+ return nil
+}
+
+func (tilelib *tileLibrary) loadTileVariants(tvs []TileVariant, variantmap map[tileLibRef]tileVariantID) error {
+ for _, tv := range tvs {
+ // Assign a new variant ID (unique across all inputs)
+ // for each input variant.
+ variantmap[tileLibRef{Tag: tv.Tag, Variant: tv.Variant}] = tilelib.getRef(tv.Tag, tv.Sequence).Variant
+ }
+ return nil
+}
+
+func (tilelib *tileLibrary) loadCompactGenomes(cgs []CompactGenome, variantmap map[tileLibRef]tileVariantID, onLoadGenome func(CompactGenome)) error {
+ log.Debugf("loadCompactGenomes: %d", len(cgs))
+ var wg sync.WaitGroup
+ errs := make(chan error, 1)
+ for _, cg := range cgs {
+ wg.Add(1)
+ cg := cg
+ go func() {
+ defer wg.Done()
+ for i, variant := range cg.Variants {
+ if len(errs) > 0 {
+ return
+ }
+ if variant == 0 {
+ continue
+ }
+ tag := tagID(i / 2)
+ newvariant, ok := variantmap[tileLibRef{Tag: tag, Variant: variant}]
+ if !ok {
+ err := fmt.Errorf("oops: genome %q has variant %d for tag %d, but that variant was not in its library", cg.Name, variant, tag)
+ select {
+ case errs <- err:
+ default:
+ }
+ return
+ }
+ log.Tracef("loadCompactGenomes: cg %s tag %d variant %d => %d", cg.Name, tag, variant, newvariant)
+ cg.Variants[i] = newvariant
+ }
+ if onLoadGenome != nil {
+ onLoadGenome(cg)
+ }
+ if tilelib.encoder != nil {
+ err := tilelib.encoder.Encode(LibraryEntry{
+ CompactGenomes: []CompactGenome{cg},
+ })
+ if err != nil {
+ select {
+ case errs <- err:
+ default:
+ }
+ return
+ }
+ }
+ if tilelib.compactGenomes != nil {
+ tilelib.mtx.Lock()
+ defer tilelib.mtx.Unlock()
+ tilelib.compactGenomes[cg.Name] = cg.Variants
+ }
+ }()
+ }
+ wg.Wait()
+ go close(errs)
+ return <-errs
+}
+
+func (tilelib *tileLibrary) loadCompactSequences(cseqs []CompactSequence, variantmap map[tileLibRef]tileVariantID) error {
+ log.Debugf("loadCompactSequences: %d", len(cseqs))
+ for _, cseq := range cseqs {
+ for _, tseq := range cseq.TileSequences {
+ for i, libref := range tseq {
+ if libref.Variant == 0 {
+ // No variant (e.g., import
+ // dropped tiles with
+ // no-calls) = no translation.
+ continue
+ }
+ v, ok := variantmap[libref]
+ if !ok {
+ return fmt.Errorf("oops: CompactSequence %q has variant %d for tag %d, but that variant was not in its library", cseq.Name, libref.Variant, libref.Tag)
+ }
+ tseq[i].Variant = v
+ }
+ }
+ if tilelib.encoder != nil {
+ if err := tilelib.encoder.Encode(LibraryEntry{
+ CompactSequences: []CompactSequence{cseq},
+ }); err != nil {
+ return err
+ }
+ }
+ }
+ tilelib.mtx.Lock()
+ defer tilelib.mtx.Unlock()
+ if tilelib.refseqs == nil {
+ tilelib.refseqs = map[string]map[string][]tileLibRef{}
+ }
+ for _, cseq := range cseqs {
+ tilelib.refseqs[cseq.Name] = cseq.TileSequences
+ }
+ return nil
+}
+
+func (tilelib *tileLibrary) LoadDir(ctx context.Context, path string, onLoadGenome func(CompactGenome)) error {
+ var files []string
+ var walk func(string) error
+ walk = func(path string) error {
+ f, err := open(path)
+ if err != nil {
+ return err
+ }
+ defer f.Close()
+ fis, err := f.Readdir(-1)
+ if err != nil {
+ files = append(files, path)
+ return nil
+ }
+ for _, fi := range fis {
+ if fi.Name() == "." || fi.Name() == ".." {
+ continue
+ } else if child := path + "/" + fi.Name(); fi.IsDir() {
+ err = walk(child)
+ if err != nil {
+ return err
+ }
+ } else if strings.HasSuffix(child, ".gob") || strings.HasSuffix(child, ".gob.gz") {
+ files = append(files, child)
+ }
+ }
+ return nil
+ }
+ log.Infof("LoadDir: walk dir %s", path)
+ err := walk(path)
+ if err != nil {
+ return err
+ }
+ ctx, cancel := context.WithCancel(ctx)
+ defer cancel()
+ var mtx sync.Mutex
+ cgs := []CompactGenome{}
+ cseqs := []CompactSequence{}
+ variantmap := map[tileLibRef]tileVariantID{}
+ errs := make(chan error, len(files))
+ log.Infof("LoadDir: read %d files", len(files))
+ for _, path := range files {
+ path := path
+ go func() {
+ f, err := open(path)
+ if err != nil {
+ errs <- err
+ return
+ }
+ defer f.Close()
+ defer log.Infof("LoadDir: finished reading %s", path)
+ errs <- DecodeLibrary(f, strings.HasSuffix(path, ".gz"), func(ent *LibraryEntry) error {
+ if ctx.Err() != nil {
+ return ctx.Err()
+ }
+ if len(ent.TagSet) > 0 {
+ mtx.Lock()
+ if tilelib.taglib == nil || tilelib.taglib.Len() != len(ent.TagSet) {
+ // load first set of tags, or
+ // report mismatch if 2 sets
+ // have different #tags.
+ if err := tilelib.loadTagSet(ent.TagSet); err != nil {
+ mtx.Unlock()
+ return err
+ }
+ }
+ mtx.Unlock()
+ }
+ variantmapadd := map[tileLibRef]tileVariantID{}
+ for _, tv := range ent.TileVariants {
+ variantmapadd[tileLibRef{Tag: tv.Tag, Variant: tv.Variant}] = tilelib.getRef(tv.Tag, tv.Sequence).Variant
+ }
+ mtx.Lock()
+ cgs = append(cgs, ent.CompactGenomes...)
+ cseqs = append(cseqs, ent.CompactSequences...)
+ for k, v := range variantmapadd {
+ variantmap[k] = v
+ }
+ mtx.Unlock()
+ return nil
+ })
+ }()
+ }
+ for range files {
+ err := <-errs
+ if err != nil {
+ return err
+ }
+ }
+ log.Info("LoadDir: loadCompactGenomes")
+ err = tilelib.loadCompactGenomes(cgs, variantmap, onLoadGenome)
+ if err != nil {
+ return err
+ }
+ log.Info("LoadDir: loadCompactSequences")
+ err = tilelib.loadCompactSequences(cseqs, variantmap)
+ if err != nil {
+ return err
+ }
+ log.Info("LoadDir done")
+ return nil
+}
+
+func (tilelib *tileLibrary) WriteDir(dir string) error {
+ nfiles := 128
+ files := make([]*os.File, nfiles)
+ for i := range files {
+ f, err := os.OpenFile(fmt.Sprintf("%s/library.%04d.gob.gz", dir, i), os.O_CREATE|os.O_WRONLY, 0666)
+ if err != nil {
+ return err
+ }
+ defer f.Close()
+ files[i] = f
+ }
+ bufws := make([]*bufio.Writer, nfiles)
+ for i := range bufws {
+ bufws[i] = bufio.NewWriterSize(files[i], 1<<26)
+ }
+ zws := make([]*pgzip.Writer, nfiles)
+ for i := range zws {
+ zws[i] = pgzip.NewWriter(bufws[i])
+ defer zws[i].Close()
+ }
+ encoders := make([]*gob.Encoder, nfiles)
+ for i := range encoders {
+ encoders[i] = gob.NewEncoder(zws[i])
+ }
+
+ cgnames := make([]string, 0, len(tilelib.compactGenomes))
+ for name := range tilelib.compactGenomes {
+ cgnames = append(cgnames, name)
+ }
+ sort.Strings(cgnames)
+
+ log.Infof("WriteDir: writing %d files", nfiles)
+ ctx, cancel := context.WithCancel(context.Background())
+ defer cancel()
+ errs := make(chan error, nfiles)
+ for start := range files {
+ start := start
+ go func() {
+ err := encoders[start].Encode(LibraryEntry{TagSet: tilelib.taglib.Tags()})
+ if err != nil {
+ errs <- err
+ return
+ }
+ if start == 0 {
+ // For now, just write all the refs to
+ // the first file
+ for name, tseqs := range tilelib.refseqs {
+ err := encoders[start].Encode(LibraryEntry{CompactSequences: []CompactSequence{{
+ Name: name,
+ TileSequences: tseqs,
+ }}})
+ if err != nil {
+ errs <- err
+ return
+ }
+ }
+ }
+ for i := start; i < len(cgnames); i += nfiles {
+ err := encoders[start].Encode(LibraryEntry{CompactGenomes: []CompactGenome{{
+ Name: cgnames[i],
+ Variants: tilelib.compactGenomes[cgnames[i]],
+ }}})
+ if err != nil {
+ errs <- err
+ return
+ }
+ }
+ tvs := []TileVariant{}
+ for tag := start; tag < len(tilelib.variant) && ctx.Err() == nil; tag += nfiles {
+ tvs = tvs[:0]
+ for idx, hash := range tilelib.variant[tag] {
+ tvs = append(tvs, TileVariant{
+ Tag: tagID(tag),
+ Variant: tileVariantID(idx + 1),
+ Blake2b: hash,
+ Sequence: tilelib.seq[hash],
+ })
+ }
+ err := encoders[start].Encode(LibraryEntry{TileVariants: tvs})
+ if err != nil {
+ errs <- err
+ return
+ }
+ }
+ errs <- nil
+ }()
+ }
+ for range files {
+ err := <-errs
+ if err != nil {
+ return err
+ }
+ }
+ log.Info("WriteDir: flushing")
+ for i := range zws {
+ err := zws[i].Close()
+ if err != nil {
+ return err
+ }
+ err = bufws[i].Flush()
+ if err != nil {
+ return err
+ }
+ err = files[i].Close()
+ if err != nil {
+ return err
+ }
+ }
+ log.Info("WriteDir: done")
+ return nil
+}
+
+// Load library data from rdr. Tile variants might be renumbered in
+// the process; in that case, genomes variants will be renumbered to
+// match.
+//
+// If onLoadGenome is non-nil, call it on each CompactGenome entry.
+func (tilelib *tileLibrary) LoadGob(ctx context.Context, rdr io.Reader, gz bool, onLoadGenome func(CompactGenome)) error {
+ cgs := []CompactGenome{}
+ cseqs := []CompactSequence{}
+ variantmap := map[tileLibRef]tileVariantID{}
+ err := DecodeLibrary(rdr, gz, func(ent *LibraryEntry) error {
+ if ctx.Err() != nil {
+ return ctx.Err()
+ }
+ if err := tilelib.loadTagSet(ent.TagSet); err != nil {
+ return err
+ }
+ if err := tilelib.loadTileVariants(ent.TileVariants, variantmap); err != nil {
+ return err
+ }
+ cgs = append(cgs, ent.CompactGenomes...)
+ cseqs = append(cseqs, ent.CompactSequences...)
+ return nil
+ })
+ if err != nil {
+ return err
+ }
+ if ctx.Err() != nil {
+ return ctx.Err()
+ }
+ err = tilelib.loadCompactGenomes(cgs, variantmap, onLoadGenome)
+ if err != nil {
+ return err
+ }
+ err = tilelib.loadCompactSequences(cseqs, variantmap)
+ if err != nil {
+ return err
+ }
+ return nil
+}
+
+func (tilelib *tileLibrary) dump(out io.Writer) {
+ printTV := func(tag int, variant tileVariantID) {
+ if variant < 1 {
+ fmt.Fprintf(out, " -")
+ } else if tag >= len(tilelib.variant) {
+ fmt.Fprintf(out, " (!tag=%d)", tag)
+ } else if int(variant) > len(tilelib.variant[tag]) {
+ fmt.Fprintf(out, " (tag=%d,!variant=%d)", tag, variant)