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         taglib         *tagLibrary
  54         variant        [][][blake2b.Size256]byte
  55         // count [][]int
  56         // seq map[[blake2b.Size]byte][]byte
  57         variants int
  58         // if non-nil, write out any tile variants added while tiling
  59         encoder *gob.Encoder
  60         // if non-nil, call this func upon loading a genome
  61         onLoadGenome func(CompactGenome)
  62
  63         mtx sync.Mutex
  64 }
  65
  66 func (tilelib *tileLibrary) loadTagSet(newtagset [][]byte) error {
  67         // Loading a tagset means either passing it through to the
  68         // output (if it's the first one we've seen), or just ensuring
  69         // it doesn't disagree with what we already have.
  70         if len(newtagset) == 0 {
  71                 return nil
  72         }
  73         tilelib.mtx.Lock()
  74         defer tilelib.mtx.Unlock()
  75         if tilelib.taglib == nil || tilelib.taglib.Len() == 0 {
  76                 tilelib.taglib = &tagLibrary{}
  77                 err := tilelib.taglib.setTags(newtagset)
  78                 if err != nil {
  79                         return err
  80                 }
  81                 if tilelib.encoder != nil {
  82                         err = tilelib.encoder.Encode(LibraryEntry{
  83                                 TagSet: newtagset,
  84                         })
  85                         if err != nil {
  86                                 return err
  87                         }
  88                 }
  89         } else if tilelib.taglib.Len() != len(newtagset) {
  90                 return fmt.Errorf("cannot merge libraries with differing tagsets")
  91         } else {
  92                 current := tilelib.taglib.Tags()
  93                 for i := range newtagset {
  94                         if !bytes.Equal(newtagset[i], current[i]) {
  95                                 return fmt.Errorf("cannot merge libraries with differing tagsets")
  96                         }
  97                 }
  98         }
  99         return nil
 100 }
 101
 102 func (tilelib *tileLibrary) loadTileVariants(tvs []TileVariant, variantmap map[tileLibRef]tileVariantID) error {
 103         for _, tv := range tvs {
 104                 // Assign a new variant ID (unique across all inputs)
 105                 // for each input variant.
 106                 variantmap[tileLibRef{tag: tv.Tag, variant: tv.Variant}] = tilelib.getRef(tv.Tag, tv.Sequence).variant
 107         }
 108         return nil
 109 }
 110
 111 func (tilelib *tileLibrary) loadGenomes(genomes map[string][]tileVariantID, variantmap map[tileLibRef]tileVariantID, onLoadGenome func(CompactGenome)) error {
 112         var wg sync.WaitGroup
 113         errs := make(chan error, 1)
 114         for name, variants := range genomes {
 115                 name, variants := name, variants
 116                 wg.Add(1)
 117                 go func() {
 118                         defer wg.Done()
 119                         for i, variant := range variants {
 120                                 if len(errs) > 0 {
 121                                         return
 122                                 }
 123                                 if variant == 0 {
 124                                         continue
 125                                 }
 126                                 tag := tagID(i / 2)
 127                                 newvariant, ok := variantmap[tileLibRef{tag: tag, variant: variant}]
 128                                 if !ok {
 129                                         err := fmt.Errorf("oops: genome %q has variant %d for tag %d, but that variant was not in its library", name, variant, tag)
 130                                         select {
 131                                         case errs <- err:
 132                                         default:
 133                                         }
 134                                         return
 135                                 }
 136                                 variants[i] = newvariant
 137                         }
 138                         if tilelib.encoder != nil {
 139                                 for name, variants := range genomes {
 140                                         cg := CompactGenome{
 141                                                 Name:     name,
 142                                                 Variants: variants,
 143                                         }
 144                                         if onLoadGenome != nil {
 145                                                 onLoadGenome(cg)
 146                                         }
 147                                         err := tilelib.encoder.Encode(LibraryEntry{
 148                                                 CompactGenomes: []CompactGenome{cg},
 149                                         })
 150                                         if err != nil {
 151                                                 select {
 152                                                 case errs <- err:
 153                                                 default:
 154                                                 }
 155                                                 return
 156                                         }
 157                                 }
 158                         }
 159                 }()
 160         }
 161         wg.Wait()
 162         go close(errs)
 163         return <-errs
 164 }
 165
 166 func (tilelib *tileLibrary) LoadGob(ctx context.Context, rdr io.Reader, onLoadGenome func(CompactGenome)) error {
 167         genomes := map[string][]tileVariantID{}
 168         variantmap := map[tileLibRef]tileVariantID{}
 169         err := DecodeLibrary(rdr, func(ent *LibraryEntry) error {
 170                 if ctx.Err() != nil {
 171                         return ctx.Err()
 172                 }
 173                 if err := tilelib.loadTagSet(ent.TagSet); err != nil {
 174                         return err
 175                 } else if err = tilelib.loadTileVariants(ent.TileVariants, variantmap); err != nil {
 176                         return err
 177                 } else {
 178                         for _, cg := range ent.CompactGenomes {
 179                                 genomes[cg.Name] = cg.Variants
 180                         }
 181                         return nil
 182                 }
 183         })
 184         if err != nil {
 185                 return err
 186         }
 187         if ctx.Err() != nil {
 188                 return ctx.Err()
 189         }
 190         err = tilelib.loadGenomes(genomes, variantmap, onLoadGenome)
 191         if err != nil {
 192                 return err
 193         }
 194         return nil
 195 }
 196
 197 func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader) (tileSeq, error) {
 198         ret := tileSeq{}
 199         type jobT struct {
 200                 label string
 201                 fasta []byte
 202         }
 203         todo := make(chan jobT)
 204         scanner := bufio.NewScanner(rdr)
 205         go func() {
 206                 defer close(todo)
 207                 var fasta []byte
 208                 var seqlabel string
 209                 for scanner.Scan() {
 210                         buf := scanner.Bytes()
 211                         if len(buf) > 0 && buf[0] == '>' {
 212                                 todo <- jobT{seqlabel, fasta}
 213                                 seqlabel, fasta = string(buf[1:]), nil
 214                                 log.Debugf("%s %s reading fasta", filelabel, seqlabel)
 215                         } else {
 216                                 fasta = append(fasta, bytes.ToLower(buf)...)
 217                         }
 218                 }
 219                 todo <- jobT{seqlabel, fasta}
 220         }()
 221         type foundtag struct {
 222                 pos    int
 223                 tagid  tagID
 224                 taglen int
 225         }
 226         found := make([]foundtag, 2000000)
 227         path := make([]tileLibRef, 2000000)
 228         totalFoundTags := 0
 229         totalPathLen := 0
 230         skippedSequences := 0
 231         for job := range todo {
 232                 if len(job.fasta) == 0 {
 233                         continue
 234                 } else if strings.Contains(job.label, "_") {
 235                         skippedSequences++
 236                         continue
 237                 }
 238                 log.Debugf("%s %s tiling", filelabel, job.label)
 239
 240                 found = found[:0]
 241                 tilelib.taglib.FindAll(job.fasta, func(tagid tagID, pos, taglen int) {
 242                         found = append(found, foundtag{pos: pos, tagid: tagid, taglen: taglen})
 243                 })
 244                 totalFoundTags += len(found)
 245
 246                 skipped := 0
 247                 path = path[:0]
 248                 last := foundtag{tagid: -1}
 249                 if tilelib.skipOOO {
 250                         keep := longestIncreasingSubsequence(len(found), func(i int) int { return int(found[i].tagid) })
 251                         for i, x := range keep {
 252                                 found[i] = found[x]
 253                         }
 254                         skipped = len(found) - len(keep)
 255                         found = found[:len(keep)]
 256                 }
 257                 for i, f := range found {
 258                         log.Tracef("%s %s found[%d] == %#v", filelabel, job.label, i, f)
 259                         if last.taglen > 0 {
 260                                 path = append(path, tilelib.getRef(last.tagid, job.fasta[last.pos:f.pos+f.taglen]))
 261                         }
 262                         last = f
 263                 }
 264                 if last.taglen > 0 {
 265                         path = append(path, tilelib.getRef(last.tagid, job.fasta[last.pos:]))
 266                 }
 267
 268                 pathcopy := make([]tileLibRef, len(path))
 269                 copy(pathcopy, path)
 270                 ret[job.label] = pathcopy
 271                 log.Debugf("%s %s tiled with path len %d, skipped %d", filelabel, job.label, len(path), skipped)
 272                 totalPathLen += len(path)
 273         }
 274         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)
 275         return ret, scanner.Err()
 276 }
 277
 278 func (tilelib *tileLibrary) Len() int {
 279         tilelib.mtx.Lock()
 280         defer tilelib.mtx.Unlock()
 281         return tilelib.variants
 282 }
 283
 284 // Return a tileLibRef for a tile with the given tag and sequence,
 285 // adding the sequence to the library if needed.
 286 func (tilelib *tileLibrary) getRef(tag tagID, seq []byte) tileLibRef {
 287         if !tilelib.includeNoCalls {
 288                 for _, b := range seq {
 289                         if b != 'a' && b != 'c' && b != 'g' && b != 't' {
 290                                 // return "tile not found" if seq has any
 291                                 // no-calls
 292                                 return tileLibRef{tag: tag}
 293                         }
 294                 }
 295         }
 296         tilelib.mtx.Lock()
 297         // if tilelib.seq == nil {
 298         //      tilelib.seq = map[[blake2b.Size]byte][]byte{}
 299         // }
 300         if tilelib.variant == nil && tilelib.taglib != nil {
 301                 tilelib.variant = make([][][blake2b.Size256]byte, tilelib.taglib.Len())
 302         }
 303         if int(tag) >= len(tilelib.variant) {
 304                 // If we haven't seen the tag library yet (as in a
 305                 // merge), tilelib.taglib.Len() is zero. We can still
 306                 // behave correctly, we just need to expand the
 307                 // tilelib.variant slice as needed.
 308                 if int(tag) >= cap(tilelib.variant) {
 309                         // Allocate 2x capacity.
 310                         newslice := make([][][blake2b.Size256]byte, int(tag)+1, (int(tag)+1)*2)
 311                         copy(newslice, tilelib.variant)
 312                         tilelib.variant = newslice[:int(tag)+1]
 313                 } else {
 314                         // Use previously allocated capacity, avoiding
 315                         // copy.
 316                         tilelib.variant = tilelib.variant[:int(tag)+1]
 317                 }
 318         }
 319         seqhash := blake2b.Sum256(seq)
 320         for i, varhash := range tilelib.variant[tag] {
 321                 if varhash == seqhash {
 322                         tilelib.mtx.Unlock()
 323                         return tileLibRef{tag: tag, variant: tileVariantID(i + 1)}
 324                 }
 325         }
 326         tilelib.variants++
 327         tilelib.variant[tag] = append(tilelib.variant[tag], seqhash)
 328         // tilelib.seq[seqhash] = append([]byte(nil), seq...)
 329         variant := tileVariantID(len(tilelib.variant[tag]))
 330         tilelib.mtx.Unlock()
 331
 332         if tilelib.encoder != nil {
 333                 tilelib.encoder.Encode(LibraryEntry{
 334                         TileVariants: []TileVariant{{
 335                                 Tag:      tag,
 336                                 Variant:  variant,
 337                                 Blake2b:  seqhash,
 338                                 Sequence: seq,
 339                         }},
 340                 })
 341         }
 342         return tileLibRef{tag: tag, variant: variant}
 343 }