+// Align genome tiles to reference tiles, write diffs to outw, and (if
+// bedw is not nil) write tile coverage to bedw.
+func (cmd *exporter) exportSeq(outw, bedw io.Writer, taglen int, seqname string, reftiles []tileLibRef, tileVariant map[tileLibRef]TileVariant, cgs []CompactGenome) {
+ refpos := 0
+ variantAt := map[int][]hgvs.Variant{} // variantAt[chromOffset][genomeIndex*2+phase]
+ for refstep, libref := range reftiles {
+ reftile := tileVariant[libref]
+ coverage := int64(0) // number of ref bases that are called in genomes -- max is len(reftile.Sequence)*len(cgs)*2
+ for cgidx, cg := range cgs {
+ for phase := 0; phase < 2; phase++ {
+ if len(cg.Variants) <= int(libref.Tag)*2+phase {
+ continue
+ }
+ variant := cg.Variants[int(libref.Tag)*2+phase]
+ if variant == 0 {
+ continue
+ }
+ genometile := tileVariant[tileLibRef{Tag: libref.Tag, Variant: variant}]
+ if variant == libref.Variant {
+ continue
+ }
+ refSequence := reftile.Sequence
+ // If needed, extend the reference
+ // sequence up to the tag at the end
+ // of the genometile sequence.
+ refstepend := refstep + 1
+ for refstepend < len(reftiles) && len(refSequence) >= taglen && !bytes.EqualFold(refSequence[len(refSequence)-taglen:], genometile.Sequence[len(genometile.Sequence)-taglen:]) {
+ if &refSequence[0] == &reftile.Sequence[0] {
+ refSequence = append([]byte(nil), refSequence...)
+ }
+ refSequence = append(refSequence, tileVariant[reftiles[refstepend]].Sequence...)
+ refstepend++
+ }
+ // (TODO: handle no-calls)
+ vars, _ := hgvs.Diff(strings.ToUpper(string(refSequence)), strings.ToUpper(string(genometile.Sequence)), time.Second)
+ for _, v := range vars {
+ if cmd.outputFormat.PadLeft {
+ v = v.PadLeft()
+ }
+ v.Position += refpos
+ log.Debugf("%s seq %s phase %d tag %d tile diff %s\n", cg.Name, seqname, phase, libref.Tag, v.String())
+ varslice := variantAt[v.Position]
+ if varslice == nil {
+ varslice = make([]hgvs.Variant, len(cgs)*2)
+ variantAt[v.Position] = varslice
+ }
+ varslice[cgidx*2+phase] = v
+ }
+ coverage += int64(len(reftile.Sequence))
+ }
+ }
+ refpos += len(reftile.Sequence) - taglen
+
+ // Flush entries from variantAt that are behind
+ // refpos. Flush all entries if this is the last
+ // reftile of the path/chromosome.
+ var flushpos []int
+ lastrefstep := refstep == len(reftiles)-1
+ for pos := range variantAt {
+ if lastrefstep || pos <= refpos {
+ flushpos = append(flushpos, pos)
+ }
+ }
+ sort.Slice(flushpos, func(i, j int) bool { return flushpos[i] < flushpos[j] })
+ for _, pos := range flushpos {
+ varslice := variantAt[pos]
+ delete(variantAt, pos)
+ for i := range varslice {
+ if varslice[i].Position == 0 {
+ varslice[i].Position = pos
+ }
+ }
+ cmd.outputFormat.Print(outw, seqname, varslice)
+ }
+ if bedw != nil && len(reftile.Sequence) > 0 {
+ tilestart := refpos - len(reftile.Sequence) + taglen
+ tileend := refpos
+ if !lastrefstep {
+ tileend += taglen
+ }
+ thickstart := tilestart + taglen
+ if refstep == 0 {
+ thickstart = 0
+ }
+ thickend := refpos
+ // coverage score, 0 to 1000
+ score := 1000 * coverage / int64(len(reftile.Sequence)) / int64(len(cgs)) / 2
+ fmt.Fprintf(bedw, "%s %d %d %d %d . %d %d\n",
+ seqname, tilestart, tileend,
+ libref.Tag,
+ score,
+ thickstart, thickend)
+ }
+ }
+}
+