tilelib.go

   1 package main
   2
   3 import (
   4         "bufio"
   5         "bytes"
   6         "context"
   7         "encoding/gob"
   8         "fmt"
   9         "io"
  10         "strings"
  11         "sync"
  12
  13         log "github.com/sirupsen/logrus"
  14         "golang.org/x/crypto/blake2b"
  15 )
  16
  17 type tileVariantID uint16 // 1-based
  18
  19 type tileLibRef struct {
  20         Tag     tagID
  21         Variant tileVariantID
  22 }
  23
  24 type tileSeq map[string][]tileLibRef
  25
  26 func (tseq tileSeq) Variants() ([]tileVariantID, int, int) {
  27         maxtag := 0
  28         for _, refs := range tseq {
  29                 for _, ref := range refs {
  30                         if maxtag < int(ref.Tag) {
  31                                 maxtag = int(ref.Tag)
  32                         }
  33                 }
  34         }
  35         vars := make([]tileVariantID, maxtag+1)
  36         var kept, dropped int
  37         for _, refs := range tseq {
  38                 for _, ref := range refs {
  39                         if vars[int(ref.Tag)] != 0 {
  40                                 dropped++
  41                         } else {
  42                                 kept++
  43                         }
  44                         vars[int(ref.Tag)] = ref.Variant
  45                 }
  46         }
  47         return vars, kept, dropped
  48 }
  49
  50 type tileLibrary struct {
  51         includeNoCalls      bool
  52         skipOOO             bool
  53         retainTileSequences bool
  54
  55         taglib         *tagLibrary
  56         variant        [][][blake2b.Size256]byte
  57         refseqs        map[string]map[string][]tileLibRef
  58         compactGenomes map[string][]tileVariantID
  59         // count [][]int
  60         seq      map[[blake2b.Size256]byte][]byte
  61         variants int
  62         // if non-nil, write out any tile variants added while tiling
  63         encoder *gob.Encoder
  64
  65         mtx sync.Mutex
  66 }
  67
  68 func (tilelib *tileLibrary) loadTagSet(newtagset [][]byte) error {
  69         // Loading a tagset means either passing it through to the
  70         // output (if it's the first one we've seen), or just ensuring
  71         // it doesn't disagree with what we already have.
  72         if len(newtagset) == 0 {
  73                 return nil
  74         }
  75         tilelib.mtx.Lock()
  76         defer tilelib.mtx.Unlock()
  77         if tilelib.taglib == nil || tilelib.taglib.Len() == 0 {
  78                 tilelib.taglib = &tagLibrary{}
  79                 err := tilelib.taglib.setTags(newtagset)
  80                 if err != nil {
  81                         return err
  82                 }
  83                 if tilelib.encoder != nil {
  84                         err = tilelib.encoder.Encode(LibraryEntry{
  85                                 TagSet: newtagset,
  86                         })
  87                         if err != nil {
  88                                 return err
  89                         }
  90                 }
  91         } else if tilelib.taglib.Len() != len(newtagset) {
  92                 return fmt.Errorf("cannot merge libraries with differing tagsets")
  93         } else {
  94                 current := tilelib.taglib.Tags()
  95                 for i := range newtagset {
  96                         if !bytes.Equal(newtagset[i], current[i]) {
  97                                 return fmt.Errorf("cannot merge libraries with differing tagsets")
  98                         }
  99                 }
 100         }
 101         return nil
 102 }
 103
 104 func (tilelib *tileLibrary) loadTileVariants(tvs []TileVariant, variantmap map[tileLibRef]tileVariantID) error {
 105         for _, tv := range tvs {
 106                 // Assign a new variant ID (unique across all inputs)
 107                 // for each input variant.
 108                 variantmap[tileLibRef{Tag: tv.Tag, Variant: tv.Variant}] = tilelib.getRef(tv.Tag, tv.Sequence).Variant
 109         }
 110         return nil
 111 }
 112
 113 func (tilelib *tileLibrary) loadCompactGenomes(cgs []CompactGenome, variantmap map[tileLibRef]tileVariantID, onLoadGenome func(CompactGenome)) error {
 114         log.Debugf("loadCompactGenomes: %d", len(cgs))
 115         var wg sync.WaitGroup
 116         errs := make(chan error, 1)
 117         for _, cg := range cgs {
 118                 wg.Add(1)
 119                 cg := cg
 120                 go func() {
 121                         defer wg.Done()
 122                         for i, variant := range cg.Variants {
 123                                 if len(errs) > 0 {
 124                                         return
 125                                 }
 126                                 if variant == 0 {
 127                                         continue
 128                                 }
 129                                 tag := tagID(i / 2)
 130                                 newvariant, ok := variantmap[tileLibRef{Tag: tag, Variant: variant}]
 131                                 if !ok {
 132                                         err := fmt.Errorf("oops: genome %q has variant %d for tag %d, but that variant was not in its library", cg.Name, variant, tag)
 133                                         select {
 134                                         case errs <- err:
 135                                         default:
 136                                         }
 137                                         return
 138                                 }
 139                                 log.Tracef("loadCompactGenomes: cg %s tag %d variant %d => %d", cg.Name, tag, variant, newvariant)
 140                                 cg.Variants[i] = newvariant
 141                         }
 142                         if onLoadGenome != nil {
 143                                 onLoadGenome(cg)
 144                         }
 145                         if tilelib.encoder != nil {
 146                                 err := tilelib.encoder.Encode(LibraryEntry{
 147                                         CompactGenomes: []CompactGenome{cg},
 148                                 })
 149                                 if err != nil {
 150                                         select {
 151                                         case errs <- err:
 152                                         default:
 153                                         }
 154                                         return
 155                                 }
 156                         }
 157                         if tilelib.compactGenomes != nil {
 158                                 tilelib.mtx.Lock()
 159                                 defer tilelib.mtx.Unlock()
 160                                 tilelib.compactGenomes[cg.Name] = cg.Variants
 161                         }
 162                 }()
 163         }
 164         wg.Wait()
 165         go close(errs)
 166         return <-errs
 167 }
 168
 169 func (tilelib *tileLibrary) loadCompactSequences(cseqs []CompactSequence, variantmap map[tileLibRef]tileVariantID) error {
 170         log.Debugf("loadCompactSequences: %d", len(cseqs))
 171         for _, cseq := range cseqs {
 172                 for _, tseq := range cseq.TileSequences {
 173                         for i, libref := range tseq {
 174                                 if libref.Variant == 0 {
 175                                         // No variant (e.g., import
 176                                         // dropped tiles with
 177                                         // no-calls) = no translation.
 178                                         continue
 179                                 }
 180                                 v, ok := variantmap[libref]
 181                                 if !ok {
 182                                         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)
 183                                 }
 184                                 tseq[i].Variant = v
 185                         }
 186                 }
 187                 if tilelib.encoder != nil {
 188                         if err := tilelib.encoder.Encode(LibraryEntry{
 189                                 CompactSequences: []CompactSequence{cseq},
 190                         }); err != nil {
 191                                 return err
 192                         }
 193                 }
 194         }
 195         tilelib.mtx.Lock()
 196         defer tilelib.mtx.Unlock()
 197         if tilelib.refseqs == nil {
 198                 tilelib.refseqs = map[string]map[string][]tileLibRef{}
 199         }
 200         for _, cseq := range cseqs {
 201                 tilelib.refseqs[cseq.Name] = cseq.TileSequences
 202         }
 203         return nil
 204 }
 205
 206 // Load library data from rdr. Tile variants might be renumbered in
 207 // the process; in that case, genomes variants will be renumbered to
 208 // match.
 209 //
 210 // If onLoadGenome is non-nil, call it on each CompactGenome entry.
 211 func (tilelib *tileLibrary) LoadGob(ctx context.Context, rdr io.Reader, onLoadGenome func(CompactGenome)) error {
 212         cgs := []CompactGenome{}
 213         cseqs := []CompactSequence{}
 214         variantmap := map[tileLibRef]tileVariantID{}
 215         err := DecodeLibrary(rdr, func(ent *LibraryEntry) error {
 216                 if ctx.Err() != nil {
 217                         return ctx.Err()
 218                 }
 219                 if err := tilelib.loadTagSet(ent.TagSet); err != nil {
 220                         return err
 221                 }
 222                 if err := tilelib.loadTileVariants(ent.TileVariants, variantmap); err != nil {
 223                         return err
 224                 }
 225                 cgs = append(cgs, ent.CompactGenomes...)
 226                 cseqs = append(cseqs, ent.CompactSequences...)
 227                 return nil
 228         })
 229         if err != nil {
 230                 return err
 231         }
 232         if ctx.Err() != nil {
 233                 return ctx.Err()
 234         }
 235         err = tilelib.loadCompactGenomes(cgs, variantmap, onLoadGenome)
 236         if err != nil {
 237                 return err
 238         }
 239         err = tilelib.loadCompactSequences(cseqs, variantmap)
 240         if err != nil {
 241                 return err
 242         }
 243         return nil
 244 }
 245
 246 type importStats struct {
 247         InputFile              string
 248         InputLabel             string
 249         InputLength            int
 250         InputCoverage          int
 251         TileCoverage           int
 252         PathLength             int
 253         DroppedOutOfOrderTiles int
 254 }
 255
 256 func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader) (tileSeq, []importStats, error) {
 257         ret := tileSeq{}
 258         type jobT struct {
 259                 label string
 260                 fasta []byte
 261         }
 262         todo := make(chan jobT)
 263         scanner := bufio.NewScanner(rdr)
 264         go func() {
 265                 defer close(todo)
 266                 var fasta []byte
 267                 var seqlabel string
 268                 for scanner.Scan() {
 269                         buf := scanner.Bytes()
 270                         if len(buf) > 0 && buf[0] == '>' {
 271                                 todo <- jobT{seqlabel, fasta}
 272                                 seqlabel, fasta = strings.SplitN(string(buf[1:]), " ", 2)[0], nil
 273                                 log.Debugf("%s %s reading fasta", filelabel, seqlabel)
 274                         } else {
 275                                 fasta = append(fasta, bytes.ToLower(buf)...)
 276                         }
 277                 }
 278                 todo <- jobT{seqlabel, fasta}
 279         }()
 280         type foundtag struct {
 281                 pos    int
 282                 tagid  tagID
 283                 taglen int
 284         }
 285         found := make([]foundtag, 2000000)
 286         path := make([]tileLibRef, 2000000)
 287         totalFoundTags := 0
 288         totalPathLen := 0
 289         skippedSequences := 0
 290         stats := make([]importStats, 0, len(todo))
 291         for job := range todo {
 292                 if len(job.fasta) == 0 {
 293                         continue
 294                 } else if strings.Contains(job.label, "_") {
 295                         skippedSequences++
 296                         continue
 297                 }
 298                 log.Debugf("%s %s tiling", filelabel, job.label)
 299
 300                 found = found[:0]
 301                 tilelib.taglib.FindAll(job.fasta, func(tagid tagID, pos, taglen int) {
 302                         found = append(found, foundtag{pos: pos, tagid: tagid, taglen: taglen})
 303                 })
 304                 totalFoundTags += len(found)
 305
 306                 basesOut := 0
 307                 skipped := 0
 308                 path = path[:0]
 309                 last := foundtag{tagid: -1}
 310                 if tilelib.skipOOO {
 311                         keep := longestIncreasingSubsequence(len(found), func(i int) int { return int(found[i].tagid) })
 312                         for i, x := range keep {
 313                                 found[i] = found[x]
 314                         }
 315                         skipped = len(found) - len(keep)
 316                         found = found[:len(keep)]
 317                 }
 318                 for i, f := range found {
 319                         log.Tracef("%s %s found[%d] == %#v", filelabel, job.label, i, f)
 320                         if last.tagid < 0 {
 321                                 // first tag in sequence
 322                                 last = foundtag{tagid: f.tagid}
 323                                 continue
 324                         }
 325                         libref := tilelib.getRef(last.tagid, job.fasta[last.pos:f.pos+f.taglen])
 326                         path = append(path, libref)
 327                         if libref.Variant > 0 {
 328                                 // Count output coverage from
 329                                 // the end of the previous tag
 330                                 // (if any) to the end of the
 331                                 // current tag, IOW don't
 332                                 // double-count coverage for
 333                                 // the previous tag.
 334                                 basesOut += countBases(job.fasta[last.pos+last.taglen : f.pos+f.taglen])
 335                         } else {
 336                                 // If we dropped this tile
 337                                 // (because !includeNoCalls),
 338                                 // set taglen=0 so the
 339                                 // overlapping tag is counted
 340                                 // toward coverage on the
 341                                 // following tile.
 342                                 f.taglen = 0
 343                         }
 344                         last = f
 345                 }
 346                 if last.tagid < 0 {
 347                         log.Warnf("%s %s no tags found", filelabel, job.label)
 348                 } else {
 349                         libref := tilelib.getRef(last.tagid, job.fasta[last.pos:])
 350                         path = append(path, libref)
 351                         if libref.Variant > 0 {
 352                                 basesOut += countBases(job.fasta[last.pos+last.taglen:])
 353                         }
 354                 }
 355
 356                 pathcopy := make([]tileLibRef, len(path))
 357                 copy(pathcopy, path)
 358                 ret[job.label] = pathcopy
 359
 360                 basesIn := countBases(job.fasta)
 361                 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)
 362                 stats = append(stats, importStats{
 363                         InputFile:              filelabel,
 364                         InputLabel:             job.label,
 365                         InputLength:            len(job.fasta),
 366                         InputCoverage:          basesIn,
 367                         TileCoverage:           basesOut,
 368                         PathLength:             len(path),
 369                         DroppedOutOfOrderTiles: skipped,
 370                 })
 371
 372                 totalPathLen += len(path)
 373         }
 374         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)
 375         return ret, stats, scanner.Err()
 376 }
 377
 378 func (tilelib *tileLibrary) Len() int {
 379         tilelib.mtx.Lock()
 380         defer tilelib.mtx.Unlock()
 381         return tilelib.variants
 382 }
 383
 384 // Return a tileLibRef for a tile with the given tag and sequence,
 385 // adding the sequence to the library if needed.
 386 func (tilelib *tileLibrary) getRef(tag tagID, seq []byte) tileLibRef {
 387         if !tilelib.includeNoCalls {
 388                 for _, b := range seq {
 389                         if b != 'a' && b != 'c' && b != 'g' && b != 't' {
 390                                 // return "tile not found" if seq has any
 391                                 // no-calls
 392                                 return tileLibRef{Tag: tag}
 393                         }
 394                 }
 395         }
 396         tilelib.mtx.Lock()
 397         if tilelib.variant == nil && tilelib.taglib != nil {
 398                 tilelib.variant = make([][][blake2b.Size256]byte, tilelib.taglib.Len())
 399         }
 400         if int(tag) >= len(tilelib.variant) {
 401                 // If we haven't seen the tag library yet (as in a
 402                 // merge), tilelib.taglib.Len() is zero. We can still
 403                 // behave correctly, we just need to expand the
 404                 // tilelib.variant slice as needed.
 405                 if int(tag) >= cap(tilelib.variant) {
 406                         // Allocate 2x capacity.
 407                         newslice := make([][][blake2b.Size256]byte, int(tag)+1, (int(tag)+1)*2)
 408                         copy(newslice, tilelib.variant)
 409                         tilelib.variant = newslice[:int(tag)+1]
 410                 } else {
 411                         // Use previously allocated capacity, avoiding
 412                         // copy.
 413                         tilelib.variant = tilelib.variant[:int(tag)+1]
 414                 }
 415         }
 416         seqhash := blake2b.Sum256(seq)
 417         for i, varhash := range tilelib.variant[tag] {
 418                 if varhash == seqhash {
 419                         tilelib.mtx.Unlock()
 420                         return tileLibRef{Tag: tag, Variant: tileVariantID(i + 1)}
 421                 }
 422         }
 423         tilelib.variants++
 424         tilelib.variant[tag] = append(tilelib.variant[tag], seqhash)
 425         if tilelib.retainTileSequences {
 426                 if tilelib.seq == nil {
 427                         tilelib.seq = map[[blake2b.Size256]byte][]byte{}
 428                 }
 429                 tilelib.seq[seqhash] = append([]byte(nil), seq...)
 430         }
 431         variant := tileVariantID(len(tilelib.variant[tag]))
 432         tilelib.mtx.Unlock()
 433
 434         if tilelib.encoder != nil {
 435                 tilelib.encoder.Encode(LibraryEntry{
 436                         TileVariants: []TileVariant{{
 437                                 Tag:      tag,
 438                                 Variant:  variant,
 439                                 Blake2b:  seqhash,
 440                                 Sequence: seq,
 441                         }},
 442                 })
 443         }
 444         return tileLibRef{Tag: tag, Variant: variant}
 445 }
 446
 447 func (tilelib *tileLibrary) TileVariantSequence(libref tileLibRef) []byte {
 448         if libref.Variant == 0 || len(tilelib.variant) <= int(libref.Tag) || len(tilelib.variant[libref.Tag]) < int(libref.Variant) {
 449                 return nil
 450         }
 451         return tilelib.seq[tilelib.variant[libref.Tag][libref.Variant-1]]
 452 }
 453
 454 func countBases(seq []byte) int {
 455         n := 0
 456         for _, c := range seq {
 457                 if isbase[c] {
 458                         n++
 459                 }
 460         }
 461         return n
 462 }