-package lightning
-
-import (
- "bufio"
- "bytes"
- "context"
- "encoding/gob"
- "fmt"
- "io"
- "os"
- "regexp"
- "runtime"
- "sort"
- "strings"
- "sync"
- "sync/atomic"
-
- "github.com/klauspost/pgzip"
- log "github.com/sirupsen/logrus"
- "golang.org/x/crypto/blake2b"
-)
-
-type tileVariantID uint16 // 1-based
-
-type tileLibRef struct {
- Tag tagID
- Variant tileVariantID
-}
-
-type tileSeq map[string][]tileLibRef
-
-func (tseq tileSeq) Variants() ([]tileVariantID, int, int) {
- maxtag := 0
- for _, refs := range tseq {
- for _, ref := range refs {
- if maxtag < int(ref.Tag) {
- maxtag = int(ref.Tag)
- }
- }
- }
- vars := make([]tileVariantID, maxtag+1)
- var kept, dropped int
- for _, refs := range tseq {
- for _, ref := range refs {
- if vars[int(ref.Tag)] != 0 {
- dropped++
- } else {
- kept++
- }
- vars[int(ref.Tag)] = ref.Variant
- }
- }
- return vars, kept, dropped
-}
-
-type tileLibrary struct {
- retainNoCalls bool
- skipOOO bool
- retainTileSequences bool
-
- taglib *tagLibrary
- variant [][][blake2b.Size256]byte
- refseqs map[string]map[string][]tileLibRef
- compactGenomes map[string][]tileVariantID
- seq2 map[[2]byte]map[[blake2b.Size256]byte][]byte
- seq2lock map[[2]byte]sync.Locker
- variants int64
- // if non-nil, write out any tile variants added while tiling
- encoder *gob.Encoder
-
- mtx sync.RWMutex
- vlock []sync.Locker
-}
-
-func (tilelib *tileLibrary) loadTagSet(newtagset [][]byte) error {
- // Loading a tagset means either passing it through to the
- // output (if it's the first one we've seen), or just ensuring
- // it doesn't disagree with what we already have.
- if len(newtagset) == 0 {
- return nil
- }
- tilelib.mtx.Lock()
- defer tilelib.mtx.Unlock()
- if tilelib.taglib == nil || tilelib.taglib.Len() == 0 {
- tilelib.taglib = &tagLibrary{}
- err := tilelib.taglib.setTags(newtagset)
- if err != nil {
- return err
- }
- if tilelib.encoder != nil {
- err = tilelib.encoder.Encode(LibraryEntry{
- TagSet: newtagset,
- })
- if err != nil {
- return err
- }
- }
- } else if tilelib.taglib.Len() != len(newtagset) {
- return fmt.Errorf("cannot merge libraries with differing tagsets")
- } else {
- current := tilelib.taglib.Tags()
- for i := range newtagset {
- if !bytes.Equal(newtagset[i], current[i]) {
- return fmt.Errorf("cannot merge libraries with differing tagsets")
- }
- }
- }
- 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
- allcgs := make([][]CompactGenome, len(files))
- allcseqs := make([][]CompactSequence, len(files))
- allvariantmap := map[tileLibRef]tileVariantID{}
- errs := make(chan error, len(files))
- log.Infof("LoadDir: read %d files", len(files))
- for fileno, path := range files {
- fileno, path := fileno, path
- go func() {
- f, err := open(path)
- if err != nil {
- errs <- err
- return
- }
- defer f.Close()
- defer log.Infof("LoadDir: finished reading %s", path)
-
- var variantmap = map[tileLibRef]tileVariantID{}
- var cgs []CompactGenome
- var cseqs []CompactSequence
- 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()
- }
- for _, tv := range ent.TileVariants {
- variantmap[tileLibRef{Tag: tv.Tag, Variant: tv.Variant}] = tilelib.getRef(tv.Tag, tv.Sequence).Variant
- }
- cgs = append(cgs, ent.CompactGenomes...)
- cseqs = append(cseqs, ent.CompactSequences...)
- return nil
- })
- allcgs[fileno] = cgs
- allcseqs[fileno] = cseqs
- mtx.Lock()
- defer mtx.Unlock()
- for k, v := range variantmap {
- allvariantmap[k] = v
- }
- }()
- }
- for range files {
- err := <-errs
- if err != nil {
- return err
- }
- }
-
- log.Info("LoadDir: loadCompactGenomes")
- var flatcgs []CompactGenome
- for _, cgs := range allcgs {
- flatcgs = append(flatcgs, cgs...)
- }
- err = tilelib.loadCompactGenomes(flatcgs, allvariantmap, onLoadGenome)
- if err != nil {
- return err
- }
-
- log.Info("LoadDir: loadCompactSequences")
- var flatcseqs []CompactSequence
- for _, cseqs := range allcseqs {
- flatcseqs = append(flatcseqs, cseqs...)
- }
- err = tilelib.loadCompactSequences(flatcseqs, allvariantmap)
- 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.hashSequence(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)
- } else {
- fmt.Fprintf(out, " %x", tilelib.variant[tag][variant-1][:8])
- }
- }
- for refname, refseqs := range tilelib.refseqs {
- for seqname, seq := range refseqs {
- fmt.Fprintf(out, "ref %s %s", refname, seqname)
- for _, libref := range seq {
- printTV(int(libref.Tag), libref.Variant)
- }
- fmt.Fprintf(out, "\n")
- }
- }
- for name, cg := range tilelib.compactGenomes {
- fmt.Fprintf(out, "cg %s", name)
- for tag, variant := range cg {
- printTV(tag/2, variant)
- }
- fmt.Fprintf(out, "\n")
- }
-}
-
-type importStats struct {
- InputFile string
- InputLabel string
- InputLength int
- InputCoverage int
- PathLength int
- DroppedOutOfOrderTiles int
-}
-
-func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader, matchChromosome *regexp.Regexp) (tileSeq, []importStats, error) {
- ret := tileSeq{}
- type jobT struct {
- label string
- fasta []byte
- }
- todo := make(chan jobT, 1)
- scanner := bufio.NewScanner(rdr)
- go func() {
- defer close(todo)
- var fasta []byte
- var seqlabel string
- for scanner.Scan() {
- buf := scanner.Bytes()
- if len(buf) > 0 && buf[0] == '>' {
- todo <- jobT{seqlabel, append([]byte(nil), fasta...)}
- seqlabel, fasta = strings.SplitN(string(buf[1:]), " ", 2)[0], fasta[:0]
- log.Debugf("%s %s reading fasta", filelabel, seqlabel)
- } else {
- fasta = append(fasta, bytes.ToLower(buf)...)
- }
- }
- todo <- jobT{seqlabel, fasta}
- }()
- type foundtag struct {
- pos int
- tagid tagID
- }
- found := make([]foundtag, 2000000)
- path := make([]tileLibRef, 2000000)
- totalFoundTags := 0
- totalPathLen := 0
- skippedSequences := 0
- taglen := tilelib.taglib.TagLen()
- var stats []importStats
- for job := range todo {
- if len(job.fasta) == 0 {
- continue
- } else if !matchChromosome.MatchString(job.label) {
- skippedSequences++
- continue
- }
- log.Debugf("%s %s tiling", filelabel, job.label)
-
- found = found[:0]
- tilelib.taglib.FindAll(job.fasta, func(tagid tagID, pos, taglen int) {
- found = append(found, foundtag{pos: pos, tagid: tagid})
- })
- totalFoundTags += len(found)
- if len(found) == 0 {
- log.Warnf("%s %s no tags found", filelabel, job.label)
- }
-
- skipped := 0
- if tilelib.skipOOO {
- log.Infof("%s %s keeping longest increasing subsequence", filelabel, job.label)
- keep := longestIncreasingSubsequence(len(found), func(i int) int { return int(found[i].tagid) })
- for i, x := range keep {
- found[i] = found[x]
- }
- skipped = len(found) - len(keep)
- found = found[:len(keep)]
- }
-
- log.Infof("%s %s getting %d librefs", filelabel, job.label, len(found))
- throttle := &throttle{Max: runtime.NumCPU()}
- path = path[:len(found)]
- var lowquality int64
- for i, f := range found {
- i, f := i, f
- throttle.Acquire()
- go func() {
- defer throttle.Release()
- var startpos, endpos int
- if i == 0 {
- startpos = 0
- } else {
- startpos = f.pos
- }
- if i == len(found)-1 {
- endpos = len(job.fasta)
- } else {
- endpos = found[i+1].pos + taglen
- }
- path[i] = tilelib.getRef(f.tagid, job.fasta[startpos:endpos])
- if countBases(job.fasta[startpos:endpos]) != endpos-startpos {
- atomic.AddInt64(&lowquality, 1)
- }
- }()
- }
- throttle.Wait()
-
- log.Infof("%s %s copying path", filelabel, job.label)
-
- pathcopy := make([]tileLibRef, len(path))
- copy(pathcopy, path)
- ret[job.label] = pathcopy
-
- basesIn := countBases(job.fasta)
- log.Infof("%s %s fasta in %d coverage in %d path len %d low-quality %d skipped-out-of-order %d", filelabel, job.label, len(job.fasta), basesIn, len(path), lowquality, skipped)
- stats = append(stats, importStats{
- InputFile: filelabel,
- InputLabel: job.label,
- InputLength: len(job.fasta),
- InputCoverage: basesIn,
- PathLength: len(path),
- DroppedOutOfOrderTiles: skipped,
- })
-
- totalPathLen += len(path)
- }
- log.Printf("%s tiled with total path len %d in %d sequences (skipped %d sequences that did not match chromosome regexp, skipped %d out-of-order tags)", filelabel, totalPathLen, len(ret), skippedSequences, totalFoundTags-totalPathLen)
- return ret, stats, scanner.Err()
-}
-
-func (tilelib *tileLibrary) Len() int64 {
- return atomic.LoadInt64(&tilelib.variants)
-}
-
-// Return a tileLibRef for a tile with the given tag and sequence,
-// adding the sequence to the library if needed.
-func (tilelib *tileLibrary) getRef(tag tagID, seq []byte) tileLibRef {
- dropSeq := false
- if !tilelib.retainNoCalls {
- for _, b := range seq {
- if b != 'a' && b != 'c' && b != 'g' && b != 't' {
- dropSeq = true
- break
- }
- }
- }
- seqhash := blake2b.Sum256(seq)
- var vlock sync.Locker
-
- tilelib.mtx.RLock()
- if len(tilelib.vlock) > int(tag) {
- vlock = tilelib.vlock[tag]
- }
- tilelib.mtx.RUnlock()
-
- if vlock != nil {
- vlock.Lock()
- for i, varhash := range tilelib.variant[tag] {
- if varhash == seqhash {
- vlock.Unlock()
- return tileLibRef{Tag: tag, Variant: tileVariantID(i + 1)}
- }
- }
- vlock.Unlock()
- } else {
- tilelib.mtx.Lock()
- if tilelib.variant == nil && tilelib.taglib != nil {
- tilelib.variant = make([][][blake2b.Size256]byte, tilelib.taglib.Len())
- tilelib.vlock = make([]sync.Locker, tilelib.taglib.Len())
- for i := range tilelib.vlock {
- tilelib.vlock[i] = new(sync.Mutex)
- }
- }
- if int(tag) >= len(tilelib.variant) {
- oldlen := len(tilelib.vlock)
- for i := 0; i < oldlen; i++ {
- tilelib.vlock[i].Lock()
- }
- // If we haven't seen the tag library yet (as
- // in a merge), tilelib.taglib.Len() is
- // zero. We can still behave correctly, we
- // just need to expand the tilelib.variant and
- // tilelib.vlock slices as needed.
- if int(tag) >= cap(tilelib.variant) {
- // Allocate 2x capacity.
- newslice := make([][][blake2b.Size256]byte, int(tag)+1, (int(tag)+1)*2)
- copy(newslice, tilelib.variant)
- tilelib.variant = newslice[:int(tag)+1]
- newvlock := make([]sync.Locker, int(tag)+1, (int(tag)+1)*2)
- copy(newvlock, tilelib.vlock)
- tilelib.vlock = newvlock[:int(tag)+1]
- } else {
- // Use previously allocated capacity,
- // avoiding copy.
- tilelib.variant = tilelib.variant[:int(tag)+1]
- tilelib.vlock = tilelib.vlock[:int(tag)+1]
- }
- for i := oldlen; i < len(tilelib.vlock); i++ {
- tilelib.vlock[i] = new(sync.Mutex)
- }
- for i := 0; i < oldlen; i++ {
- tilelib.vlock[i].Unlock()
- }
- }
- vlock = tilelib.vlock[tag]
- tilelib.mtx.Unlock()
- }
-
- vlock.Lock()
- for i, varhash := range tilelib.variant[tag] {
- if varhash == seqhash {
- vlock.Unlock()
- return tileLibRef{Tag: tag, Variant: tileVariantID(i + 1)}
- }
- }
- atomic.AddInt64(&tilelib.variants, 1)
- tilelib.variant[tag] = append(tilelib.variant[tag], seqhash)
- variant := tileVariantID(len(tilelib.variant[tag]))
- vlock.Unlock()
-
- if tilelib.retainTileSequences && !dropSeq {
- seqCopy := append([]byte(nil), seq...)
- if tilelib.seq2 == nil {
- tilelib.mtx.Lock()
- if tilelib.seq2 == nil {
- tilelib.seq2lock = map[[2]byte]sync.Locker{}
- m := map[[2]byte]map[[blake2b.Size256]byte][]byte{}
- var k [2]byte
- for i := 0; i < 256; i++ {
- k[0] = byte(i)
- for j := 0; j < 256; j++ {
- k[1] = byte(j)
- m[k] = map[[blake2b.Size256]byte][]byte{}
- tilelib.seq2lock[k] = &sync.Mutex{}
- }
- }
- tilelib.seq2 = m
- }
- tilelib.mtx.Unlock()
- }
- var k [2]byte
- copy(k[:], seqhash[:])
- locker := tilelib.seq2lock[k]
- locker.Lock()
- tilelib.seq2[k][seqhash] = seqCopy
- locker.Unlock()
- }
-
- if tilelib.encoder != nil {
- saveSeq := seq
- if dropSeq {
- // Save the hash, but not the sequence
- saveSeq = nil
- }
- tilelib.encoder.Encode(LibraryEntry{
- TileVariants: []TileVariant{{
- Tag: tag,
- Variant: variant,
- Blake2b: seqhash,
- Sequence: saveSeq,
- }},
- })
- }
- return tileLibRef{Tag: tag, Variant: variant}
-}
-
-func (tilelib *tileLibrary) hashSequence(hash [blake2b.Size256]byte) []byte {
- var partition [2]byte
- copy(partition[:], hash[:])
- return tilelib.seq2[partition][hash]
-}
-
-func (tilelib *tileLibrary) TileVariantSequence(libref tileLibRef) []byte {
- if libref.Variant == 0 || len(tilelib.variant) <= int(libref.Tag) || len(tilelib.variant[libref.Tag]) < int(libref.Variant) {
- return nil
- }
- return tilelib.hashSequence(tilelib.variant[libref.Tag][libref.Variant-1])
-}
-
-// Tidy deletes unreferenced tile variants and renumbers variants so
-// more common variants have smaller IDs.
-func (tilelib *tileLibrary) Tidy() {
- log.Print("Tidy: compute inref")
- inref := map[tileLibRef]bool{}
- for _, refseq := range tilelib.refseqs {
- for _, librefs := range refseq {
- for _, libref := range librefs {
- inref[libref] = true
- }
- }
- }
- log.Print("Tidy: compute remap")
- remap := make([][]tileVariantID, len(tilelib.variant))
- throttle := throttle{Max: runtime.NumCPU() + 1}
- for tag, oldvariants := range tilelib.variant {
- tag, oldvariants := tagID(tag), oldvariants
- if tag%1000000 == 0 {
- log.Printf("Tidy: tag %d", tag)
- }
- throttle.Acquire()
- go func() {
- defer throttle.Release()
- uses := make([]int, len(oldvariants))
- for _, cg := range tilelib.compactGenomes {
- for phase := 0; phase < 2; phase++ {
- cgi := int(tag)*2 + phase
- if cgi < len(cg) && cg[cgi] > 0 {
- uses[cg[cgi]-1]++
- }
- }
- }
-
- // Compute desired order of variants:
- // neworder[x] == index in oldvariants that
- // should move to position x.
- neworder := make([]int, len(oldvariants))
- for i := range neworder {
- neworder[i] = i
- }
- sort.Slice(neworder, func(i, j int) bool {
- if cmp := uses[neworder[i]] - uses[neworder[j]]; cmp != 0 {
- return cmp > 0
- } else {
- return bytes.Compare(oldvariants[neworder[i]][:], oldvariants[neworder[j]][:]) < 0
- }
- })
-
- // Replace tilelib.variant[tag] with a new
- // re-ordered slice of hashes, and make a
- // mapping from old to new variant IDs.
- remaptag := make([]tileVariantID, len(oldvariants)+1)
- newvariants := make([][blake2b.Size256]byte, 0, len(neworder))
- for _, oldi := range neworder {
- if uses[oldi] > 0 || inref[tileLibRef{Tag: tag, Variant: tileVariantID(oldi + 1)}] {
- newvariants = append(newvariants, oldvariants[oldi])
- remaptag[oldi+1] = tileVariantID(len(newvariants))
- }
- }
- tilelib.variant[tag] = newvariants
- remap[tag] = remaptag
- }()
- }
- throttle.Wait()
-
- // Apply remap to genomes and reference sequences, so they
- // refer to the same tile variants using the changed IDs.
- log.Print("Tidy: apply remap")
- var wg sync.WaitGroup
- for _, cg := range tilelib.compactGenomes {
- cg := cg
- wg.Add(1)
- go func() {
- defer wg.Done()
- for idx, variant := range cg {
- cg[idx] = remap[tagID(idx/2)][variant]
- }
- }()
- }
- for _, refcs := range tilelib.refseqs {
- for _, refseq := range refcs {
- refseq := refseq
- wg.Add(1)
- go func() {
- defer wg.Done()
- for i, tv := range refseq {
- refseq[i].Variant = remap[tv.Tag][tv.Variant]
- }
- }()
- }
- }
- wg.Wait()
- log.Print("Tidy: done")
-}
-
-func countBases(seq []byte) int {
- n := 0
- for _, c := range seq {
- if isbase[c] {
- n++
- }
- }
- return n
-}
projects / lightning.git / blobdiff