17 log "github.com/sirupsen/logrus"
18 "golang.org/x/crypto/blake2b"
21 type tileVariantID uint16 // 1-based
23 type tileLibRef struct {
28 type tileSeq map[string][]tileLibRef
30 func (tseq tileSeq) Variants() ([]tileVariantID, int, int) {
32 for _, refs := range tseq {
33 for _, ref := range refs {
34 if maxtag < int(ref.Tag) {
39 vars := make([]tileVariantID, maxtag+1)
41 for _, refs := range tseq {
42 for _, ref := range refs {
43 if vars[int(ref.Tag)] != 0 {
48 vars[int(ref.Tag)] = ref.Variant
51 return vars, kept, dropped
54 type tileLibrary struct {
57 retainTileSequences bool
60 variant [][][blake2b.Size256]byte
61 refseqs map[string]map[string][]tileLibRef
62 compactGenomes map[string][]tileVariantID
64 seq map[[blake2b.Size256]byte][]byte
66 // if non-nil, write out any tile variants added while tiling
73 func (tilelib *tileLibrary) loadTagSet(newtagset [][]byte) error {
74 // Loading a tagset means either passing it through to the
75 // output (if it's the first one we've seen), or just ensuring
76 // it doesn't disagree with what we already have.
77 if len(newtagset) == 0 {
81 defer tilelib.mtx.Unlock()
82 if tilelib.taglib == nil || tilelib.taglib.Len() == 0 {
83 tilelib.taglib = &tagLibrary{}
84 err := tilelib.taglib.setTags(newtagset)
88 if tilelib.encoder != nil {
89 err = tilelib.encoder.Encode(LibraryEntry{
96 } else if tilelib.taglib.Len() != len(newtagset) {
97 return fmt.Errorf("cannot merge libraries with differing tagsets")
99 current := tilelib.taglib.Tags()
100 for i := range newtagset {
101 if !bytes.Equal(newtagset[i], current[i]) {
102 return fmt.Errorf("cannot merge libraries with differing tagsets")
109 func (tilelib *tileLibrary) loadTileVariants(tvs []TileVariant, variantmap map[tileLibRef]tileVariantID) error {
110 for _, tv := range tvs {
111 // Assign a new variant ID (unique across all inputs)
112 // for each input variant.
113 variantmap[tileLibRef{Tag: tv.Tag, Variant: tv.Variant}] = tilelib.getRef(tv.Tag, tv.Sequence).Variant
118 func (tilelib *tileLibrary) loadCompactGenomes(cgs []CompactGenome, variantmap map[tileLibRef]tileVariantID, onLoadGenome func(CompactGenome)) error {
119 log.Debugf("loadCompactGenomes: %d", len(cgs))
120 var wg sync.WaitGroup
121 errs := make(chan error, 1)
122 for _, cg := range cgs {
127 for i, variant := range cg.Variants {
135 newvariant, ok := variantmap[tileLibRef{Tag: tag, Variant: variant}]
137 err := fmt.Errorf("oops: genome %q has variant %d for tag %d, but that variant was not in its library", cg.Name, variant, tag)
144 log.Tracef("loadCompactGenomes: cg %s tag %d variant %d => %d", cg.Name, tag, variant, newvariant)
145 cg.Variants[i] = newvariant
147 if onLoadGenome != nil {
150 if tilelib.encoder != nil {
151 err := tilelib.encoder.Encode(LibraryEntry{
152 CompactGenomes: []CompactGenome{cg},
162 if tilelib.compactGenomes != nil {
164 defer tilelib.mtx.Unlock()
165 tilelib.compactGenomes[cg.Name] = cg.Variants
174 func (tilelib *tileLibrary) loadCompactSequences(cseqs []CompactSequence, variantmap map[tileLibRef]tileVariantID) error {
175 log.Debugf("loadCompactSequences: %d", len(cseqs))
176 for _, cseq := range cseqs {
177 for _, tseq := range cseq.TileSequences {
178 for i, libref := range tseq {
179 if libref.Variant == 0 {
180 // No variant (e.g., import
181 // dropped tiles with
182 // no-calls) = no translation.
185 v, ok := variantmap[libref]
187 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)
192 if tilelib.encoder != nil {
193 if err := tilelib.encoder.Encode(LibraryEntry{
194 CompactSequences: []CompactSequence{cseq},
201 defer tilelib.mtx.Unlock()
202 if tilelib.refseqs == nil {
203 tilelib.refseqs = map[string]map[string][]tileLibRef{}
205 for _, cseq := range cseqs {
206 tilelib.refseqs[cseq.Name] = cseq.TileSequences
211 // Load library data from rdr. Tile variants might be renumbered in
212 // the process; in that case, genomes variants will be renumbered to
215 // If onLoadGenome is non-nil, call it on each CompactGenome entry.
216 func (tilelib *tileLibrary) LoadGob(ctx context.Context, rdr io.Reader, gz bool, onLoadGenome func(CompactGenome)) error {
217 cgs := []CompactGenome{}
218 cseqs := []CompactSequence{}
219 variantmap := map[tileLibRef]tileVariantID{}
220 err := DecodeLibrary(rdr, gz, func(ent *LibraryEntry) error {
221 if ctx.Err() != nil {
224 if err := tilelib.loadTagSet(ent.TagSet); err != nil {
227 if err := tilelib.loadTileVariants(ent.TileVariants, variantmap); err != nil {
230 cgs = append(cgs, ent.CompactGenomes...)
231 cseqs = append(cseqs, ent.CompactSequences...)
237 if ctx.Err() != nil {
240 err = tilelib.loadCompactGenomes(cgs, variantmap, onLoadGenome)
244 err = tilelib.loadCompactSequences(cseqs, variantmap)
251 type importStats struct {
258 DroppedOutOfOrderTiles int
261 func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader, matchChromosome *regexp.Regexp) (tileSeq, []importStats, error) {
267 todo := make(chan jobT)
268 scanner := bufio.NewScanner(rdr)
274 buf := scanner.Bytes()
275 if len(buf) > 0 && buf[0] == '>' {
276 todo <- jobT{seqlabel, fasta}
277 seqlabel, fasta = strings.SplitN(string(buf[1:]), " ", 2)[0], nil
278 log.Debugf("%s %s reading fasta", filelabel, seqlabel)
280 fasta = append(fasta, bytes.ToLower(buf)...)
283 todo <- jobT{seqlabel, fasta}
285 type foundtag struct {
290 found := make([]foundtag, 2000000)
291 path := make([]tileLibRef, 2000000)
294 skippedSequences := 0
295 stats := make([]importStats, 0, len(todo))
296 for job := range todo {
297 if len(job.fasta) == 0 {
299 } else if !matchChromosome.MatchString(job.label) {
303 log.Debugf("%s %s tiling", filelabel, job.label)
306 tilelib.taglib.FindAll(job.fasta, func(tagid tagID, pos, taglen int) {
307 found = append(found, foundtag{pos: pos, tagid: tagid, taglen: taglen})
309 totalFoundTags += len(found)
314 last := foundtag{tagid: -1}
316 keep := longestIncreasingSubsequence(len(found), func(i int) int { return int(found[i].tagid) })
317 for i, x := range keep {
320 skipped = len(found) - len(keep)
321 found = found[:len(keep)]
323 for i, f := range found {
324 log.Tracef("%s %s found[%d] == %#v", filelabel, job.label, i, f)
326 // first tag in sequence
327 last = foundtag{tagid: f.tagid}
330 libref := tilelib.getRef(last.tagid, job.fasta[last.pos:f.pos+f.taglen])
331 path = append(path, libref)
332 if libref.Variant > 0 {
333 // Count output coverage from
334 // the end of the previous tag
335 // (if any) to the end of the
336 // current tag, IOW don't
337 // double-count coverage for
339 basesOut += countBases(job.fasta[last.pos+last.taglen : f.pos+f.taglen])
341 // If we dropped this tile
342 // (because !retainNoCalls),
343 // set taglen=0 so the
344 // overlapping tag is counted
345 // toward coverage on the
352 log.Warnf("%s %s no tags found", filelabel, job.label)
354 libref := tilelib.getRef(last.tagid, job.fasta[last.pos:])
355 path = append(path, libref)
356 if libref.Variant > 0 {
357 basesOut += countBases(job.fasta[last.pos+last.taglen:])
361 pathcopy := make([]tileLibRef, len(path))
363 ret[job.label] = pathcopy
365 basesIn := countBases(job.fasta)
366 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)
367 stats = append(stats, importStats{
368 InputFile: filelabel,
369 InputLabel: job.label,
370 InputLength: len(job.fasta),
371 InputCoverage: basesIn,
372 TileCoverage: basesOut,
373 PathLength: len(path),
374 DroppedOutOfOrderTiles: skipped,
377 totalPathLen += len(path)
379 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)
380 return ret, stats, scanner.Err()
383 func (tilelib *tileLibrary) Len() int64 {
384 return atomic.LoadInt64(&tilelib.variants)
387 // Return a tileLibRef for a tile with the given tag and sequence,
388 // adding the sequence to the library if needed.
389 func (tilelib *tileLibrary) getRef(tag tagID, seq []byte) tileLibRef {
391 if !tilelib.retainNoCalls {
392 for _, b := range seq {
393 if b != 'a' && b != 'c' && b != 'g' && b != 't' {
399 seqhash := blake2b.Sum256(seq)
401 if int(tag) < len(tilelib.variant) {
402 for i, varhash := range tilelib.variant[tag] {
403 if varhash == seqhash {
404 tilelib.mtx.RUnlock()
405 return tileLibRef{Tag: tag, Variant: tileVariantID(i + 1)}
409 var vlock sync.Locker
410 if len(tilelib.vlock) > int(tag) {
411 vlock = tilelib.vlock[tag]
413 tilelib.mtx.RUnlock()
416 if tilelib.variant == nil && tilelib.taglib != nil {
417 tilelib.variant = make([][][blake2b.Size256]byte, tilelib.taglib.Len())
418 tilelib.vlock = make([]sync.Locker, tilelib.taglib.Len())
419 for i := range tilelib.vlock {
420 tilelib.vlock[i] = &sync.Mutex{}
423 if int(tag) >= len(tilelib.variant) {
424 oldlen := len(tilelib.variant)
425 // If we haven't seen the tag library yet (as
426 // in a merge), tilelib.taglib.Len() is
427 // zero. We can still behave correctly, we
428 // just need to expand the tilelib.variant
430 if int(tag) >= cap(tilelib.variant) {
431 // Allocate 2x capacity.
432 newslice := make([][][blake2b.Size256]byte, int(tag)+1, (int(tag)+1)*2)
433 copy(newslice, tilelib.variant)
434 tilelib.variant = newslice[:int(tag)+1]
435 newvlock := make([]sync.Locker, int(tag)+1, (int(tag)+1)*2)
436 copy(newvlock, tilelib.vlock)
437 tilelib.vlock = newvlock[:int(tag)+1]
439 // Use previously allocated capacity,
441 tilelib.variant = tilelib.variant[:int(tag)+1]
442 tilelib.vlock = tilelib.vlock[:int(tag)+1]
444 for i := oldlen; i < len(tilelib.variant); i++ {
445 tilelib.vlock[i] = &sync.Mutex{}
448 vlock = tilelib.vlock[tag]
454 for i, varhash := range tilelib.variant[tag] {
455 if varhash == seqhash {
457 tilelib.mtx.RUnlock()
458 return tileLibRef{Tag: tag, Variant: tileVariantID(i + 1)}
461 atomic.AddInt64(&tilelib.variants, 1)
462 tilelib.variant[tag] = append(tilelib.variant[tag], seqhash)
463 if tilelib.retainTileSequences && !dropSeq {
464 if tilelib.seq == nil {
465 tilelib.seq = map[[blake2b.Size256]byte][]byte{}
467 tilelib.seq[seqhash] = append([]byte(nil), seq...)
469 variant := tileVariantID(len(tilelib.variant[tag]))
471 tilelib.mtx.RUnlock()
473 if tilelib.encoder != nil {
476 // Save the hash, but not the sequence
479 tilelib.encoder.Encode(LibraryEntry{
480 TileVariants: []TileVariant{{
488 return tileLibRef{Tag: tag, Variant: variant}
491 func (tilelib *tileLibrary) TileVariantSequence(libref tileLibRef) []byte {
492 if libref.Variant == 0 || len(tilelib.variant) <= int(libref.Tag) || len(tilelib.variant[libref.Tag]) < int(libref.Variant) {
495 return tilelib.seq[tilelib.variant[libref.Tag][libref.Variant-1]]
498 // Tidy deletes unreferenced tile variants and renumbers variants so
499 // more common variants have smaller IDs.
500 func (tilelib *tileLibrary) Tidy() {
501 log.Print("Tidy: compute inref")
502 inref := map[tileLibRef]bool{}
503 for _, refseq := range tilelib.refseqs {
504 for _, librefs := range refseq {
505 for _, libref := range librefs {
510 log.Print("Tidy: compute remap")
511 remap := make([][]tileVariantID, len(tilelib.variant))
512 throttle := throttle{Max: runtime.NumCPU() + 1}
513 for tag, oldvariants := range tilelib.variant {
514 tag, oldvariants := tagID(tag), oldvariants
515 if tag%1000000 == 0 {
516 log.Printf("Tidy: tag %d", tag)
520 defer throttle.Release()
521 uses := make([]int, len(oldvariants))
522 for _, cg := range tilelib.compactGenomes {
523 for phase := 0; phase < 2; phase++ {
524 cgi := int(tag)*2 + phase
525 if cgi < len(cg) && cg[cgi] > 0 {
531 // Compute desired order of variants:
532 // neworder[x] == index in oldvariants that
533 // should move to position x.
534 neworder := make([]int, len(oldvariants))
535 for i := range neworder {
538 sort.Slice(neworder, func(i, j int) bool {
539 if cmp := uses[neworder[i]] - uses[neworder[j]]; cmp != 0 {
542 return bytes.Compare(oldvariants[neworder[i]][:], oldvariants[neworder[j]][:]) < 0
546 // Replace tilelib.variant[tag] with a new
547 // re-ordered slice of hashes, and make a
548 // mapping from old to new variant IDs.
549 remaptag := make([]tileVariantID, len(oldvariants)+1)
550 newvariants := make([][blake2b.Size256]byte, 0, len(neworder))
551 for _, oldi := range neworder {
552 if uses[oldi] > 0 || inref[tileLibRef{Tag: tag, Variant: tileVariantID(oldi + 1)}] {
553 newvariants = append(newvariants, oldvariants[oldi])
554 remaptag[oldi+1] = tileVariantID(len(newvariants))
557 tilelib.variant[tag] = newvariants
558 remap[tag] = remaptag
563 // Apply remap to genomes and reference sequences, so they
564 // refer to the same tile variants using the changed IDs.
565 log.Print("Tidy: apply remap")
566 for _, cg := range tilelib.compactGenomes {
567 for idx, variant := range cg {
568 cg[idx] = remap[tagID(idx/2)][variant]
571 for _, refcs := range tilelib.refseqs {
572 for _, refseq := range refcs {
573 for i, tv := range refseq {
574 refseq[i].Variant = remap[tv.Tag][tv.Variant]
578 log.Print("Tidy: done")
581 func countBases(seq []byte) int {
583 for _, c := range seq {