1 // Copyright (C) The Lightning Authors. All rights reserved.
3 // SPDX-License-Identifier: AGPL-3.0
27 "git.arvados.org/arvados.git/sdk/go/arvados"
28 "github.com/arvados/lightning/hgvs"
29 "github.com/kshedden/gonpy"
30 log "github.com/sirupsen/logrus"
31 "golang.org/x/crypto/blake2b"
34 type sliceNumpy struct {
43 func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
47 fmt.Fprintf(stderr, "%s\n", err)
50 flags := flag.NewFlagSet("", flag.ContinueOnError)
51 flags.SetOutput(stderr)
52 pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
53 runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
54 projectUUID := flags.String("project", "", "project `UUID` for output data")
55 priority := flags.Int("priority", 500, "container request priority")
56 inputDir := flags.String("input-dir", "./in", "input `directory`")
57 outputDir := flags.String("output-dir", "./out", "output `directory`")
58 ref := flags.String("ref", "", "reference name (if blank, choose last one that appears in input)")
59 regionsFilename := flags.String("regions", "", "only output columns/annotations that intersect regions in specified bed `file`")
60 expandRegions := flags.Int("expand-regions", 0, "expand specified regions by `N` base pairs on each side`")
61 mergeOutput := flags.Bool("merge-output", false, "merge output into one matrix.npy and one matrix.annotations.csv")
62 hgvsSingle := flags.Bool("single-hgvs-matrix", false, "also generate hgvs-based matrix")
63 hgvsChunked := flags.Bool("chunked-hgvs-matrix", false, "also generate hgvs-based matrix per chromosome")
64 flags.IntVar(&cmd.threads, "threads", 16, "number of memory-hungry assembly threads")
65 flags.StringVar(&cmd.chi2CasesFile, "chi2-cases-file", "", "text file indicating positive cases (for Χ² test)")
66 flags.Float64Var(&cmd.chi2PValue, "chi2-p-value", 1, "do Χ² test and omit columns with p-value above this threshold")
67 cmd.filter.Flags(flags)
68 err = flags.Parse(args)
69 if err == flag.ErrHelp {
72 } else if err != nil {
78 log.Println(http.ListenAndServe(*pprof, nil))
82 if cmd.chi2CasesFile == "" && cmd.chi2PValue != 1 {
83 log.Errorf("cannot use provided -chi2-p-value=%f because -chi2-cases-file= value is empty", cmd.chi2PValue)
88 runner := arvadosContainerRunner{
89 Name: "lightning slice-numpy",
90 Client: arvados.NewClientFromEnv(),
91 ProjectUUID: *projectUUID,
98 err = runner.TranslatePaths(inputDir, regionsFilename, &cmd.chi2CasesFile)
102 runner.Args = []string{"slice-numpy", "-local=true",
104 "-input-dir=" + *inputDir,
105 "-output-dir=/mnt/output",
106 "-threads=" + fmt.Sprintf("%d", cmd.threads),
107 "-regions=" + *regionsFilename,
108 "-expand-regions=" + fmt.Sprintf("%d", *expandRegions),
109 "-merge-output=" + fmt.Sprintf("%v", *mergeOutput),
110 "-single-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsSingle),
111 "-chunked-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsChunked),
112 "-chi2-cases-file=" + cmd.chi2CasesFile,
113 "-chi2-p-value=" + fmt.Sprintf("%f", cmd.chi2PValue),
115 runner.Args = append(runner.Args, cmd.filter.Args()...)
117 output, err = runner.Run()
121 fmt.Fprintln(stdout, output)
125 infiles, err := allGobFiles(*inputDir)
129 if len(infiles) == 0 {
130 err = fmt.Errorf("no input files found in %s", *inputDir)
133 sort.Strings(infiles)
136 var refseq map[string][]tileLibRef
137 var reftiledata = make(map[tileLibRef][]byte, 11000000)
138 in0, err := open(infiles[0])
143 matchGenome, err := regexp.Compile(cmd.filter.MatchGenome)
145 err = fmt.Errorf("-match-genome: invalid regexp: %q", cmd.filter.MatchGenome)
150 DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
151 if len(ent.TagSet) > 0 {
152 taglen = len(ent.TagSet[0])
154 for _, cseq := range ent.CompactSequences {
155 if cseq.Name == *ref || *ref == "" {
156 refseq = cseq.TileSequences
159 for _, cg := range ent.CompactGenomes {
160 if matchGenome.MatchString(cg.Name) {
161 cgnames = append(cgnames, cg.Name)
164 for _, tv := range ent.TileVariants {
166 reftiledata[tileLibRef{tv.Tag, tv.Variant}] = tv.Sequence
176 err = fmt.Errorf("%s: reference sequence not found", infiles[0])
180 err = fmt.Errorf("tagset not found")
183 if len(cgnames) == 0 {
184 err = fmt.Errorf("no genomes found matching regexp %q", cmd.filter.MatchGenome)
187 sort.Strings(cgnames)
189 cmd.minCoverage = int(math.Ceil(cmd.filter.MinCoverage * float64(len(cgnames))))
191 if cmd.chi2CasesFile != "" {
192 f, err2 := open(cmd.chi2CasesFile)
197 buf, err2 := io.ReadAll(f)
203 cmd.chi2Cases = make([]bool, len(cgnames))
205 for _, pattern := range bytes.Split(buf, []byte{'\n'}) {
206 if len(pattern) == 0 {
209 pattern := string(pattern)
211 for i, name := range cgnames {
212 if !strings.Contains(name, pattern) {
215 cmd.chi2Cases[i] = true
218 log.Warnf("pattern %q in cases file matches multiple genome IDs: %q, %q", pattern, cgnames[idx], name)
224 log.Warnf("pattern %q in cases file does not match any genome IDs", pattern)
228 log.Printf("%d cases, %d controls", ncases, len(cgnames)-ncases)
232 labelsFilename := *outputDir + "/labels.csv"
233 log.Infof("writing labels to %s", labelsFilename)
235 f, err = os.Create(labelsFilename)
240 for i, name := range cgnames {
241 _, err = fmt.Fprintf(f, "%d,%q\n", i, trimFilenameForLabel(name))
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...
261 isdup := map[tagID]bool{}
262 reftile := map[tagID]*reftileinfo{}
263 for seqname, cseq := range refseq {
265 for _, libref := range cseq {
266 tiledata := reftiledata[libref]
267 if len(tiledata) == 0 {
268 err = fmt.Errorf("missing tiledata for tag %d variant %d in %s in ref", libref.Tag, libref.Variant, seqname)
271 if isdup[libref.Tag] {
272 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
273 } else if reftile[libref.Tag] != nil {
274 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)
275 delete(reftile, libref.Tag)
276 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
277 isdup[libref.Tag] = true
279 reftile[libref.Tag] = &reftileinfo{
281 variant: libref.Variant,
286 pos += len(tiledata) - taglen
288 log.Printf("... %s done, len %d", seqname, pos+taglen)
292 if *regionsFilename != "" {
293 log.Printf("loading regions from %s", *regionsFilename)
294 mask, err = makeMask(*regionsFilename, *expandRegions)
298 log.Printf("before applying mask, len(reftile) == %d", len(reftile))
299 log.Printf("deleting reftile entries for regions outside %d intervals", mask.Len())
300 for tag, rt := range reftile {
301 if !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(rt.tiledata)) {
305 log.Printf("after applying mask, len(reftile) == %d", len(reftile))
308 type hgvsColSet map[hgvs.Variant][2][]int8
309 encodeHGVS := throttle{Max: len(refseq)}
310 encodeHGVSTodo := map[string]chan hgvsColSet{}
311 tmpHGVSCols := map[string]*os.File{}
313 for seqname := range refseq {
315 f, err = os.Create(*outputDir + "/tmp." + seqname + ".gob")
319 defer os.Remove(f.Name())
320 bufw := bufio.NewWriterSize(f, 1<<24)
321 enc := gob.NewEncoder(bufw)
322 tmpHGVSCols[seqname] = f
323 todo := make(chan hgvsColSet, 128)
324 encodeHGVSTodo[seqname] = todo
325 encodeHGVS.Go(func() error {
326 for colset := range todo {
327 err := enc.Encode(colset)
329 encodeHGVS.Report(err)
340 var toMerge [][]int16
341 if *mergeOutput || *hgvsSingle {
342 toMerge = make([][]int16, len(infiles))
345 throttleMem := throttle{Max: cmd.threads} // TODO: estimate using mem and data size
346 throttleNumpyMem := throttle{Max: cmd.threads/2 + 1}
347 log.Info("generating annotations and numpy matrix for each slice")
349 for infileIdx, infile := range infiles {
350 infileIdx, infile := infileIdx, infile
351 throttleMem.Go(func() error {
352 seq := make(map[tagID][]TileVariant, 50000)
353 cgs := make(map[string]CompactGenome, len(cgnames))
354 f, err := open(infile)
359 log.Infof("%04d: reading %s", infileIdx, infile)
360 err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
361 for _, tv := range ent.TileVariants {
365 if mask != nil && reftile[tv.Tag] == nil {
371 variants := seq[tv.Tag]
372 if len(variants) == 0 {
373 variants = make([]TileVariant, 100)
375 for len(variants) <= int(tv.Variant) {
376 variants = append(variants, TileVariant{})
378 variants[int(tv.Variant)] = tv
379 seq[tv.Tag] = variants
381 for _, cg := range ent.CompactGenomes {
382 if !matchGenome.MatchString(cg.Name) {
385 // pad to full slice size
386 // to avoid out-of-bounds
388 if sliceSize := 2 * int(cg.EndTag-cg.StartTag); len(cg.Variants) < sliceSize {
389 cg.Variants = append(cg.Variants, make([]tileVariantID, sliceSize-len(cg.Variants))...)
398 tagstart := cgs[cgnames[0]].StartTag
399 tagend := cgs[cgnames[0]].EndTag
403 log.Infof("%04d: renumber/dedup variants for tags %d-%d", infileIdx, tagstart, tagend)
404 variantRemap := make([][]tileVariantID, tagend-tagstart)
405 throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
406 for tag, variants := range seq {
407 tag, variants := tag, variants
408 throttleCPU.Acquire()
410 defer throttleCPU.Release()
411 count := make(map[[blake2b.Size256]byte]int, len(variants))
415 count[blake2b.Sum256(rt.tiledata)] = 0
418 for _, cg := range cgs {
419 idx := int(tag-tagstart) * 2
420 for allele := 0; allele < 2; allele++ {
421 v := cg.Variants[idx+allele]
422 if v > 0 && len(variants[v].Sequence) > 0 {
423 count[variants[v].Blake2b]++
427 // hash[i] will be the hash of
428 // the variant(s) that should
429 // be at rank i (0-based).
430 hash := make([][blake2b.Size256]byte, 0, len(count))
431 for b := range count {
432 hash = append(hash, b)
434 sort.Slice(hash, func(i, j int) bool {
435 bi, bj := &hash[i], &hash[j]
436 if ci, cj := count[*bi], count[*bj]; ci != cj {
439 return bytes.Compare((*bi)[:], (*bj)[:]) < 0
442 // rank[b] will be the 1-based
443 // new variant number for
444 // variants whose hash is b.
445 rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
446 for i, h := range hash {
447 rank[h] = tileVariantID(i + 1)
449 // remap[v] will be the new
450 // variant number for original
452 remap := make([]tileVariantID, len(variants))
453 for i, tv := range variants {
454 remap[i] = rank[tv.Blake2b]
456 variantRemap[tag-tagstart] = remap
458 rt.variant = rank[blake2b.Sum256(rt.tiledata)]
464 annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
465 log.Infof("%04d: writing %s", infileIdx, annotationsFilename)
466 annof, err := os.Create(annotationsFilename)
470 annow := bufio.NewWriterSize(annof, 1<<20)
472 for tag := tagstart; tag < tagend; tag++ {
473 rt, ok := reftile[tag]
478 // Excluded by specified
479 // regions, or reference does
480 // not use any variant of this
481 // tile. (TODO: log this?
482 // mention it in annotations?)
485 fmt.Fprintf(annow, "%d,%d,%d,=,%s,%d,,,\n", tag, outcol, rt.variant, rt.seqname, rt.pos)
487 reftilestr := strings.ToUpper(string(rt.tiledata))
488 remap := variantRemap[tag-tagstart]
489 maxv := tileVariantID(0)
490 for _, v := range remap {
495 done := make([]bool, maxv+1)
496 variantDiffs := make([][]hgvs.Variant, maxv+1)
497 for v, tv := range variants {
499 if v == rt.variant || done[v] {
504 if len(tv.Sequence) < taglen || !bytes.HasSuffix(rt.tiledata, tv.Sequence[len(tv.Sequence)-taglen:]) {
505 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
508 if lendiff := len(rt.tiledata) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
509 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
512 diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
513 for i := range diffs {
514 diffs[i].Position += rt.pos
516 for _, diff := range diffs {
517 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)
520 variantDiffs[v] = diffs
524 // We can now determine, for each HGVS
525 // variant (diff) in this reftile
526 // region, whether a given genome
527 // phase/allele (1) has the variant, (0) has
528 // =ref or a different variant in that
529 // position, or (-1) is lacking
530 // coverage / couldn't be diffed.
531 hgvsCol := hgvsColSet{}
532 for _, diffs := range variantDiffs {
533 for _, diff := range diffs {
534 if _, ok := hgvsCol[diff]; ok {
537 hgvsCol[diff] = [2][]int8{
538 make([]int8, len(cgnames)),
539 make([]int8, len(cgnames)),
543 for row, name := range cgnames {
544 variants := cgs[name].Variants[(tag-tagstart)*2:]
545 for ph := 0; ph < 2; ph++ {
547 if int(v) >= len(remap) {
553 // hgvsCol[*][ph][row] is already 0
554 } else if len(variantDiffs[v]) == 0 {
555 // lacking coverage / couldn't be diffed
556 for _, col := range hgvsCol {
560 for _, diff := range variantDiffs[v] {
561 hgvsCol[diff][ph][row] = 1
566 for diff, colpair := range hgvsCol {
567 allele2homhet(colpair)
568 if !cmd.filterHGVScolpair(colpair) {
569 delete(hgvsCol, diff)
572 if len(hgvsCol) > 0 {
573 encodeHGVSTodo[rt.seqname] <- hgvsCol
587 log.Infof("%04d: preparing numpy", infileIdx)
588 throttleNumpyMem.Acquire()
591 out := make([]int16, rows*cols)
592 for row, name := range cgnames {
593 out := out[row*cols:]
595 for col, v := range cgs[name].Variants {
596 tag := tagstart + tagID(col/2)
597 if mask != nil && reftile[tag] == nil {
600 if variants, ok := seq[tag]; ok && len(variants) > int(v) && len(variants[v].Sequence) > 0 {
601 out[outcol] = int16(variantRemap[tag-tagstart][v])
611 throttleNumpyMem.Release()
613 if *mergeOutput || *hgvsSingle {
614 log.Infof("%04d: matrix fragment %d rows x %d cols", infileIdx, rows, cols)
615 toMerge[infileIdx] = out
618 fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
619 err = writeNumpyInt16(fnm, out, rows, cols)
625 log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
629 if err = throttleMem.Wait(); err != nil {
634 log.Info("flushing hgvsCols temp files")
635 for seqname := range refseq {
636 close(encodeHGVSTodo[seqname])
638 err = encodeHGVS.Wait()
642 for seqname := range refseq {
643 log.Infof("%s: reading hgvsCols from temp file", seqname)
644 f := tmpHGVSCols[seqname]
645 _, err = f.Seek(0, io.SeekStart)
649 var hgvsCols hgvsColSet
650 dec := gob.NewDecoder(bufio.NewReaderSize(f, 1<<24))
652 err = dec.Decode(&hgvsCols)
657 log.Infof("%s: sorting %d hgvs variants", seqname, len(hgvsCols))
658 variants := make([]hgvs.Variant, 0, len(hgvsCols))
659 for v := range hgvsCols {
660 variants = append(variants, v)
662 sort.Slice(variants, func(i, j int) bool {
663 vi, vj := &variants[i], &variants[j]
664 if vi.Position != vj.Position {
665 return vi.Position < vj.Position
666 } else if vi.Ref != vj.Ref {
667 return vi.Ref < vj.Ref
669 return vi.New < vj.New
673 cols := len(variants) * 2
674 log.Infof("%s: building hgvs matrix (rows=%d, cols=%d, mem=%d)", seqname, rows, cols, rows*cols)
675 out := make([]int8, rows*cols)
676 for varIdx, variant := range variants {
677 hgvsCols := hgvsCols[variant]
678 for row := range cgnames {
679 for ph := 0; ph < 2; ph++ {
680 out[row*cols+varIdx+ph] = hgvsCols[ph][row]
684 err = writeNumpyInt8(fmt.Sprintf("%s/hgvs.%s.npy", *outputDir, seqname), out, rows, cols)
690 fnm := fmt.Sprintf("%s/hgvs.%s.annotations.csv", *outputDir, seqname)
691 log.Infof("%s: writing hgvs column labels to %s", seqname, fnm)
692 var hgvsLabels bytes.Buffer
693 for varIdx, variant := range variants {
694 fmt.Fprintf(&hgvsLabels, "%d,%s:g.%s\n", varIdx, seqname, variant.String())
696 err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0666)
703 if *mergeOutput || *hgvsSingle {
704 var annow *bufio.Writer
707 annoFilename := fmt.Sprintf("%s/matrix.annotations.csv", *outputDir)
708 annof, err = os.Create(annoFilename)
712 annow = bufio.NewWriterSize(annof, 1<<20)
717 for _, chunk := range toMerge {
718 cols += len(chunk) / rows
720 log.Infof("merging output matrix (rows=%d, cols=%d, mem=%d) and annotations", rows, cols, rows*cols*2)
723 out = make([]int16, rows*cols)
725 hgvsCols := map[string][2][]int16{} // hgvs -> [[g0,g1,g2,...], [g0,g1,g2,...]] (slice of genomes for each phase)
727 for outIdx, chunk := range toMerge {
728 chunkcols := len(chunk) / rows
730 for row := 0; row < rows; row++ {
731 copy(out[row*cols+startcol:], chunk[row*chunkcols:(row+1)*chunkcols])
734 toMerge[outIdx] = nil
736 annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, outIdx)
737 log.Infof("reading %s", annotationsFilename)
738 buf, err := os.ReadFile(annotationsFilename)
743 err = os.Remove(annotationsFilename)
748 for _, line := range bytes.Split(buf, []byte{'\n'}) {
752 fields := bytes.SplitN(line, []byte{','}, 9)
753 tag, _ := strconv.Atoi(string(fields[0]))
754 incol, _ := strconv.Atoi(string(fields[1]))
755 tileVariant, _ := strconv.Atoi(string(fields[2]))
756 hgvsID := string(fields[3])
757 seqname := string(fields[4])
758 pos, _ := strconv.Atoi(string(fields[5]))
761 // Null entry for un-diffable
766 // Null entry for ref tile
769 if mask != nil && !mask.Check(strings.TrimPrefix(seqname, "chr"), pos, pos+len(refseq)) {
770 // The tile intersects one of
771 // the selected regions, but
772 // this particular HGVS
776 hgvsColPair := hgvsCols[hgvsID]
777 if hgvsColPair[0] == nil {
778 // values in new columns start
779 // out as -1 ("no data yet")
780 // or 0 ("=ref") here, may
781 // change to 1 ("hgvs variant
782 // present") below, either on
783 // this line or a future line.
784 hgvsColPair = [2][]int16{make([]int16, len(cgnames)), make([]int16, len(cgnames))}
785 rt, ok := reftile[tagID(tag)]
787 err = fmt.Errorf("bug: seeing annotations for tag %d, but it has no reftile entry", tag)
790 for ph := 0; ph < 2; ph++ {
791 for row := 0; row < rows; row++ {
792 v := chunk[row*chunkcols+incol*2+ph]
793 if tileVariantID(v) == rt.variant {
794 hgvsColPair[ph][row] = 0
796 hgvsColPair[ph][row] = -1
800 hgvsCols[hgvsID] = hgvsColPair
802 hgvsref := hgvs.Variant{
807 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])
811 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])
813 for ph := 0; ph < 2; ph++ {
814 for row := 0; row < rows; row++ {
815 v := chunk[row*chunkcols+incol*2+ph]
816 if int(v) == tileVariant {
817 hgvsColPair[ph][row] = 1
823 startcol += chunkcols
834 err = writeNumpyInt16(fmt.Sprintf("%s/matrix.npy", *outputDir), out, rows, cols)
842 cols = len(hgvsCols) * 2
843 log.Printf("building hgvs-based matrix: %d rows x %d cols", rows, cols)
844 out = make([]int16, rows*cols)
845 hgvsIDs := make([]string, 0, cols/2)
846 for hgvsID := range hgvsCols {
847 hgvsIDs = append(hgvsIDs, hgvsID)
849 sort.Strings(hgvsIDs)
850 var hgvsLabels bytes.Buffer
851 for idx, hgvsID := range hgvsIDs {
852 fmt.Fprintf(&hgvsLabels, "%d,%s\n", idx, hgvsID)
853 for ph := 0; ph < 2; ph++ {
854 hgvscol := hgvsCols[hgvsID][ph]
855 for row, val := range hgvscol {
856 out[row*cols+idx*2+ph] = val
860 err = writeNumpyInt16(fmt.Sprintf("%s/hgvs.npy", *outputDir), out, rows, cols)
865 fnm := fmt.Sprintf("%s/hgvs.annotations.csv", *outputDir)
866 log.Printf("writing hgvs labels: %s", fnm)
867 err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0777)
876 func (cmd *sliceNumpy) filterHGVScolpair(colpair [2][]int8) bool {
877 if cmd.chi2PValue >= 1 {
880 col0 := make([]bool, 0, len(cmd.chi2Cases))
881 col1 := make([]bool, 0, len(cmd.chi2Cases))
882 cases := make([]bool, 0, len(cmd.chi2Cases))
883 for i, c := range cmd.chi2Cases {
884 if colpair[0][i] < 0 {
887 col0 = append(col0, colpair[0][i] != 0)
888 col1 = append(col1, colpair[1][i] != 0)
889 cases = append(cases, c)
891 return len(cases) >= cmd.minCoverage &&
892 (pvalue(cases, col0) <= cmd.chi2PValue || pvalue(cases, col1) <= cmd.chi2PValue)
895 func writeNumpyInt16(fnm string, out []int16, rows, cols int) error {
896 output, err := os.Create(fnm)
901 bufw := bufio.NewWriterSize(output, 1<<26)
902 npw, err := gonpy.NewWriter(nopCloser{bufw})
906 log.WithFields(log.Fields{
910 }).Infof("writing numpy: %s", fnm)
911 npw.Shape = []int{rows, cols}
917 return output.Close()
920 func writeNumpyInt8(fnm string, out []int8, rows, cols int) error {
921 output, err := os.Create(fnm)
926 bufw := bufio.NewWriterSize(output, 1<<26)
927 npw, err := gonpy.NewWriter(nopCloser{bufw})
931 log.WithFields(log.Fields{
935 }).Infof("writing numpy: %s", fnm)
936 npw.Shape = []int{rows, cols}
942 return output.Close()
945 func allele2homhet(colpair [2][]int8) {
946 a, b := colpair[0], colpair[1]
947 for i, av := range a {
949 if av < 0 || bv < 0 {
952 } else if av > 0 && bv > 0 {
955 } else if av > 0 || bv > 0 {
959 // ref (or a different variant in same position)
960 // (this is a no-op) a[i], b[i] = 0, 0