
229 log.Infof("writing labels to %s", labelsFilename)
231 f, err = os.Create(labelsFilename)
236 for i, name := range cmd.cgnames {
238 if cmd.chi2Cases != nil && cmd.chi2Cases[i] {
241 _, err = fmt.Fprintf(f, "%d,%q,%d\n", i, trimFilenameForLabel(name), cc)
243 err = fmt.Errorf("write %s: %w", labelsFilename, err)
249 err = fmt.Errorf("close %s: %w", labelsFilename, err)
254 log.Info("indexing reference tiles")
255 type reftileinfo struct {
256 variant tileVariantID
257 seqname string // chr1
258 pos int // distance from start of chromosome to starttag
259 tiledata []byte // acgtggcaa...
260 excluded bool // true if excluded by regions file
261 nexttag tagID // tagID of following tile (-1 for last tag of chromosome)
263 isdup := map[tagID]bool{}
264 reftile := map[tagID]*reftileinfo{}
265 for seqname, cseq := range refseq {
267 lastreftag := tagID(-1)
268 for _, libref := range cseq {
269 if cmd.filter.MaxTag >= 0 && libref.Tag > tagID(cmd.filter.MaxTag) {
272 tiledata := reftiledata[libref]
273 if len(tiledata) == 0 {
274 err = fmt.Errorf("missing tiledata for tag %d variant %d in %s in ref", libref.Tag, libref.Variant, seqname)
277 foundthistag := false
278 taglib.FindAll(tiledata[:len(tiledata)-1], func(tagid tagID, offset, _ int) {
279 if !foundthistag && tagid == libref.Tag {
283 if dupref, ok := reftile[tagid]; ok {
284 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique, also found inside %+v from %s @ %d", tileLibRef{Tag: tagid, Variant: dupref.variant}, dupref.seqname, dupref.pos, libref, seqname, pos+offset+1)
285 delete(reftile, tagid)
287 log.Printf("found tag %d at offset %d inside tile variant %+v on %s @ %d", tagid, offset, libref, seqname, pos+offset+1)
291 if isdup[libref.Tag] {
292 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
293 } else if reftile[libref.Tag] != nil {
294 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", tileLibRef{Tag: libref.Tag, Variant: reftile[libref.Tag].variant}, reftile[libref.Tag].seqname, reftile[libref.Tag].pos)
295 delete(reftile, libref.Tag)
296 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
297 isdup[libref.Tag] = true
299 reftile[libref.Tag] = &reftileinfo{
301 variant: libref.Variant,
307 reftile[lastreftag].nexttag = libref.Tag
309 lastreftag = libref.Tag
311 pos += len(tiledata) - taglen
313 log.Printf("... %s done, len %d", seqname, pos+taglen)
317 if *regionsFilename != "" {
318 log.Printf("loading regions from %s", *regionsFilename)
319 mask, err = makeMask(*regionsFilename, *expandRegions)
323 log.Printf("before applying mask, len(reftile) == %d", len(reftile))
324 log.Printf("deleting reftile entries for regions outside %d intervals", mask.Len())
325 for _, rt := range reftile {
326 if !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(rt.tiledata)) {
330 log.Printf("after applying mask, len(reftile) == %d", len(reftile))
333 type hgvsColSet map[hgvs.Variant][2][]int8
334 encodeHGVS := throttle{Max: len(refseq)}
335 encodeHGVSTodo := map[string]chan hgvsColSet{}
336 tmpHGVSCols := map[string]*os.File{}
338 for seqname := range refseq {
340 f, err = os.Create(*outputDir + "/tmp." + seqname + ".gob")
344 defer os.Remove(f.Name())
345 bufw := bufio.NewWriterSize(f, 1<<24)
346 enc := gob.NewEncoder(bufw)
347 tmpHGVSCols[seqname] = f
348 todo := make(chan hgvsColSet, 128)
349 encodeHGVSTodo[seqname] = todo
350 encodeHGVS.Go(func() error {
351 for colset := range todo {
352 err := enc.Encode(colset)
354 encodeHGVS.Report(err)
365 var toMerge [][]int16
366 if *mergeOutput || *hgvsSingle {
367 toMerge = make([][]int16, len(infiles))
369 var onehotIndirect [][2][]uint32 // [chunkIndex][axis][index]
370 var onehotChunkSize []uint32
371 var onehotXrefs [][]onehotXref
373 onehotIndirect = make([][2][]uint32, len(infiles))
374 onehotChunkSize = make([]uint32, len(infiles))
375 onehotXrefs = make([][]onehotXref, len(infiles))
377 chunkStartTag := make([]tagID, len(infiles))
379 throttleMem := throttle{Max: cmd.threads} // TODO: estimate using mem and data size
380 throttleNumpyMem := throttle{Max: cmd.threads/2 + 1}
381 log.Info("generating annotations and numpy matrix for each slice")
382 var errSkip = errors.New("skip infile")
384 for infileIdx, infile := range infiles {
385 infileIdx, infile := infileIdx, infile
386 throttleMem.Go(func() error {
387 seq := make(map[tagID][]TileVariant, 50000)
388 cgs := make(map[string]CompactGenome, len(cmd.cgnames))
389 f, err := open(infile)
394 log.Infof("%04d: reading %s", infileIdx, infile)
395 err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
396 for _, tv := range ent.TileVariants {
401 // corresponding ref tile, if
402 // mask is in play (we can't
403 // determine coordinates for
405 if mask != nil && reftile[tv.Tag] == nil {
409 // corresponding ref tile is
410 // outside target regions --
411 // unless it's a potential
413 if mask != nil && reftile[tv.Tag].excluded &&
414 (int(tv.Tag+1) >= len(tagset) ||
415 (bytes.HasSuffix(tv.Sequence, tagset[tv.Tag+1]) && reftile[tv.Tag+1] != nil && !reftile[tv.Tag+1].excluded)) {
418 if tv.Tag == cmd.debugTag {
419 log.Printf("infile %d %s tag %d variant %d hash %x", infileIdx, infile, tv.Tag, tv.Variant, tv.Blake2b[:3])
421 variants := seq[tv.Tag]
422 if len(variants) == 0 {
423 variants = make([]TileVariant, 100)
425 for len(variants) <= int(tv.Variant) {
426 variants = append(variants, TileVariant{})
428 variants[int(tv.Variant)] = tv
429 seq[tv.Tag] = variants
431 for _, cg := range ent.CompactGenomes {
432 if cmd.filter.MaxTag >= 0 && cg.StartTag > tagID(cmd.filter.MaxTag) {
435 if !matchGenome.MatchString(cg.Name) {
438 // pad to full slice size
439 // to avoid out-of-bounds
441 if sliceSize := 2 * int(cg.EndTag-cg.StartTag); len(cg.Variants) < sliceSize {
442 cg.Variants = append(cg.Variants, make([]tileVariantID, sliceSize-len(cg.Variants))...)
450 } else if err != nil {
453 tagstart := cgs[cmd.cgnames[0]].StartTag
454 tagend := cgs[cmd.cgnames[0]].EndTag
455 chunkStartTag[infileIdx] = tagstart
459 log.Infof("%04d: renumber/dedup variants for tags %d-%d", infileIdx, tagstart, tagend)
460 variantRemap := make([][]tileVariantID, tagend-tagstart)
461 throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
462 for tag, variants := range seq {
463 tag, variants := tag, variants
464 throttleCPU.Go(func() error {
465 count := make(map[[blake2b.Size256]byte]int, len(variants))
469 count[blake2b.Sum256(rt.tiledata)] = 0
472 for cgname, cg := range cgs {
473 idx := int(tag-tagstart) * 2
474 for allele := 0; allele < 2; allele++ {
475 v := cg.Variants[idx+allele]
476 if v > 0 && len(variants[v].Sequence) > 0 {
477 count[variants[v].Blake2b]++
479 if v > 0 && tag == cmd.debugTag {
480 log.Printf("tag %d cg %s allele %d tv %d hash %x count is now %d", tag, cgname, allele, v, variants[v].Blake2b[:3], count[variants[v].Blake2b])
484 // hash[i] will be the hash of
485 // the variant(s) that should
486 // be at rank i (0-based).
487 hash := make([][blake2b.Size256]byte, 0, len(count))
488 for b := range count {
489 hash = append(hash, b)
491 sort.Slice(hash, func(i, j int) bool {
492 bi, bj := &hash[i], &hash[j]
493 if ci, cj := count[*bi], count[*bj]; ci != cj {
496 return bytes.Compare((*bi)[:], (*bj)[:]) < 0
499 // rank[b] will be the 1-based
500 // new variant number for
501 // variants whose hash is b.
502 rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
503 for i, h := range hash {
504 rank[h] = tileVariantID(i + 1)
506 if tag == cmd.debugTag {
507 for h, r := range rank {
508 log.Printf("tag %d rank(%x) = %v", tag, h[:3], r)
511 // remap[v] will be the new
512 // variant number for original
514 remap := make([]tileVariantID, len(variants))
515 for i, tv := range variants {
516 remap[i] = rank[tv.Blake2b]
518 if tag == cmd.debugTag {
519 for in, out := range remap {
521 log.Printf("tag %d remap %d => %d", tag, in, out)
525 variantRemap[tag-tagstart] = remap
527 refrank := rank[blake2b.Sum256(rt.tiledata)]
528 if tag == cmd.debugTag {
529 log.Printf("tag %d reftile variant %d => %d", tag, rt.variant, refrank)
538 var onehotChunk [][]int8
539 var onehotXref []onehotXref
541 annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
542 log.Infof("%04d: writing %s", infileIdx, annotationsFilename)
543 annof, err := os.Create(annotationsFilename)
547 annow := bufio.NewWriterSize(annof, 1<<20)
549 for tag := tagstart; tag < tagend; tag++ {
551 if rt == nil && mask != nil {
552 // With no ref tile, we don't
553 // have coordinates to say
554 // this is in the desired
555 // regions -- so it's not.
556 // TODO: handle ref spanning
560 if rt != nil && rt.excluded {
561 // TODO: don't skip yet --
562 // first check for spanning
563 // tile variants that
564 // intersect non-excluded ref
568 if cmd.filter.MaxTag >= 0 && tag > tagID(cmd.filter.MaxTag) {
571 remap := variantRemap[tag-tagstart]
572 maxv := tileVariantID(0)
573 for _, v := range remap {
578 if *onehotChunked || *onehotSingle {
579 onehot, xrefs := cmd.tv2homhet(cgs, maxv, remap, tag, tagstart, seq)
580 if tag == cmd.debugTag {
581 log.WithFields(logrus.Fields{
584 }).Info("tv2homhet()")
586 onehotChunk = append(onehotChunk, onehot...)
587 onehotXref = append(onehotXref, xrefs...)
590 // Reference does not use any
591 // variant of this tile
593 // TODO: diff against the
594 // relevant portion of the
595 // ref's spanning tile
599 fmt.Fprintf(annow, "%d,%d,%d,=,%s,%d,,,\n", tag, outcol, rt.variant, rt.seqname, rt.pos)
601 reftilestr := strings.ToUpper(string(rt.tiledata))
603 done := make([]bool, maxv+1)
604 variantDiffs := make([][]hgvs.Variant, maxv+1)
605 for v, tv := range variants {
607 if v == rt.variant || done[v] {
612 if len(tv.Sequence) < taglen {
615 // if reftilestr doesn't end
616 // in the same tag as tv,
617 // extend reftilestr with
618 // following ref tiles until
619 // it does (up to an arbitrary
620 // sanity-check limit)
621 reftilestr := reftilestr
622 endtagstr := strings.ToUpper(string(tv.Sequence[len(tv.Sequence)-taglen:]))
623 for i, rt := 0, rt; i < annotationMaxTileSpan && !strings.HasSuffix(reftilestr, endtagstr) && rt.nexttag >= 0; i++ {
624 rt = reftile[rt.nexttag]
625 reftilestr += strings.ToUpper(string(rt.tiledata[taglen:]))
627 if mask != nil && !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(reftilestr)) {
630 if !strings.HasSuffix(reftilestr, endtagstr) {
631 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
634 if lendiff := len(reftilestr) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
635 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
638 diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
639 for i := range diffs {
640 diffs[i].Position += rt.pos
642 for _, diff := range diffs {
643 fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s,%s,%d,%s,%s,%s\n", tag, outcol, v, rt.seqname, diff.String(), rt.seqname, diff.Position, diff.Ref, diff.New, diff.Left)
646 variantDiffs[v] = diffs
650 // We can now determine, for each HGVS
651 // variant (diff) in this reftile
652 // region, whether a given genome
653 // phase/allele (1) has the variant, (0) has
654 // =ref or a different variant in that
655 // position, or (-1) is lacking
656 // coverage / couldn't be diffed.
657 hgvsCol := hgvsColSet{}
658 for _, diffs := range variantDiffs {
659 for _, diff := range diffs {
660 if _, ok := hgvsCol[diff]; ok {
663 hgvsCol[diff] = [2][]int8{
664 make([]int8, len(cmd.cgnames)),
665 make([]int8, len(cmd.cgnames)),
669 for row, name := range cmd.cgnames {
670 variants := cgs[name].Variants[(tag-tagstart)*2:]
671 for ph := 0; ph < 2; ph++ {
673 if int(v) >= len(remap) {
679 // hgvsCol[*][ph][row] is already 0
680 } else if len(variantDiffs[v]) == 0 {
681 // lacking coverage / couldn't be diffed
682 for _, col := range hgvsCol {
686 for _, diff := range variantDiffs[v] {
687 hgvsCol[diff][ph][row] = 1
692 for diff, colpair := range hgvsCol {
693 allele2homhet(colpair)
694 if !cmd.filterHGVScolpair(colpair) {
695 delete(hgvsCol, diff)
698 if len(hgvsCol) > 0 {
699 encodeHGVSTodo[rt.seqname] <- hgvsCol
714 // transpose onehotChunk[col][row] to numpy[row*ncols+col]
715 rows := len(cmd.cgnames)
716 cols := len(onehotChunk)
717 log.Infof("%04d: preparing onehot numpy (rows=%d, cols=%d, mem=%d)", infileIdx, rows, cols, rows*cols)
718 throttleNumpyMem.Acquire()
719 out := onehotcols2int8(onehotChunk)
720 fnm := fmt.Sprintf("%s/onehot.%04d.npy", *outputDir, infileIdx)
721 err = writeNumpyInt8(fnm, out, rows, cols)
725 fnm = fmt.Sprintf("%s/onehot-columns.%04d.npy", *outputDir, infileIdx)
726 err = writeNumpyInt32(fnm, onehotXref2int32(onehotXref), 4, len(onehotXref))
731 throttleNumpyMem.Release()
734 onehotIndirect[infileIdx] = onehotChunk2Indirect(onehotChunk)
735 onehotChunkSize[infileIdx] = uint32(len(onehotChunk))
736 onehotXrefs[infileIdx] = onehotXref
737 n := len(onehotIndirect[infileIdx][0])
738 log.Infof("%04d: keeping onehot coordinates in memory (n=%d, mem=%d)", infileIdx, n, n*8*2)
740 if !(*onehotSingle || *onehotChunked) || *mergeOutput || *hgvsSingle {
741 log.Infof("%04d: preparing numpy (rows=%d, cols=%d)", infileIdx, len(cmd.cgnames), 2*outcol)
742 throttleNumpyMem.Acquire()
743 rows := len(cmd.cgnames)
745 out := make([]int16, rows*cols)
746 for row, name := range cmd.cgnames {
748 for col, v := range cgs[name].Variants {
749 tag := tagstart + tagID(col/2)
750 if cmd.filter.MaxTag >= 0 && tag > tagID(cmd.filter.MaxTag) {
753 if rt := reftile[tag]; rt == nil || rt.excluded {
757 out[outidx] = 0 // tag not found / spanning tile
758 } else if variants, ok := seq[tag]; ok && int(v) < len(variants) && len(variants[v].Sequence) > 0 {
759 out[outidx] = int16(variantRemap[tag-tagstart][v])
761 out[outidx] = -1 // low quality tile variant
763 if tag == cmd.debugTag {
764 log.Printf("tag %d row %d col %d outidx %d v %d out %d", tag, row, col, outidx, v, out[outidx])
772 throttleNumpyMem.Release()
773 if *mergeOutput || *hgvsSingle {
774 log.Infof("%04d: matrix fragment %d rows x %d cols", infileIdx, rows, cols)
775 toMerge[infileIdx] = out
777 if !*mergeOutput && !*onehotChunked && !*onehotSingle {
778 fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
779 err = writeNumpyInt16(fnm, out, rows, cols)
786 log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
790 if err = throttleMem.Wait(); err != nil {
795 log.Info("flushing hgvsCols temp files")
796 for seqname := range refseq {
797 close(encodeHGVSTodo[seqname])
799 err = encodeHGVS.Wait()
803 for seqname := range refseq {
804 log.Infof("%s: reading hgvsCols from temp file", seqname)
805 f := tmpHGVSCols[seqname]
806 _, err = f.Seek(0, io.SeekStart)
810 var hgvsCols hgvsColSet
811 dec := gob.NewDecoder(bufio.NewReaderSize(f, 1<<24))
813 err = dec.Decode(&hgvsCols)
818 log.Infof("%s: sorting %d hgvs variants", seqname, len(hgvsCols))
819 variants := make([]hgvs.Variant, 0, len(hgvsCols))
820 for v := range hgvsCols {
821 variants = append(variants, v)
823 sort.Slice(variants, func(i, j int) bool {
824 vi, vj := &variants[i], &variants[j]
825 if vi.Position != vj.Position {
826 return vi.Position < vj.Position
827 } else if vi.Ref != vj.Ref {
828 return vi.Ref < vj.Ref
830 return vi.New < vj.New
833 rows := len(cmd.cgnames)
834 cols := len(variants) * 2
835 log.Infof("%s: building hgvs matrix (rows=%d, cols=%d, mem=%d)", seqname, rows, cols, rows*cols)
836 out := make([]int8, rows*cols)
837 for varIdx, variant := range variants {
838 hgvsCols := hgvsCols[variant]
839 for row := range cmd.cgnames {
840 for ph := 0; ph < 2; ph++ {
841 out[row*cols+varIdx+ph] = hgvsCols[ph][row]
845 err = writeNumpyInt8(fmt.Sprintf("%s/hgvs.%s.npy", *outputDir, seqname), out, rows, cols)
851 fnm := fmt.Sprintf("%s/hgvs.%s.annotations.csv", *outputDir, seqname)
852 log.Infof("%s: writing hgvs column labels to %s", seqname, fnm)
853 var hgvsLabels bytes.Buffer
854 for varIdx, variant := range variants {
855 fmt.Fprintf(&hgvsLabels, "%d,%s:g.%s\n", varIdx, seqname, variant.String())
857 err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0666)
864 if *mergeOutput || *hgvsSingle {
865 var annow *bufio.Writer
868 annoFilename := fmt.Sprintf("%s/matrix.annotations.csv", *outputDir)
869 annof, err = os.Create(annoFilename)
873 annow = bufio.NewWriterSize(annof, 1<<20)
876 rows := len(cmd.cgnames)
878 for _, chunk := range toMerge {
879 cols += len(chunk) / rows
881 log.Infof("merging output matrix (rows=%d, cols=%d, mem=%d) and annotations", rows, cols, rows*cols*2)
884 out = make([]int16, rows*cols)
886 hgvsCols := map[string][2][]int16{} // hgvs -> [[g0,g1,g2,...], [g0,g1,g2,...]] (slice of genomes for each phase)
888 for outIdx, chunk := range toMerge {
889 chunkcols := len(chunk) / rows
891 for row := 0; row < rows; row++ {
892 copy(out[row*cols+startcol:], chunk[row*chunkcols:(row+1)*chunkcols])
895 toMerge[outIdx] = nil
897 annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, outIdx)
898 log.Infof("reading %s", annotationsFilename)
899 buf, err := os.ReadFile(annotationsFilename)
904 err = os.Remove(annotationsFilename)
909 for _, line := range bytes.Split(buf, []byte{'\n'}) {
913 fields := bytes.SplitN(line, []byte{','}, 9)
914 tag, _ := strconv.Atoi(string(fields[0]))
915 incol, _ := strconv.Atoi(string(fields[1]))
916 tileVariant, _ := strconv.Atoi(string(fields[2]))
917 hgvsID := string(fields[3])
918 seqname := string(fields[4])
919 pos, _ := strconv.Atoi(string(fields[5]))
922 // Null entry for un-diffable
927 // Null entry for ref tile
930 if mask != nil && !mask.Check(strings.TrimPrefix(seqname, "chr"), pos, pos+len(refseq)) {
931 // The tile intersects one of
932 // the selected regions, but
933 // this particular HGVS
937 hgvsColPair := hgvsCols[hgvsID]
938 if hgvsColPair[0] == nil {
939 // values in new columns start
940 // out as -1 ("no data yet")
941 // or 0 ("=ref") here, may
942 // change to 1 ("hgvs variant
943 // present") below, either on
944 // this line or a future line.
945 hgvsColPair = [2][]int16{make([]int16, len(cmd.cgnames)), make([]int16, len(cmd.cgnames))}
946 rt, ok := reftile[tagID(tag)]
948 err = fmt.Errorf("bug: seeing annotations for tag %d, but it has no reftile entry", tag)
951 for ph := 0; ph < 2; ph++ {
952 for row := 0; row < rows; row++ {
953 v := chunk[row*chunkcols+incol*2+ph]
954 if tileVariantID(v) == rt.variant {
955 hgvsColPair[ph][row] = 0
957 hgvsColPair[ph][row] = -1
961 hgvsCols[hgvsID] = hgvsColPair
963 hgvsref := hgvs.Variant{
968 fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s,%s,%d,%s,%s,%s\n", tag, incol+startcol/2, rt.variant, seqname, hgvsref.String(), seqname, pos, refseq, refseq, fields[8])
972 fmt.Fprintf(annow, "%d,%d,%d,%s,%s,%d,%s,%s,%s\n", tag, incol+startcol/2, tileVariant, hgvsID, seqname, pos, refseq, fields[7], fields[8])
974 for ph := 0; ph < 2; ph++ {
975 for row := 0; row < rows; row++ {
976 v := chunk[row*chunkcols+incol*2+ph]
977 if int(v) == tileVariant {
978 hgvsColPair[ph][row] = 1
984 startcol += chunkcols
995 err = writeNumpyInt16(fmt.Sprintf("%s/matrix.npy", *outputDir), out, rows, cols)
1003 cols = len(hgvsCols) * 2
1004 log.Printf("building hgvs-based matrix: %d rows x %d cols", rows, cols)
1005 out = make([]int16, rows*cols)
1006 hgvsIDs := make([]string, 0, cols/2)
1007 for hgvsID := range hgvsCols {
1008 hgvsIDs = append(hgvsIDs, hgvsID)
1010 sort.Strings(hgvsIDs)
1011 var hgvsLabels bytes.Buffer
1012 for idx, hgvsID := range hgvsIDs {
1013 fmt.Fprintf(&hgvsLabels, "%d,%s\n", idx, hgvsID)
1014 for ph := 0; ph < 2; ph++ {
1015 hgvscol := hgvsCols[hgvsID][ph]
1016 for row, val := range hgvscol {
1017 out[row*cols+idx*2+ph] = val
1021 err = writeNumpyInt16(fmt.Sprintf("%s/hgvs.npy", *outputDir), out, rows, cols)
1026 fnm := fmt.Sprintf("%s/hgvs.annotations.csv", *outputDir)
1027 log.Printf("writing hgvs labels: %s", fnm)
1028 err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0777)
1036 for _, part := range onehotIndirect {
1037 nzCount += len(part[0])
1039 onehot := make([]uint32, nzCount*2) // [r,r,r,...,c,c,c,...]
1040 var xrefs []onehotXref
1041 chunkOffset := uint32(0)
1043 for i, part := range onehotIndirect {
1044 for i := range part[1] {
1045 part[1][i] += chunkOffset
1047 copy(onehot[outcol:], part[0])
1048 copy(onehot[outcol+nzCount:], part[1])
1049 xrefs = append(xrefs, onehotXrefs[i]...)
1051 outcol += len(part[0])
1052 chunkOffset += onehotChunkSize[i]
1056 onehotXrefs[i] = nil
1057 debug.FreeOSMemory()
1059 fnm := fmt.Sprintf("%s/onehot.npy", *outputDir)
1060 err = writeNumpyUint32(fnm, onehot, 2, nzCount)
1064 fnm = fmt.Sprintf("%s/onehot-columns.npy", *outputDir)
1065 err = writeNumpyInt32(fnm, onehotXref2int32(xrefs), 5, len(xrefs))
1070 if !*mergeOutput && !*onehotChunked && !*onehotSingle {
1071 tagoffsetFilename := *outputDir + "/chunk-tag-offset.csv"
1072 log.Infof("writing tag offsets to %s", tagoffsetFilename)
1074 f, err = os.Create(tagoffsetFilename)
1079 for idx, offset := range chunkStartTag {
1080 _, err = fmt.Fprintf(f, "%q,%d\n", fmt.Sprintf("matrix.%04d.npy", idx), offset)
1082 err = fmt.Errorf("write %s: %w", tagoffsetFilename, err)
1088 err = fmt.Errorf("close %s: %w", tagoffsetFilename, err)
1095 // Read case/control files, remove non-case/control entries from
1096 // cmd.cgnames, and build cmd.chi2Cases.
1097 func (cmd *sliceNumpy) useCaseControlFiles() error {
1098 if cmd.chi2CaseControlFile == "" {
1101 infiles, err := allFiles(cmd.chi2CaseControlFile, nil)
1105 // index in cmd.cgnames => case(true) / control(false)
1106 cc := map[int]bool{}
1107 for _, infile := range infiles {
1108 f, err := open(infile)
1112 buf, err := io.ReadAll(f)
1118 for _, tsv := range bytes.Split(buf, []byte{'\n'}) {
1122 split := strings.Split(string(tsv), "\t")
1125 for col, name := range split {
1126 if name == cmd.chi2CaseControlColumn {
1132 return fmt.Errorf("%s: no column named %q in header row %q", infile, cmd.chi2CaseControlColumn, tsv)
1136 if len(split) <= ccCol {
1141 for i, name := range cmd.cgnames {
1142 if strings.Contains(name, pattern) {
1144 log.Warnf("pattern %q in %s matches multiple genome IDs (%qs, %q)", pattern, infile, cmd.cgnames[found], name)
1150 log.Warnf("pattern %q in %s does not match any genome IDs", pattern, infile)
1153 if split[ccCol] == "0" {
1156 if split[ccCol] == "1" {
1161 allnames := cmd.cgnames
1165 for i, name := range allnames {
1166 if cc, ok := cc[i]; ok {
1167 cmd.cgnames = append(cmd.cgnames, name)
1168 cmd.chi2Cases = append(cmd.chi2Cases, cc)
1174 log.Printf("%d cases, %d controls, %d neither (dropped)", ncases, len(cmd.cgnames)-ncases, len(allnames)-len(cmd.cgnames))
1178 func (cmd *sliceNumpy) filterHGVScolpair(colpair [2][]int8) bool {
1179 if cmd.chi2PValue >= 1 {
1182 col0 := make([]bool, 0, len(cmd.chi2Cases))
1183 col1 := make([]bool, 0, len(cmd.chi2Cases))
1184 cases := make([]bool, 0, len(cmd.chi2Cases))
1185 for i, c := range cmd.chi2Cases {
1186 if colpair[0][i] < 0 {
1189 col0 = append(col0, colpair[0][i] != 0)
1190 col1 = append(col1, colpair[1][i] != 0)
1191 cases = append(cases, c)
1193 return len(cases) >= cmd.minCoverage &&
1194 (pvalue(col0, cases) <= cmd.chi2PValue || pvalue(col1, cases) <= cmd.chi2PValue)
1197 func writeNumpyUint32(fnm string, out []uint32, rows, cols int) error {
1198 output, err := os.Create(fnm)
1202 defer output.Close()
1203 bufw := bufio.NewWriterSize(output, 1<<26)
1204 npw, err := gonpy.NewWriter(nopCloser{bufw})
1208 log.WithFields(log.Fields{
1212 "bytes": rows * cols * 4,
1213 }).Infof("writing numpy: %s", fnm)
1214 npw.Shape = []int{rows, cols}
1215 npw.WriteUint32(out)
1220 return output.Close()
1223 func writeNumpyInt32(fnm string, out []int32, rows, cols int) error {
1224 output, err := os.Create(fnm)
1228 defer output.Close()
1229 bufw := bufio.NewWriterSize(output, 1<<26)
1230 npw, err := gonpy.NewWriter(nopCloser{bufw})
1234 log.WithFields(log.Fields{
1238 "bytes": rows * cols * 4,
1239 }).Infof("writing numpy: %s", fnm)
1240 npw.Shape = []int{rows, cols}
1246 return output.Close()
1249 func writeNumpyInt16(fnm string, out []int16, rows, cols int) error {
1250 output, err := os.Create(fnm)
1254 defer output.Close()
1255 bufw := bufio.NewWriterSize(output, 1<<26)
1256 npw, err := gonpy.NewWriter(nopCloser{bufw})
1260 log.WithFields(log.Fields{
1264 "bytes": rows * cols * 2,
1265 }).Infof("writing numpy: %s", fnm)
1266 npw.Shape = []int{rows, cols}
1272 return output.Close()
1275 func writeNumpyInt8(fnm string, out []int8, rows, cols int) error {
1276 output, err := os.Create(fnm)
1280 defer output.Close()
1281 bufw := bufio.NewWriterSize(output, 1<<26)
1282 npw, err := gonpy.NewWriter(nopCloser{bufw})
1286 log.WithFields(log.Fields{
1290 "bytes": rows * cols,
1291 }).Infof("writing numpy: %s", fnm)
1292 npw.Shape = []int{rows, cols}
1298 return output.Close()
1301 func allele2homhet(colpair [2][]int8) {
1302 a, b := colpair[0], colpair[1]
1303 for i, av := range a {
1305 if av < 0 || bv < 0 {
1308 } else if av > 0 && bv > 0 {
1311 } else if av > 0 || bv > 0 {
1315 // ref (or a different variant in same position)
1316 // (this is a no-op) a[i], b[i] = 0, 0
1321 type onehotXref struct {
1323 variant tileVariantID
1328 const onehotXrefSize = unsafe.Sizeof(onehotXref{})
1330 // Build onehot matrix (m[tileVariantIndex][genome] == 0 or 1) for all
1331 // variants of a single tile/tag#.
1333 // Return nil if no tile variant passes Χ² filter.
1334 func (cmd *sliceNumpy) tv2homhet(cgs map[string]CompactGenome, maxv tileVariantID, remap []tileVariantID, tag, chunkstarttag tagID, seq map[tagID][]TileVariant) ([][]int8, []onehotXref) {
1335 if tag == cmd.debugTag {
1336 tv := make([]tileVariantID, len(cmd.cgnames)*2)
1337 for i, name := range cmd.cgnames {
1338 copy(tv[i*2:(i+1)*2], cgs[name].Variants[(tag-chunkstarttag)*2:])
1340 log.WithFields(logrus.Fields{
1341 "cgs[i].Variants[tag*2+j]": tv,
1345 "chunkstarttag": chunkstarttag,
1346 }).Info("tv2homhet()")
1348 if maxv < 1 || (maxv < 2 && !cmd.includeVariant1) {
1349 // everyone has the most common variant (of the variants we don't drop)
1352 tagoffset := tag - chunkstarttag
1354 for _, cg := range cgs {
1356 for _, v := range cg.Variants[tagoffset*2 : tagoffset*2+2] {
1357 if v > 0 && int(v) < len(seq[tag]) && len(seq[tag][v].Sequence) > 0 {
1365 if coverage < cmd.minCoverage {
1368 obs := make([][]bool, (maxv+1)*2) // 2 slices (hom + het) for each variant#
1369 for i := range obs {
1370 obs[i] = make([]bool, len(cmd.cgnames))
1372 for cgid, name := range cmd.cgnames {
1373 cgvars := cgs[name].Variants[tagoffset*2:]
1374 tv0, tv1 := remap[cgvars[0]], remap[cgvars[1]]
1375 for v := tileVariantID(1); v <= maxv; v++ {
1376 if tv0 == v && tv1 == v {
1377 obs[v*2][cgid] = true
1378 } else if tv0 == v || tv1 == v {
1379 obs[v*2+1][cgid] = true
1384 var xref []onehotXref
1385 for col := 2; col < len(obs); col++ {
1386 // col 0,1 correspond to tile variant 0, i.e.,
1387 // no-call; col 2,3 correspond to the most common
1388 // variant; so we (normally) start at col 4.
1389 if col < 4 && !cmd.includeVariant1 {
1392 p := pvalue(obs[col], cmd.chi2Cases)
1393 if cmd.chi2PValue < 1 && !(p < cmd.chi2PValue) {
1396 onehot = append(onehot, bool2int8(obs[col]))
1397 xref = append(xref, onehotXref{
1399 variant: tileVariantID(col >> 1),
1407 func bool2int8(in []bool) []int8 {
1408 out := make([]int8, len(in))
1409 for i, v := range in {
1417 // convert a []onehotXref with length N to a numpy-style []int32
1418 // matrix with N columns, one row per field of onehotXref struct.
1420 // Hom/het row contains hom=0, het=1.
1422 // P-value row contains 1000000x actual p-value.
1423 func onehotXref2int32(xrefs []onehotXref) []int32 {
1425 xdata := make([]int32, 5*xcols)
1426 for i, xref := range xrefs {
1427 xdata[i] = int32(xref.tag)
1428 xdata[xcols+i] = int32(xref.variant)
1430 xdata[xcols*2+i] = 1
1432 xdata[xcols*3+i] = int32(xref.pvalue * 1000000)
1433 xdata[xcols*4+i] = int32(-math.Log10(xref.pvalue) * 1000000)
1438 // transpose onehot data from in[col][row] to numpy-style
1439 // out[row*cols+col].
1440 func onehotcols2int8(in [][]int8) []int8 {
1446 out := make([]int8, rows*cols)
1447 for row := 0; row < rows; row++ {
1448 outrow := out[row*cols:]
1449 for col, incol := range in {
1450 outrow[col] = incol[row]
1456 // Return [2][]uint32{rowIndices, colIndices} indicating which
1457 // elements of matrixT[c][r] have non-zero values.
1458 func onehotChunk2Indirect(matrixT [][]int8) [2][]uint32 {
1460 for c, col := range matrixT {
1461 for r, val := range col {
1463 nz[0] = append(nz[0], uint32(r))
1464 nz[1] = append(nz[1], uint32(c))