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 onlyPCA := flags.Bool("pca", false, "generate pca matrix")
76 debugTag := flags.Int("debug-tag", -1, "log debugging details about specified tag")
77 flags.IntVar(&cmd.threads, "threads", 16, "number of memory-hungry assembly threads")
78 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)")
79 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)")
80 flags.Float64Var(&cmd.chi2PValue, "chi2-p-value", 1, "do Χ² test and omit columns with p-value above this threshold")
81 flags.BoolVar(&cmd.includeVariant1, "include-variant-1", false, "include most common variant when building one-hot matrix")
82 cmd.filter.Flags(flags)
83 err = flags.Parse(args)
84 if err == flag.ErrHelp {
87 } else if err != nil {
93 log.Println(http.ListenAndServe(*pprof, nil))
97 if cmd.chi2PValue != 1 && (cmd.chi2CaseControlFile == "" || cmd.chi2CaseControlColumn == "") {
98 log.Errorf("cannot use provided -chi2-p-value=%f because -chi2-case-control-file= or -chi2-case-control-column= value is empty", cmd.chi2PValue)
102 cmd.debugTag = tagID(*debugTag)
105 runner := arvadosContainerRunner{
106 Name: "lightning slice-numpy",
107 Client: arvados.NewClientFromEnv(),
108 ProjectUUID: *projectUUID,
115 err = runner.TranslatePaths(inputDir, regionsFilename, &cmd.chi2CaseControlFile)
119 runner.Args = []string{"slice-numpy", "-local=true",
121 "-input-dir=" + *inputDir,
122 "-output-dir=/mnt/output",
123 "-threads=" + fmt.Sprintf("%d", cmd.threads),
124 "-regions=" + *regionsFilename,
125 "-expand-regions=" + fmt.Sprintf("%d", *expandRegions),
126 "-merge-output=" + fmt.Sprintf("%v", *mergeOutput),
127 "-single-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsSingle),
128 "-chunked-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsChunked),
129 "-single-onehot=" + fmt.Sprintf("%v", *onehotSingle),
130 "-chunked-onehot=" + fmt.Sprintf("%v", *onehotChunked),
131 "-pca=" + fmt.Sprintf("%v", *onlyPCA),
132 "-chi2-case-control-file=" + cmd.chi2CaseControlFile,
133 "-chi2-case-control-column=" + cmd.chi2CaseControlColumn,
134 "-chi2-p-value=" + fmt.Sprintf("%f", cmd.chi2PValue),
135 "-include-variant-1=" + fmt.Sprintf("%v", cmd.includeVariant1),
136 "-debug-tag=" + fmt.Sprintf("%d", cmd.debugTag),
138 runner.Args = append(runner.Args, cmd.filter.Args()...)
140 output, err = runner.Run()
144 fmt.Fprintln(stdout, output)
148 infiles, err := allFiles(*inputDir, matchGobFile)
152 if len(infiles) == 0 {
153 err = fmt.Errorf("no input files found in %s", *inputDir)
156 sort.Strings(infiles)
158 var refseq map[string][]tileLibRef
159 var reftiledata = make(map[tileLibRef][]byte, 11000000)
160 in0, err := open(infiles[0])
165 matchGenome, err := regexp.Compile(cmd.filter.MatchGenome)
167 err = fmt.Errorf("-match-genome: invalid regexp: %q", cmd.filter.MatchGenome)
173 err = DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
174 if len(ent.TagSet) > 0 {
177 for _, cseq := range ent.CompactSequences {
178 if cseq.Name == *ref || *ref == "" {
179 refseq = cseq.TileSequences
182 for _, cg := range ent.CompactGenomes {
183 if matchGenome.MatchString(cg.Name) {
184 cmd.cgnames = append(cmd.cgnames, cg.Name)
187 for _, tv := range ent.TileVariants {
189 reftiledata[tileLibRef{tv.Tag, tv.Variant}] = tv.Sequence
199 err = fmt.Errorf("%s: reference sequence not found", infiles[0])
202 if len(tagset) == 0 {
203 err = fmt.Errorf("tagset not found")
207 taglib := &tagLibrary{}
208 err = taglib.setTags(tagset)
212 taglen := taglib.TagLen()
214 if len(cmd.cgnames) == 0 {
215 err = fmt.Errorf("no genomes found matching regexp %q", cmd.filter.MatchGenome)
218 sort.Strings(cmd.cgnames)
219 err = cmd.useCaseControlFiles()
223 if len(cmd.cgnames) == 0 {
224 err = fmt.Errorf("fatal: 0 cases, 0 controls, nothing to do")
227 if cmd.filter.MinCoverage == 1 {
228 // In the generic formula below, floating point
229 // arithmetic can effectively push the coverage
230 // threshold above 1.0, which is impossible/useless.
231 // 1.0 needs to mean exactly 100% coverage.
232 cmd.minCoverage = len(cmd.cgnames)
234 cmd.minCoverage = int(math.Ceil(cmd.filter.MinCoverage * float64(len(cmd.cgnames))))
238 labelsFilename := *outputDir + "/samples.csv"
239 log.Infof("writing labels to %s", labelsFilename)
241 f, err = os.Create(labelsFilename)
246 for i, name := range cmd.cgnames {
248 if cmd.chi2Cases != nil && cmd.chi2Cases[i] {
251 _, err = fmt.Fprintf(f, "%d,%q,%d\n", i, trimFilenameForLabel(name), cc)
253 err = fmt.Errorf("write %s: %w", labelsFilename, err)
259 err = fmt.Errorf("close %s: %w", labelsFilename, err)
264 log.Info("indexing reference tiles")
265 type reftileinfo struct {
266 variant tileVariantID
267 seqname string // chr1
268 pos int // distance from start of chromosome to starttag
269 tiledata []byte // acgtggcaa...
270 excluded bool // true if excluded by regions file
271 nexttag tagID // tagID of following tile (-1 for last tag of chromosome)
273 isdup := map[tagID]bool{}
274 reftile := map[tagID]*reftileinfo{}
275 for seqname, cseq := range refseq {
277 lastreftag := tagID(-1)
278 for _, libref := range cseq {
279 if cmd.filter.MaxTag >= 0 && libref.Tag > tagID(cmd.filter.MaxTag) {
282 tiledata := reftiledata[libref]
283 if len(tiledata) == 0 {
284 err = fmt.Errorf("missing tiledata for tag %d variant %d in %s in ref", libref.Tag, libref.Variant, seqname)
287 foundthistag := false
288 taglib.FindAll(tiledata[:len(tiledata)-1], func(tagid tagID, offset, _ int) {
289 if !foundthistag && tagid == libref.Tag {
293 if dupref, ok := reftile[tagid]; ok {
294 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)
295 delete(reftile, tagid)
297 log.Printf("found tag %d at offset %d inside tile variant %+v on %s @ %d", tagid, offset, libref, seqname, pos+offset+1)
301 if isdup[libref.Tag] {
302 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
303 } else if reftile[libref.Tag] != nil {
304 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)
305 delete(reftile, libref.Tag)
306 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
307 isdup[libref.Tag] = true
309 reftile[libref.Tag] = &reftileinfo{
311 variant: libref.Variant,
317 reftile[lastreftag].nexttag = libref.Tag
319 lastreftag = libref.Tag
321 pos += len(tiledata) - taglen
323 log.Printf("... %s done, len %d", seqname, pos+taglen)
327 if *regionsFilename != "" {
328 log.Printf("loading regions from %s", *regionsFilename)
329 mask, err = makeMask(*regionsFilename, *expandRegions)
333 log.Printf("before applying mask, len(reftile) == %d", len(reftile))
334 log.Printf("deleting reftile entries for regions outside %d intervals", mask.Len())
335 for _, rt := range reftile {
336 if !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(rt.tiledata)) {
340 log.Printf("after applying mask, len(reftile) == %d", len(reftile))
343 type hgvsColSet map[hgvs.Variant][2][]int8
344 encodeHGVS := throttle{Max: len(refseq)}
345 encodeHGVSTodo := map[string]chan hgvsColSet{}
346 tmpHGVSCols := map[string]*os.File{}
348 for seqname := range refseq {
350 f, err = os.Create(*outputDir + "/tmp." + seqname + ".gob")
354 defer os.Remove(f.Name())
355 bufw := bufio.NewWriterSize(f, 1<<24)
356 enc := gob.NewEncoder(bufw)
357 tmpHGVSCols[seqname] = f
358 todo := make(chan hgvsColSet, 128)
359 encodeHGVSTodo[seqname] = todo
360 encodeHGVS.Go(func() error {
361 for colset := range todo {
362 err := enc.Encode(colset)
364 encodeHGVS.Report(err)
375 var toMerge [][]int16
376 if *mergeOutput || *hgvsSingle {
377 toMerge = make([][]int16, len(infiles))
379 var onehotIndirect [][2][]uint32 // [chunkIndex][axis][index]
380 var onehotChunkSize []uint32
381 var onehotXrefs [][]onehotXref
382 if *onehotSingle || *onlyPCA {
383 onehotIndirect = make([][2][]uint32, len(infiles))
384 onehotChunkSize = make([]uint32, len(infiles))
385 onehotXrefs = make([][]onehotXref, len(infiles))
387 chunkStartTag := make([]tagID, len(infiles))
389 throttleMem := throttle{Max: cmd.threads} // TODO: estimate using mem and data size
390 throttleNumpyMem := throttle{Max: cmd.threads/2 + 1}
391 log.Info("generating annotations and numpy matrix for each slice")
392 var errSkip = errors.New("skip infile")
394 for infileIdx, infile := range infiles {
395 infileIdx, infile := infileIdx, infile
396 throttleMem.Go(func() error {
397 seq := make(map[tagID][]TileVariant, 50000)
398 cgs := make(map[string]CompactGenome, len(cmd.cgnames))
399 f, err := open(infile)
404 log.Infof("%04d: reading %s", infileIdx, infile)
405 err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
406 for _, tv := range ent.TileVariants {
411 // corresponding ref tile, if
412 // mask is in play (we can't
413 // determine coordinates for
415 if mask != nil && reftile[tv.Tag] == nil {
419 // corresponding ref tile is
420 // outside target regions --
421 // unless it's a potential
423 if mask != nil && reftile[tv.Tag].excluded &&
424 (int(tv.Tag+1) >= len(tagset) ||
425 (bytes.HasSuffix(tv.Sequence, tagset[tv.Tag+1]) && reftile[tv.Tag+1] != nil && !reftile[tv.Tag+1].excluded)) {
428 if tv.Tag == cmd.debugTag {
429 log.Printf("infile %d %s tag %d variant %d hash %x", infileIdx, infile, tv.Tag, tv.Variant, tv.Blake2b[:3])
431 variants := seq[tv.Tag]
432 if len(variants) == 0 {
433 variants = make([]TileVariant, 100)
435 for len(variants) <= int(tv.Variant) {
436 variants = append(variants, TileVariant{})
438 variants[int(tv.Variant)] = tv
439 seq[tv.Tag] = variants
441 for _, cg := range ent.CompactGenomes {
442 if cmd.filter.MaxTag >= 0 && cg.StartTag > tagID(cmd.filter.MaxTag) {
445 if !matchGenome.MatchString(cg.Name) {
448 // pad to full slice size
449 // to avoid out-of-bounds
451 if sliceSize := 2 * int(cg.EndTag-cg.StartTag); len(cg.Variants) < sliceSize {
452 cg.Variants = append(cg.Variants, make([]tileVariantID, sliceSize-len(cg.Variants))...)
460 } else if err != nil {
463 tagstart := cgs[cmd.cgnames[0]].StartTag
464 tagend := cgs[cmd.cgnames[0]].EndTag
465 chunkStartTag[infileIdx] = tagstart
469 log.Infof("%04d: renumber/dedup variants for tags %d-%d", infileIdx, tagstart, tagend)
470 variantRemap := make([][]tileVariantID, tagend-tagstart)
471 throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
472 for tag, variants := range seq {
473 tag, variants := tag, variants
474 throttleCPU.Go(func() error {
476 count := make(map[[blake2b.Size256]byte]int, len(variants))
480 count[blake2b.Sum256(rt.tiledata)] = 0
483 for cgname, cg := range cgs {
484 idx := int(tag-tagstart) * 2
485 for allele := 0; allele < 2; allele++ {
486 v := cg.Variants[idx+allele]
487 if v > 0 && len(variants[v].Sequence) > 0 {
488 count[variants[v].Blake2b]++
491 if v > 0 && tag == cmd.debugTag {
492 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])
496 if alleleCoverage < cmd.minCoverage*2 {
497 idx := int(tag-tagstart) * 2
498 for _, cg := range cgs {
500 cg.Variants[idx+1] = 0
502 if tag == cmd.debugTag {
503 log.Printf("tag %d alleleCoverage %d < min %d, sample data wiped", tag, alleleCoverage, cmd.minCoverage*2)
508 // hash[i] will be the hash of
509 // the variant(s) that should
510 // be at rank i (0-based).
511 hash := make([][blake2b.Size256]byte, 0, len(count))
512 for b := range count {
513 hash = append(hash, b)
515 sort.Slice(hash, func(i, j int) bool {
516 bi, bj := &hash[i], &hash[j]
517 if ci, cj := count[*bi], count[*bj]; ci != cj {
520 return bytes.Compare((*bi)[:], (*bj)[:]) < 0
523 // rank[b] will be the 1-based
524 // new variant number for
525 // variants whose hash is b.
526 rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
527 for i, h := range hash {
528 rank[h] = tileVariantID(i + 1)
530 if tag == cmd.debugTag {
531 for h, r := range rank {
532 log.Printf("tag %d rank(%x) = %v", tag, h[:3], r)
535 // remap[v] will be the new
536 // variant number for original
538 remap := make([]tileVariantID, len(variants))
539 for i, tv := range variants {
540 remap[i] = rank[tv.Blake2b]
542 if tag == cmd.debugTag {
543 for in, out := range remap {
545 log.Printf("tag %d remap %d => %d", tag, in, out)
549 variantRemap[tag-tagstart] = remap
551 refrank := rank[blake2b.Sum256(rt.tiledata)]
552 if tag == cmd.debugTag {
553 log.Printf("tag %d reftile variant %d => %d", tag, rt.variant, refrank)
562 var onehotChunk [][]int8
563 var onehotXref []onehotXref
565 var annotationsFilename string
567 annotationsFilename = "/dev/null"
569 annotationsFilename = fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
570 log.Infof("%04d: writing %s", infileIdx, annotationsFilename)
572 annof, err := os.Create(annotationsFilename)
576 annow := bufio.NewWriterSize(annof, 1<<20)
578 for tag := tagstart; tag < tagend; tag++ {
580 if rt == nil && mask != nil {
581 // With no ref tile, we don't
582 // have coordinates to say
583 // this is in the desired
584 // regions -- so it's not.
585 // TODO: handle ref spanning
589 if rt != nil && rt.excluded {
590 // TODO: don't skip yet --
591 // first check for spanning
592 // tile variants that
593 // intersect non-excluded ref
597 if cmd.filter.MaxTag >= 0 && tag > tagID(cmd.filter.MaxTag) {
600 remap := variantRemap[tag-tagstart]
601 maxv := tileVariantID(0)
602 for _, v := range remap {
607 if *onehotChunked || *onehotSingle || *onlyPCA {
608 onehot, xrefs := cmd.tv2homhet(cgs, maxv, remap, tag, tagstart, seq)
609 if tag == cmd.debugTag {
610 log.WithFields(logrus.Fields{
613 }).Info("tv2homhet()")
615 onehotChunk = append(onehotChunk, onehot...)
616 onehotXref = append(onehotXref, xrefs...)
623 // Reference does not use any
624 // variant of this tile
626 // TODO: diff against the
627 // relevant portion of the
628 // ref's spanning tile
632 fmt.Fprintf(annow, "%d,%d,%d,=,%s,%d,,,\n", tag, outcol, rt.variant, rt.seqname, rt.pos)
634 reftilestr := strings.ToUpper(string(rt.tiledata))
636 done := make([]bool, maxv+1)
637 variantDiffs := make([][]hgvs.Variant, maxv+1)
638 for v, tv := range variants {
640 if v == 0 || v == rt.variant || done[v] {
645 if len(tv.Sequence) < taglen {
648 // if reftilestr doesn't end
649 // in the same tag as tv,
650 // extend reftilestr with
651 // following ref tiles until
652 // it does (up to an arbitrary
653 // sanity-check limit)
654 reftilestr := reftilestr
655 endtagstr := strings.ToUpper(string(tv.Sequence[len(tv.Sequence)-taglen:]))
656 for i, rt := 0, rt; i < annotationMaxTileSpan && !strings.HasSuffix(reftilestr, endtagstr) && rt.nexttag >= 0; i++ {
657 rt = reftile[rt.nexttag]
661 reftilestr += strings.ToUpper(string(rt.tiledata[taglen:]))
663 if mask != nil && !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(reftilestr)) {
666 if !strings.HasSuffix(reftilestr, endtagstr) {
667 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
670 if lendiff := len(reftilestr) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
671 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
674 diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
675 for i := range diffs {
676 diffs[i].Position += rt.pos
678 for _, diff := range diffs {
679 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)
682 variantDiffs[v] = diffs
686 // We can now determine, for each HGVS
687 // variant (diff) in this reftile
688 // region, whether a given genome
689 // phase/allele (1) has the variant, (0) has
690 // =ref or a different variant in that
691 // position, or (-1) is lacking
692 // coverage / couldn't be diffed.
693 hgvsCol := hgvsColSet{}
694 for _, diffs := range variantDiffs {
695 for _, diff := range diffs {
696 if _, ok := hgvsCol[diff]; ok {
699 hgvsCol[diff] = [2][]int8{
700 make([]int8, len(cmd.cgnames)),
701 make([]int8, len(cmd.cgnames)),
705 for row, name := range cmd.cgnames {
706 variants := cgs[name].Variants[(tag-tagstart)*2:]
707 for ph := 0; ph < 2; ph++ {
709 if int(v) >= len(remap) {
715 // hgvsCol[*][ph][row] is already 0
716 } else if len(variantDiffs[v]) == 0 {
717 // lacking coverage / couldn't be diffed
718 for _, col := range hgvsCol {
722 for _, diff := range variantDiffs[v] {
723 hgvsCol[diff][ph][row] = 1
728 for diff, colpair := range hgvsCol {
729 allele2homhet(colpair)
730 if !cmd.filterHGVScolpair(colpair) {
731 delete(hgvsCol, diff)
734 if len(hgvsCol) > 0 {
735 encodeHGVSTodo[rt.seqname] <- hgvsCol
750 // transpose onehotChunk[col][row] to numpy[row*ncols+col]
751 rows := len(cmd.cgnames)
752 cols := len(onehotChunk)
753 log.Infof("%04d: preparing onehot numpy (rows=%d, cols=%d, mem=%d)", infileIdx, rows, cols, rows*cols)
754 throttleNumpyMem.Acquire()
755 out := onehotcols2int8(onehotChunk)
756 fnm := fmt.Sprintf("%s/onehot.%04d.npy", *outputDir, infileIdx)
757 err = writeNumpyInt8(fnm, out, rows, cols)
761 fnm = fmt.Sprintf("%s/onehot-columns.%04d.npy", *outputDir, infileIdx)
762 err = writeNumpyInt32(fnm, onehotXref2int32(onehotXref), 4, len(onehotXref))
767 throttleNumpyMem.Release()
769 if *onehotSingle || *onlyPCA {
770 onehotIndirect[infileIdx] = onehotChunk2Indirect(onehotChunk)
771 onehotChunkSize[infileIdx] = uint32(len(onehotChunk))
772 onehotXrefs[infileIdx] = onehotXref
773 n := len(onehotIndirect[infileIdx][0])
774 log.Infof("%04d: keeping onehot coordinates in memory (n=%d, mem=%d)", infileIdx, n, n*8*2)
776 if !(*onehotSingle || *onehotChunked || *onlyPCA) || *mergeOutput || *hgvsSingle {
777 log.Infof("%04d: preparing numpy (rows=%d, cols=%d)", infileIdx, len(cmd.cgnames), 2*outcol)
778 throttleNumpyMem.Acquire()
779 rows := len(cmd.cgnames)
781 out := make([]int16, rows*cols)
782 for row, name := range cmd.cgnames {
784 for col, v := range cgs[name].Variants {
785 tag := tagstart + tagID(col/2)
786 if cmd.filter.MaxTag >= 0 && tag > tagID(cmd.filter.MaxTag) {
789 if rt := reftile[tag]; rt == nil || rt.excluded {
793 out[outidx] = 0 // tag not found / spanning tile
794 } else if variants, ok := seq[tag]; ok && int(v) < len(variants) && len(variants[v].Sequence) > 0 {
795 out[outidx] = int16(variantRemap[tag-tagstart][v])
797 out[outidx] = -1 // low quality tile variant
799 if tag == cmd.debugTag {
800 log.Printf("tag %d row %d col %d outidx %d v %d out %d", tag, row, col, outidx, v, out[outidx])
808 throttleNumpyMem.Release()
809 if *mergeOutput || *hgvsSingle {
810 log.Infof("%04d: matrix fragment %d rows x %d cols", infileIdx, rows, cols)
811 toMerge[infileIdx] = out
813 if !*mergeOutput && !*onehotChunked && !*onehotSingle {
814 fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
815 err = writeNumpyInt16(fnm, out, rows, cols)
822 log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
826 if err = throttleMem.Wait(); err != nil {
831 log.Info("flushing hgvsCols temp files")
832 for seqname := range refseq {
833 close(encodeHGVSTodo[seqname])
835 err = encodeHGVS.Wait()
839 for seqname := range refseq {
840 log.Infof("%s: reading hgvsCols from temp file", seqname)
841 f := tmpHGVSCols[seqname]
842 _, err = f.Seek(0, io.SeekStart)
846 var hgvsCols hgvsColSet
847 dec := gob.NewDecoder(bufio.NewReaderSize(f, 1<<24))
849 err = dec.Decode(&hgvsCols)
854 log.Infof("%s: sorting %d hgvs variants", seqname, len(hgvsCols))
855 variants := make([]hgvs.Variant, 0, len(hgvsCols))
856 for v := range hgvsCols {
857 variants = append(variants, v)
859 sort.Slice(variants, func(i, j int) bool {
860 vi, vj := &variants[i], &variants[j]
861 if vi.Position != vj.Position {
862 return vi.Position < vj.Position
863 } else if vi.Ref != vj.Ref {
864 return vi.Ref < vj.Ref
866 return vi.New < vj.New
869 rows := len(cmd.cgnames)
870 cols := len(variants) * 2
871 log.Infof("%s: building hgvs matrix (rows=%d, cols=%d, mem=%d)", seqname, rows, cols, rows*cols)
872 out := make([]int8, rows*cols)
873 for varIdx, variant := range variants {
874 hgvsCols := hgvsCols[variant]
875 for row := range cmd.cgnames {
876 for ph := 0; ph < 2; ph++ {
877 out[row*cols+varIdx+ph] = hgvsCols[ph][row]
881 err = writeNumpyInt8(fmt.Sprintf("%s/hgvs.%s.npy", *outputDir, seqname), out, rows, cols)
887 fnm := fmt.Sprintf("%s/hgvs.%s.annotations.csv", *outputDir, seqname)
888 log.Infof("%s: writing hgvs column labels to %s", seqname, fnm)
889 var hgvsLabels bytes.Buffer
890 for varIdx, variant := range variants {
891 fmt.Fprintf(&hgvsLabels, "%d,%s:g.%s\n", varIdx, seqname, variant.String())
893 err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0666)
900 if *mergeOutput || *hgvsSingle {
901 var annow *bufio.Writer
904 annoFilename := fmt.Sprintf("%s/matrix.annotations.csv", *outputDir)
905 annof, err = os.Create(annoFilename)
909 annow = bufio.NewWriterSize(annof, 1<<20)
912 rows := len(cmd.cgnames)
914 for _, chunk := range toMerge {
915 cols += len(chunk) / rows
917 log.Infof("merging output matrix (rows=%d, cols=%d, mem=%d) and annotations", rows, cols, rows*cols*2)
920 out = make([]int16, rows*cols)
922 hgvsCols := map[string][2][]int16{} // hgvs -> [[g0,g1,g2,...], [g0,g1,g2,...]] (slice of genomes for each phase)
924 for outIdx, chunk := range toMerge {
925 chunkcols := len(chunk) / rows
927 for row := 0; row < rows; row++ {
928 copy(out[row*cols+startcol:], chunk[row*chunkcols:(row+1)*chunkcols])
931 toMerge[outIdx] = nil
933 annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, outIdx)
934 log.Infof("reading %s", annotationsFilename)
935 buf, err := os.ReadFile(annotationsFilename)
940 err = os.Remove(annotationsFilename)
945 for _, line := range bytes.Split(buf, []byte{'\n'}) {
949 fields := bytes.SplitN(line, []byte{','}, 9)
950 tag, _ := strconv.Atoi(string(fields[0]))
951 incol, _ := strconv.Atoi(string(fields[1]))
952 tileVariant, _ := strconv.Atoi(string(fields[2]))
953 hgvsID := string(fields[3])
954 seqname := string(fields[4])
955 pos, _ := strconv.Atoi(string(fields[5]))
958 // Null entry for un-diffable
963 // Null entry for ref tile
966 if mask != nil && !mask.Check(strings.TrimPrefix(seqname, "chr"), pos, pos+len(refseq)) {
967 // The tile intersects one of
968 // the selected regions, but
969 // this particular HGVS
973 hgvsColPair := hgvsCols[hgvsID]
974 if hgvsColPair[0] == nil {
975 // values in new columns start
976 // out as -1 ("no data yet")
977 // or 0 ("=ref") here, may
978 // change to 1 ("hgvs variant
979 // present") below, either on
980 // this line or a future line.
981 hgvsColPair = [2][]int16{make([]int16, len(cmd.cgnames)), make([]int16, len(cmd.cgnames))}
982 rt, ok := reftile[tagID(tag)]
984 err = fmt.Errorf("bug: seeing annotations for tag %d, but it has no reftile entry", tag)
987 for ph := 0; ph < 2; ph++ {
988 for row := 0; row < rows; row++ {
989 v := chunk[row*chunkcols+incol*2+ph]
990 if tileVariantID(v) == rt.variant {
991 hgvsColPair[ph][row] = 0
993 hgvsColPair[ph][row] = -1
997 hgvsCols[hgvsID] = hgvsColPair
999 hgvsref := hgvs.Variant{
1001 Ref: string(refseq),
1002 New: string(refseq),
1004 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])
1008 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])
1010 for ph := 0; ph < 2; ph++ {
1011 for row := 0; row < rows; row++ {
1012 v := chunk[row*chunkcols+incol*2+ph]
1013 if int(v) == tileVariant {
1014 hgvsColPair[ph][row] = 1
1020 startcol += chunkcols
1031 err = writeNumpyInt16(fmt.Sprintf("%s/matrix.npy", *outputDir), out, rows, cols)
1039 cols = len(hgvsCols) * 2
1040 log.Printf("building hgvs-based matrix: %d rows x %d cols", rows, cols)
1041 out = make([]int16, rows*cols)
1042 hgvsIDs := make([]string, 0, cols/2)
1043 for hgvsID := range hgvsCols {
1044 hgvsIDs = append(hgvsIDs, hgvsID)
1046 sort.Strings(hgvsIDs)
1047 var hgvsLabels bytes.Buffer
1048 for idx, hgvsID := range hgvsIDs {
1049 fmt.Fprintf(&hgvsLabels, "%d,%s\n", idx, hgvsID)
1050 for ph := 0; ph < 2; ph++ {
1051 hgvscol := hgvsCols[hgvsID][ph]
1052 for row, val := range hgvscol {
1053 out[row*cols+idx*2+ph] = val
1057 err = writeNumpyInt16(fmt.Sprintf("%s/hgvs.npy", *outputDir), out, rows, cols)
1062 fnm := fmt.Sprintf("%s/hgvs.annotations.csv", *outputDir)
1063 log.Printf("writing hgvs labels: %s", fnm)
1064 err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0777)
1072 for _, part := range onehotIndirect {
1073 nzCount += len(part[0])
1075 onehot := make([]uint32, nzCount*2) // [r,r,r,...,c,c,c,...]
1076 var xrefs []onehotXref
1077 chunkOffset := uint32(0)
1079 for i, part := range onehotIndirect {
1080 for i := range part[1] {
1081 part[1][i] += chunkOffset
1083 copy(onehot[outcol:], part[0])
1084 copy(onehot[outcol+nzCount:], part[1])
1085 xrefs = append(xrefs, onehotXrefs[i]...)
1087 outcol += len(part[0])
1088 chunkOffset += onehotChunkSize[i]
1092 onehotXrefs[i] = nil
1093 debug.FreeOSMemory()
1095 fnm := fmt.Sprintf("%s/onehot.npy", *outputDir)
1096 err = writeNumpyUint32(fnm, onehot, 2, nzCount)
1100 fnm = fmt.Sprintf("%s/onehot-columns.npy", *outputDir)
1101 err = writeNumpyInt32(fnm, onehotXref2int32(xrefs), 5, len(xrefs))
1109 if !*mergeOutput && !*onehotChunked && !*onehotSingle && !*onlyPCA {
1110 tagoffsetFilename := *outputDir + "/chunk-tag-offset.csv"
1111 log.Infof("writing tag offsets to %s", tagoffsetFilename)
1113 f, err = os.Create(tagoffsetFilename)
1118 for idx, offset := range chunkStartTag {
1119 _, err = fmt.Fprintf(f, "%q,%d\n", fmt.Sprintf("matrix.%04d.npy", idx), offset)
1121 err = fmt.Errorf("write %s: %w", tagoffsetFilename, err)
1127 err = fmt.Errorf("close %s: %w", tagoffsetFilename, err)
1134 // Read case/control files, remove non-case/control entries from
1135 // cmd.cgnames, and build cmd.chi2Cases.
1136 func (cmd *sliceNumpy) useCaseControlFiles() error {
1137 if cmd.chi2CaseControlFile == "" {
1140 infiles, err := allFiles(cmd.chi2CaseControlFile, nil)
1144 // index in cmd.cgnames => case(true) / control(false)
1145 cc := map[int]bool{}
1146 for _, infile := range infiles {
1147 f, err := open(infile)
1151 buf, err := io.ReadAll(f)
1157 for _, tsv := range bytes.Split(buf, []byte{'\n'}) {
1161 split := strings.Split(string(tsv), "\t")
1164 for col, name := range split {
1165 if name == cmd.chi2CaseControlColumn {
1171 return fmt.Errorf("%s: no column named %q in header row %q", infile, cmd.chi2CaseControlColumn, tsv)
1175 if len(split) <= ccCol {
1180 for i, name := range cmd.cgnames {
1181 if strings.Contains(name, pattern) {
1183 log.Warnf("pattern %q in %s matches multiple genome IDs (%qs, %q)", pattern, infile, cmd.cgnames[found], name)
1189 log.Warnf("pattern %q in %s does not match any genome IDs", pattern, infile)
1192 if split[ccCol] == "0" {
1195 if split[ccCol] == "1" {
1200 allnames := cmd.cgnames
1204 for i, name := range allnames {
1205 if cc, ok := cc[i]; ok {
1206 cmd.cgnames = append(cmd.cgnames, name)
1207 cmd.chi2Cases = append(cmd.chi2Cases, cc)
1213 log.Printf("%d cases, %d controls, %d neither (dropped)", ncases, len(cmd.cgnames)-ncases, len(allnames)-len(cmd.cgnames))
1217 func (cmd *sliceNumpy) filterHGVScolpair(colpair [2][]int8) bool {
1218 if cmd.chi2PValue >= 1 {
1221 col0 := make([]bool, 0, len(cmd.chi2Cases))
1222 col1 := make([]bool, 0, len(cmd.chi2Cases))
1223 cases := make([]bool, 0, len(cmd.chi2Cases))
1224 for i, c := range cmd.chi2Cases {
1225 if colpair[0][i] < 0 {
1228 col0 = append(col0, colpair[0][i] != 0)
1229 col1 = append(col1, colpair[1][i] != 0)
1230 cases = append(cases, c)
1232 return len(cases) >= cmd.minCoverage &&
1233 (pvalue(col0, cases) <= cmd.chi2PValue || pvalue(col1, cases) <= cmd.chi2PValue)
1236 func writeNumpyUint32(fnm string, out []uint32, rows, cols int) error {
1237 output, err := os.Create(fnm)
1241 defer output.Close()
1242 bufw := bufio.NewWriterSize(output, 1<<26)
1243 npw, err := gonpy.NewWriter(nopCloser{bufw})
1247 log.WithFields(log.Fields{
1251 "bytes": rows * cols * 4,
1252 }).Infof("writing numpy: %s", fnm)
1253 npw.Shape = []int{rows, cols}
1254 npw.WriteUint32(out)
1259 return output.Close()
1262 func writeNumpyInt32(fnm string, out []int32, rows, cols int) error {
1263 output, err := os.Create(fnm)
1267 defer output.Close()
1268 bufw := bufio.NewWriterSize(output, 1<<26)
1269 npw, err := gonpy.NewWriter(nopCloser{bufw})
1273 log.WithFields(log.Fields{
1277 "bytes": rows * cols * 4,
1278 }).Infof("writing numpy: %s", fnm)
1279 npw.Shape = []int{rows, cols}
1285 return output.Close()
1288 func writeNumpyInt16(fnm string, out []int16, rows, cols int) error {
1289 output, err := os.Create(fnm)
1293 defer output.Close()
1294 bufw := bufio.NewWriterSize(output, 1<<26)
1295 npw, err := gonpy.NewWriter(nopCloser{bufw})
1299 log.WithFields(log.Fields{
1303 "bytes": rows * cols * 2,
1304 }).Infof("writing numpy: %s", fnm)
1305 npw.Shape = []int{rows, cols}
1311 return output.Close()
1314 func writeNumpyInt8(fnm string, out []int8, rows, cols int) error {
1315 output, err := os.Create(fnm)
1319 defer output.Close()
1320 bufw := bufio.NewWriterSize(output, 1<<26)
1321 npw, err := gonpy.NewWriter(nopCloser{bufw})
1325 log.WithFields(log.Fields{
1329 "bytes": rows * cols,
1330 }).Infof("writing numpy: %s", fnm)
1331 npw.Shape = []int{rows, cols}
1337 return output.Close()
1340 func allele2homhet(colpair [2][]int8) {
1341 a, b := colpair[0], colpair[1]
1342 for i, av := range a {
1344 if av < 0 || bv < 0 {
1347 } else if av > 0 && bv > 0 {
1350 } else if av > 0 || bv > 0 {
1354 // ref (or a different variant in same position)
1355 // (this is a no-op) a[i], b[i] = 0, 0
1360 type onehotXref struct {
1362 variant tileVariantID
1367 const onehotXrefSize = unsafe.Sizeof(onehotXref{})
1369 // Build onehot matrix (m[tileVariantIndex][genome] == 0 or 1) for all
1370 // variants of a single tile/tag#.
1372 // Return nil if no tile variant passes Χ² filter.
1373 func (cmd *sliceNumpy) tv2homhet(cgs map[string]CompactGenome, maxv tileVariantID, remap []tileVariantID, tag, chunkstarttag tagID, seq map[tagID][]TileVariant) ([][]int8, []onehotXref) {
1374 if tag == cmd.debugTag {
1375 tv := make([]tileVariantID, len(cmd.cgnames)*2)
1376 for i, name := range cmd.cgnames {
1377 copy(tv[i*2:(i+1)*2], cgs[name].Variants[(tag-chunkstarttag)*2:])
1379 log.WithFields(logrus.Fields{
1380 "cgs[i].Variants[tag*2+j]": tv,
1384 "chunkstarttag": chunkstarttag,
1385 }).Info("tv2homhet()")
1387 if maxv < 1 || (maxv < 2 && !cmd.includeVariant1) {
1388 // everyone has the most common variant (of the variants we don't drop)
1391 tagoffset := tag - chunkstarttag
1393 for _, cg := range cgs {
1395 for _, v := range cg.Variants[tagoffset*2 : tagoffset*2+2] {
1396 if v > 0 && int(v) < len(seq[tag]) && len(seq[tag][v].Sequence) > 0 {
1404 if coverage < cmd.minCoverage {
1407 obs := make([][]bool, (maxv+1)*2) // 2 slices (hom + het) for each variant#
1408 for i := range obs {
1409 obs[i] = make([]bool, len(cmd.cgnames))
1411 for cgid, name := range cmd.cgnames {
1412 cgvars := cgs[name].Variants[tagoffset*2:]
1413 tv0, tv1 := remap[cgvars[0]], remap[cgvars[1]]
1414 for v := tileVariantID(1); v <= maxv; v++ {
1415 if tv0 == v && tv1 == v {
1416 obs[v*2][cgid] = true
1417 } else if tv0 == v || tv1 == v {
1418 obs[v*2+1][cgid] = true
1423 var xref []onehotXref
1424 for col := 2; col < len(obs); col++ {
1425 // col 0,1 correspond to tile variant 0, i.e.,
1426 // no-call; col 2,3 correspond to the most common
1427 // variant; so we (normally) start at col 4.
1428 if col < 4 && !cmd.includeVariant1 {
1431 p := pvalue(obs[col], cmd.chi2Cases)
1432 if cmd.chi2PValue < 1 && !(p < cmd.chi2PValue) {
1435 onehot = append(onehot, bool2int8(obs[col]))
1436 xref = append(xref, onehotXref{
1438 variant: tileVariantID(col >> 1),
1446 func bool2int8(in []bool) []int8 {
1447 out := make([]int8, len(in))
1448 for i, v := range in {
1456 // convert a []onehotXref with length N to a numpy-style []int32
1457 // matrix with N columns, one row per field of onehotXref struct.
1459 // Hom/het row contains hom=0, het=1.
1461 // P-value row contains 1000000x actual p-value.
1462 func onehotXref2int32(xrefs []onehotXref) []int32 {
1464 xdata := make([]int32, 5*xcols)
1465 for i, xref := range xrefs {
1466 xdata[i] = int32(xref.tag)
1467 xdata[xcols+i] = int32(xref.variant)
1469 xdata[xcols*2+i] = 1
1471 xdata[xcols*3+i] = int32(xref.pvalue * 1000000)
1472 xdata[xcols*4+i] = int32(-math.Log10(xref.pvalue) * 1000000)
1477 // transpose onehot data from in[col][row] to numpy-style
1478 // out[row*cols+col].
1479 func onehotcols2int8(in [][]int8) []int8 {
1485 out := make([]int8, rows*cols)
1486 for row := 0; row < rows; row++ {
1487 outrow := out[row*cols:]
1488 for col, incol := range in {
1489 outrow[col] = incol[row]
1495 // Return [2][]uint32{rowIndices, colIndices} indicating which
1496 // elements of matrixT[c][r] have non-zero values.
1497 func onehotChunk2Indirect(matrixT [][]int8) [2][]uint32 {
1499 for c, col := range matrixT {
1500 for r, val := range col {
1502 nz[0] = append(nz[0], uint32(r))
1503 nz[1] = append(nz[1], uint32(c))