+ for _, seqname := range seqnames {
+ basename := "hgvs"
+ wantPrefix := ""
+ if seqname == "" {
+ cols = len(hgvsCols) * 2
+ } else {
+ basename = "hgvs." + seqname
+ wantPrefix = seqname + ":"
+ cols = 0
+ for hgvsID := range hgvsCols {
+ if strings.HasPrefix(hgvsID, wantPrefix) {
+ cols += 2
+ }
+ }
+ }
+ log.Printf("building hgvs-based matrix [%s]: %d rows x %d cols", seqname, rows, cols)
+ out = make([]int16, rows*cols)
+ hgvsIDs := make([]string, 0, cols/2)
+ for hgvsID := range hgvsCols {
+ if strings.HasPrefix(hgvsID, wantPrefix) {
+ 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/%s.npy", *outputDir, basename), out, rows, cols)
+ if err != nil {
+ return 1
+ }