import (
"bufio"
"bytes"
- "crypto/md5"
+ "context"
+ "encoding/gob"
+ "fmt"
"io"
- "log"
+ "runtime"
+ "sort"
+ "strings"
"sync"
+
+ log "github.com/sirupsen/logrus"
+ "golang.org/x/crypto/blake2b"
)
-type tileVariantID int32 // 1-based
+type tileVariantID uint16 // 1-based
type tileLibRef struct {
- tag tagID
- variant tileVariantID
+ 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 {
- taglib *tagLibrary
- variant [][][md5.Size]byte
+ retainNoCalls bool
+ skipOOO bool
+ retainTileSequences bool
+
+ taglib *tagLibrary
+ variant [][][blake2b.Size256]byte
+ refseqs map[string]map[string][]tileLibRef
+ compactGenomes map[string][]tileVariantID
// count [][]int
- // seq map[[md5.Size]byte][]byte
+ seq map[[blake2b.Size256]byte][]byte
+ variants int
+ // if non-nil, write out any tile variants added while tiling
+ encoder *gob.Encoder
mtx sync.Mutex
}
-func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader) (tileSeq, error) {
- ret := tileSeq{}
+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
- flush := func(seqlabel string, fasta []byte) {
- defer wg.Done()
- var path []tileLibRef
- if len(fasta) == 0 {
- return
- }
- tilestart := -1 // position in fasta of tile that ends here
- tiletagid := tagID(-1) // tag id starting tile that ends here
- tilelib.taglib.FindAll(fasta, func(id tagID, pos int) {
- if tilestart >= 0 {
- path = append(path, tilelib.getRef(tiletagid, fasta[tilestart:pos]))
- }
- tilestart = pos
- tiletagid = id
- })
- if tiletagid >= 0 {
- path = append(path, tilelib.getRef(tiletagid, fasta[tilestart:]))
+ 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
+ }
}
- ret[seqlabel] = path
- log.Printf("%s %s tiled with path len %d", filelabel, seqlabel, len(path))
}
- var fasta []byte
- var seqlabel string
+ 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
+}
+
+// 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
+}
+
+type importStats struct {
+ InputFile string
+ InputLabel string
+ InputLength int
+ InputCoverage int
+ TileCoverage int
+ PathLength int
+ DroppedOutOfOrderTiles int
+}
+
+func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader) (tileSeq, []importStats, error) {
+ ret := tileSeq{}
+ type jobT struct {
+ label string
+ fasta []byte
+ }
+ todo := make(chan jobT)
scanner := bufio.NewScanner(rdr)
- for scanner.Scan() {
- buf := scanner.Bytes()
- if len(buf) == 0 || buf[0] == '>' {
- wg.Add(1)
- go flush(seqlabel, fasta)
- fasta = nil
- seqlabel = string(buf[1:])
- } else {
- fasta = append(fasta, bytes.ToLower(buf)...)
+ 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, fasta}
+ seqlabel, fasta = strings.SplitN(string(buf[1:]), " ", 2)[0], nil
+ 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
+ taglen int
}
- if err := scanner.Err(); err != nil {
- return nil, err
+ found := make([]foundtag, 2000000)
+ path := make([]tileLibRef, 2000000)
+ totalFoundTags := 0
+ totalPathLen := 0
+ skippedSequences := 0
+ stats := make([]importStats, 0, len(todo))
+ for job := range todo {
+ if len(job.fasta) == 0 {
+ continue
+ } else if strings.Contains(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, taglen: taglen})
+ })
+ totalFoundTags += len(found)
+
+ basesOut := 0
+ skipped := 0
+ path = path[:0]
+ last := foundtag{tagid: -1}
+ if tilelib.skipOOO {
+ 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)]
+ }
+ for i, f := range found {
+ log.Tracef("%s %s found[%d] == %#v", filelabel, job.label, i, f)
+ if last.tagid < 0 {
+ // first tag in sequence
+ last = foundtag{tagid: f.tagid}
+ continue
+ }
+ libref := tilelib.getRef(last.tagid, job.fasta[last.pos:f.pos+f.taglen])
+ path = append(path, libref)
+ if libref.Variant > 0 {
+ // Count output coverage from
+ // the end of the previous tag
+ // (if any) to the end of the
+ // current tag, IOW don't
+ // double-count coverage for
+ // the previous tag.
+ basesOut += countBases(job.fasta[last.pos+last.taglen : f.pos+f.taglen])
+ } else {
+ // If we dropped this tile
+ // (because !retainNoCalls),
+ // set taglen=0 so the
+ // overlapping tag is counted
+ // toward coverage on the
+ // following tile.
+ f.taglen = 0
+ }
+ last = f
+ }
+ if last.tagid < 0 {
+ log.Warnf("%s %s no tags found", filelabel, job.label)
+ } else {
+ libref := tilelib.getRef(last.tagid, job.fasta[last.pos:])
+ path = append(path, libref)
+ if libref.Variant > 0 {
+ basesOut += countBases(job.fasta[last.pos+last.taglen:])
+ }
+ }
+
+ 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 coverage out %d path len %d skipped %d", filelabel, job.label, len(job.fasta), basesIn, basesOut, len(path), skipped)
+ stats = append(stats, importStats{
+ InputFile: filelabel,
+ InputLabel: job.label,
+ InputLength: len(job.fasta),
+ InputCoverage: basesIn,
+ TileCoverage: basesOut,
+ PathLength: len(path),
+ DroppedOutOfOrderTiles: skipped,
+ })
+
+ totalPathLen += len(path)
}
- wg.Add(1)
- go flush(seqlabel, fasta)
- wg.Wait()
- return ret, nil
+ log.Printf("%s tiled with total path len %d in %d sequences (skipped %d sequences with '_' in name, skipped %d out-of-order tags)", filelabel, totalPathLen, len(ret), skippedSequences, totalFoundTags-totalPathLen)
+ return ret, stats, scanner.Err()
+}
+
+func (tilelib *tileLibrary) Len() int {
+ tilelib.mtx.Lock()
+ defer tilelib.mtx.Unlock()
+ return 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
+ }
+ }
+ }
tilelib.mtx.Lock()
- defer tilelib.mtx.Unlock()
- // if tilelib.seq == nil {
- // tilelib.seq = map[[md5.Size]byte][]byte{}
- // }
- if len(tilelib.variant) <= int(tag) {
- tilelib.variant = append(tilelib.variant, make([][][md5.Size]byte, int(tag)-len(tilelib.variant)+1)...)
+ if tilelib.variant == nil && tilelib.taglib != nil {
+ tilelib.variant = make([][][blake2b.Size256]byte, tilelib.taglib.Len())
}
- seqhash := md5.Sum(seq)
+ if int(tag) >= len(tilelib.variant) {
+ // 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 slice 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]
+ } else {
+ // Use previously allocated capacity, avoiding
+ // copy.
+ tilelib.variant = tilelib.variant[:int(tag)+1]
+ }
+ }
+ seqhash := blake2b.Sum256(seq)
for i, varhash := range tilelib.variant[tag] {
if varhash == seqhash {
- return tileLibRef{tag: tag, variant: tileVariantID(i + 1)}
+ tilelib.mtx.Unlock()
+ return tileLibRef{Tag: tag, Variant: tileVariantID(i + 1)}
}
}
+ tilelib.variants++
tilelib.variant[tag] = append(tilelib.variant[tag], seqhash)
- // tilelib.seq[seqhash] = append([]byte(nil), seq...)
- return tileLibRef{tag: tag, variant: tileVariantID(len(tilelib.variant[tag]))}
+ if tilelib.retainTileSequences && !dropSeq {
+ if tilelib.seq == nil {
+ tilelib.seq = map[[blake2b.Size256]byte][]byte{}
+ }
+ tilelib.seq[seqhash] = append([]byte(nil), seq...)
+ }
+ variant := tileVariantID(len(tilelib.variant[tag]))
+ tilelib.mtx.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) 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.seq[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%10000 == 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.variants[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")
+ for _, cg := range tilelib.compactGenomes {
+ for idx, variant := range cg {
+ cg[idx] = remap[tagID(idx/2)][variant]
+ }
+ }
+ for _, refcs := range tilelib.refseqs {
+ for _, refseq := range refcs {
+ for i, tv := range refseq {
+ refseq[i].Variant = remap[tv.Tag][tv.Variant]
+ }
+ }
+ }
+ 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