+
+ if *hgvsChunked {
+ log.Info("flushing hgvsCols temp files")
+ for seqname := range refseq {
+ close(encodeHGVSTodo[seqname])
+ }
+ err = encodeHGVS.Wait()
+ if err != nil {
+ return 1
+ }
+ for seqname := range refseq {
+ log.Infof("%s: reading hgvsCols from temp file", seqname)
+ f := tmpHGVSCols[seqname]
+ _, err = f.Seek(0, io.SeekStart)
+ if err != nil {
+ return 1
+ }
+ var hgvsCols hgvsColSet
+ dec := gob.NewDecoder(bufio.NewReaderSize(f, 1<<24))
+ for err == nil {
+ err = dec.Decode(&hgvsCols)
+ }
+ if err != io.EOF {
+ return 1
+ }
+ log.Infof("%s: sorting %d hgvs variants", seqname, len(hgvsCols))
+ variants := make([]hgvs.Variant, 0, len(hgvsCols))
+ for v := range hgvsCols {
+ variants = append(variants, v)
+ }
+ sort.Slice(variants, func(i, j int) bool {
+ vi, vj := &variants[i], &variants[j]
+ if vi.Position != vj.Position {
+ return vi.Position < vj.Position
+ } else if vi.Ref != vj.Ref {
+ return vi.Ref < vj.Ref
+ } else {
+ return vi.New < vj.New
+ }
+ })
+ rows := len(cgnames)
+ cols := len(variants) * 2
+ log.Infof("%s: building hgvs matrix (rows=%d, cols=%d, mem=%d)", seqname, rows, cols, rows*cols)
+ out := make([]int8, rows*cols)
+ for varIdx, variant := range variants {
+ hgvsCols := hgvsCols[variant]
+ for row := range cgnames {
+ for ph := 0; ph < 2; ph++ {
+ out[row*cols+varIdx+ph] = hgvsCols[ph][row]
+ }
+ }
+ }
+ err = writeNumpyInt8(fmt.Sprintf("%s/hgvs.%s.npy", *outputDir, seqname), out, rows, cols)
+ if err != nil {
+ return 1
+ }
+ out = nil
+
+ fnm := fmt.Sprintf("%s/hgvs.%s.annotations.csv", *outputDir, seqname)
+ log.Infof("%s: writing hgvs column labels to %s", seqname, fnm)
+ var hgvsLabels bytes.Buffer
+ for varIdx, variant := range variants {
+ fmt.Fprintf(&hgvsLabels, "%d,%s:g.%s\n", varIdx, seqname, variant.String())
+ }
+ err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0666)
+ if err != nil {
+ return 1
+ }
+ }
+ }
+
+ if *mergeOutput || *hgvsSingle {
+ var annow *bufio.Writer
+ var annof *os.File
+ if *mergeOutput {
+ annoFilename := fmt.Sprintf("%s/matrix.annotations.csv", *outputDir)
+ annof, err = os.Create(annoFilename)
+ if err != nil {
+ return 1
+ }
+ annow = bufio.NewWriterSize(annof, 1<<20)
+ }
+
+ rows := len(cgnames)
+ cols := 0
+ for _, chunk := range toMerge {
+ cols += len(chunk) / rows
+ }
+ log.Infof("merging output matrix (rows=%d, cols=%d, mem=%d) and annotations", rows, cols, rows*cols*2)
+ var out []int16
+ if *mergeOutput {
+ out = make([]int16, rows*cols)
+ }
+ hgvsCols := map[string][2][]int16{} // hgvs -> [[g0,g1,g2,...], [g0,g1,g2,...]] (slice of genomes for each phase)
+ startcol := 0
+ for outIdx, chunk := range toMerge {
+ chunkcols := len(chunk) / rows
+ if *mergeOutput {
+ for row := 0; row < rows; row++ {
+ copy(out[row*cols+startcol:], chunk[row*chunkcols:(row+1)*chunkcols])
+ }
+ }
+ toMerge[outIdx] = nil
+
+ annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, outIdx)
+ log.Infof("reading %s", annotationsFilename)
+ buf, err := os.ReadFile(annotationsFilename)
+ if err != nil {
+ return 1
+ }
+ if *mergeOutput {
+ err = os.Remove(annotationsFilename)
+ if err != nil {
+ return 1
+ }
+ }
+ for _, line := range bytes.Split(buf, []byte{'\n'}) {
+ if len(line) == 0 {
+ continue
+ }
+ fields := bytes.SplitN(line, []byte{','}, 9)
+ tag, _ := strconv.Atoi(string(fields[0]))
+ incol, _ := strconv.Atoi(string(fields[1]))
+ tileVariant, _ := strconv.Atoi(string(fields[2]))
+ hgvsID := string(fields[3])
+ seqname := string(fields[4])
+ pos, _ := strconv.Atoi(string(fields[5]))
+ refseq := fields[6]
+ if hgvsID == "" {
+ // Null entry for un-diffable
+ // tile variant
+ continue
+ }
+ if hgvsID == "=" {
+ // Null entry for ref tile
+ continue
+ }
+ if mask != nil && !mask.Check(strings.TrimPrefix(seqname, "chr"), pos, pos+len(refseq)) {
+ // The tile intersects one of
+ // the selected regions, but
+ // this particular HGVS
+ // variant does not.
+ continue
+ }
+ hgvsColPair := hgvsCols[hgvsID]
+ if hgvsColPair[0] == nil {
+ // values in new columns start
+ // out as -1 ("no data yet")
+ // or 0 ("=ref") here, may
+ // change to 1 ("hgvs variant
+ // present") below, either on
+ // this line or a future line.
+ hgvsColPair = [2][]int16{make([]int16, len(cgnames)), make([]int16, len(cgnames))}
+ rt, ok := reftile[tagID(tag)]
+ if !ok {
+ err = fmt.Errorf("bug: seeing annotations for tag %d, but it has no reftile entry", tag)
+ return 1
+ }
+ for ph := 0; ph < 2; ph++ {
+ for row := 0; row < rows; row++ {
+ v := chunk[row*chunkcols+incol*2+ph]
+ if tileVariantID(v) == rt.variant {
+ hgvsColPair[ph][row] = 0
+ } else {
+ hgvsColPair[ph][row] = -1
+ }
+ }
+ }
+ hgvsCols[hgvsID] = hgvsColPair
+ if annow != nil {
+ hgvsref := hgvs.Variant{
+ Position: pos,
+ Ref: string(refseq),
+ New: string(refseq),
+ }
+ 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])
+ }
+ }
+ if annow != nil {
+ 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])
+ }
+ for ph := 0; ph < 2; ph++ {
+ for row := 0; row < rows; row++ {
+ v := chunk[row*chunkcols+incol*2+ph]
+ if int(v) == tileVariant {
+ hgvsColPair[ph][row] = 1
+ }
+ }
+ }
+ }
+
+ startcol += chunkcols
+ }
+ if *mergeOutput {
+ err = annow.Flush()
+ if err != nil {
+ return 1
+ }
+ err = annof.Close()
+ if err != nil {
+ return 1
+ }
+ err = writeNumpyInt16(fmt.Sprintf("%s/matrix.npy", *outputDir), out, rows, cols)
+ if err != nil {
+ return 1
+ }
+ }
+ out = nil
+
+ if *hgvsSingle {
+ cols = len(hgvsCols) * 2
+ log.Printf("building hgvs-based matrix: %d rows x %d cols", rows, cols)
+ out = make([]int16, rows*cols)
+ hgvsIDs := make([]string, 0, cols/2)
+ for hgvsID := range hgvsCols {
+ hgvsIDs = append(hgvsIDs, hgvsID)
+ }
+ sort.Strings(hgvsIDs)
+ var hgvsLabels bytes.Buffer
+ for idx, hgvsID := range hgvsIDs {
+ fmt.Fprintf(&hgvsLabels, "%d,%s\n", idx, hgvsID)
+ for ph := 0; ph < 2; ph++ {
+ hgvscol := hgvsCols[hgvsID][ph]
+ for row, val := range hgvscol {
+ out[row*cols+idx*2+ph] = val
+ }
+ }
+ }
+ err = writeNumpyInt16(fmt.Sprintf("%s/hgvs.npy", *outputDir), out, rows, cols)
+ if err != nil {
+ return 1
+ }
+
+ fnm := fmt.Sprintf("%s/hgvs.annotations.csv", *outputDir)
+ log.Printf("writing hgvs labels: %s", fnm)
+ err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0777)
+ if err != nil {
+ return 1
+ }
+ }
+ }