dump.go

   1 // Copyright (C) The Lightning Authors. All rights reserved.
   2 //
   3 // SPDX-License-Identifier: AGPL-3.0
   4
   5 package lightning
   6
   7 import (
   8         "bufio"
   9         "bytes"
  10         "flag"
  11         "fmt"
  12         "io"
  13         "net/http"
  14         _ "net/http/pprof"
  15         "os"
  16         "regexp"
  17         "runtime"
  18         "sort"
  19         "strconv"
  20         "strings"
  21         "sync"
  22         "sync/atomic"
  23
  24         "git.arvados.org/arvados.git/sdk/go/arvados"
  25         log "github.com/sirupsen/logrus"
  26         "golang.org/x/crypto/blake2b"
  27 )
  28
  29 type dump struct {
  30         filter       filter
  31         cgnames      []string
  32         selectedTags map[tagID]bool
  33 }
  34
  35 func (cmd *dump) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  36         err := cmd.run(prog, args, stdin, stdout, stderr)
  37         if err != nil {
  38                 return 1
  39         }
  40         return 0
  41 }
  42
  43 func (cmd *dump) run(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) error {
  44         flags := flag.NewFlagSet("", flag.ContinueOnError)
  45         flags.SetOutput(stderr)
  46         pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
  47         runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
  48         projectUUID := flags.String("project", "", "project `UUID` for output data")
  49         priority := flags.Int("priority", 500, "container request priority")
  50         inputDir := flags.String("input-dir", "./in", "input `directory`")
  51         outputDir := flags.String("output-dir", "./out", "output `directory`")
  52         ref := flags.String("ref", "", "reference name (if blank, choose last one that appears in input)")
  53         regionsFilename := flags.String("regions", "", "only output columns/annotations that intersect regions in specified bed `file`")
  54         expandRegions := flags.Int("expand-regions", 0, "expand specified regions by `N` base pairs on each side`")
  55         selectedTags := flags.String("tags", "", "tag numbers to dump")
  56         cmd.filter.Flags(flags)
  57         err := flags.Parse(args)
  58         if err == flag.ErrHelp {
  59                 return nil
  60         } else if err != nil {
  61                 return err
  62         } else if flags.NArg() > 0 {
  63                 return fmt.Errorf("errant command line arguments after parsed flags: %v", flags.Args())
  64         }
  65
  66         if *pprof != "" {
  67                 go func() {
  68                         log.Println(http.ListenAndServe(*pprof, nil))
  69                 }()
  70         }
  71
  72         if !*runlocal {
  73                 runner := arvadosContainerRunner{
  74                         Name:        "lightning slice-numpy",
  75                         Client:      arvados.NewClientFromEnv(),
  76                         ProjectUUID: *projectUUID,
  77                         RAM:         750000000000,
  78                         VCPUs:       96,
  79                         Priority:    *priority,
  80                         KeepCache:   2,
  81                         APIAccess:   true,
  82                 }
  83                 err = runner.TranslatePaths(inputDir, regionsFilename)
  84                 if err != nil {
  85                         return err
  86                 }
  87                 runner.Args = []string{"dump", "-local=true",
  88                         "-pprof=:6060",
  89                         "-input-dir=" + *inputDir,
  90                         "-output-dir=/mnt/output",
  91                         "-regions=" + *regionsFilename,
  92                         "-expand-regions=" + fmt.Sprintf("%d", *expandRegions),
  93                         "-tags=" + *selectedTags,
  94                 }
  95                 runner.Args = append(runner.Args, cmd.filter.Args()...)
  96                 output, err := runner.Run()
  97                 if err != nil {
  98                         return err
  99                 }
 100                 fmt.Fprintln(stdout, output)
 101                 return nil
 102         }
 103
 104         if *selectedTags != "" {
 105                 cmd.selectedTags = map[tagID]bool{}
 106                 for _, tagstr := range strings.Split(*selectedTags, ",") {
 107                         tag, err := strconv.ParseInt(tagstr, 10, 64)
 108                         if err != nil {
 109                                 return err
 110                         }
 111                         cmd.selectedTags[tagID(tag)] = true
 112                 }
 113         }
 114
 115         infiles, err := allFiles(*inputDir, matchGobFile)
 116         if err != nil {
 117                 return err
 118         }
 119         if len(infiles) == 0 {
 120                 return fmt.Errorf("no input files found in %s", *inputDir)
 121         }
 122         sort.Strings(infiles)
 123
 124         var refseq map[string][]tileLibRef
 125         var reftiledata = make(map[tileLibRef][]byte, 11000000)
 126         in0, err := open(infiles[0])
 127         if err != nil {
 128                 return err
 129         }
 130
 131         matchGenome, err := regexp.Compile(cmd.filter.MatchGenome)
 132         if err != nil {
 133                 err = fmt.Errorf("-match-genome: invalid regexp: %q", cmd.filter.MatchGenome)
 134                 return err
 135         }
 136
 137         cmd.cgnames = nil
 138         taglen := -1
 139         DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
 140                 if len(ent.TagSet) > 0 {
 141                         taglen = len(ent.TagSet[0])
 142                 }
 143                 for _, cseq := range ent.CompactSequences {
 144                         if cseq.Name == *ref || *ref == "" {
 145                                 refseq = cseq.TileSequences
 146                         }
 147                 }
 148                 for _, cg := range ent.CompactGenomes {
 149                         if matchGenome.MatchString(cg.Name) {
 150                                 cmd.cgnames = append(cmd.cgnames, cg.Name)
 151                         }
 152                 }
 153                 for _, tv := range ent.TileVariants {
 154                         if tv.Ref {
 155                                 reftiledata[tileLibRef{tv.Tag, tv.Variant}] = tv.Sequence
 156                         }
 157                 }
 158                 return nil
 159         })
 160         if err != nil {
 161                 return err
 162         }
 163         in0.Close()
 164         if refseq == nil {
 165                 return fmt.Errorf("%s: reference sequence not found", infiles[0])
 166         }
 167         if taglen < 0 {
 168                 return fmt.Errorf("tagset not found")
 169         }
 170         if len(cmd.cgnames) == 0 {
 171                 return fmt.Errorf("no genomes found matching regexp %q", cmd.filter.MatchGenome)
 172         }
 173         sort.Strings(cmd.cgnames)
 174
 175         log.Info("indexing reference tiles")
 176         type reftileinfo struct {
 177                 variant  tileVariantID
 178                 seqname  string // chr1
 179                 pos      int    // distance from start of chromosome to starttag
 180                 tiledata []byte // acgtggcaa...
 181         }
 182         isdup := map[tagID]bool{}
 183         reftile := map[tagID]*reftileinfo{}
 184         for seqname, cseq := range refseq {
 185                 pos := 0
 186                 for _, libref := range cseq {
 187                         tiledata := reftiledata[libref]
 188                         if len(tiledata) == 0 {
 189                                 return fmt.Errorf("missing tiledata for tag %d variant %d in %s in ref", libref.Tag, libref.Variant, seqname)
 190                         }
 191                         if isdup[libref.Tag] {
 192                                 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
 193                         } else if reftile[libref.Tag] != nil {
 194                                 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", tileLibRef{Tag: libref.Tag, Variant: reftile[libref.Tag].variant}, reftile[libref.Tag].seqname, reftile[libref.Tag].pos)
 195                                 delete(reftile, libref.Tag)
 196                                 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
 197                                 isdup[libref.Tag] = true
 198                         } else {
 199                                 reftile[libref.Tag] = &reftileinfo{
 200                                         seqname:  seqname,
 201                                         variant:  libref.Variant,
 202                                         tiledata: tiledata,
 203                                         pos:      pos,
 204                                 }
 205                         }
 206                         pos += len(tiledata) - taglen
 207                 }
 208                 log.Printf("... %s done, len %d", seqname, pos+taglen)
 209         }
 210
 211         var mask *mask
 212         if *regionsFilename != "" {
 213                 log.Printf("loading regions from %s", *regionsFilename)
 214                 mask, err = makeMask(*regionsFilename, *expandRegions)
 215                 if err != nil {
 216                         return err
 217                 }
 218                 log.Printf("before applying mask, len(reftile) == %d", len(reftile))
 219                 log.Printf("deleting reftile entries for regions outside %d intervals", mask.Len())
 220                 for tag, rt := range reftile {
 221                         if !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(rt.tiledata)) {
 222                                 delete(reftile, tag)
 223                         }
 224                 }
 225                 log.Printf("after applying mask, len(reftile) == %d", len(reftile))
 226         }
 227
 228         if cmd.selectedTags != nil {
 229                 log.Printf("deleting reftile entries other than %d selected tags", len(cmd.selectedTags))
 230                 for tag := range reftile {
 231                         if !cmd.selectedTags[tag] {
 232                                 delete(reftile, tag)
 233                         }
 234                 }
 235                 log.Printf("after applying selected tags, len(reftile) == %d", len(reftile))
 236         }
 237
 238         dumpVariantsName := fmt.Sprintf("%s/variants.csv", *outputDir)
 239         log.Infof("writing %s", dumpVariantsName)
 240         dumpVariantsF, err := os.Create(dumpVariantsName)
 241         if err != nil {
 242                 return err
 243         }
 244         dumpVariantsW := bufio.NewWriterSize(dumpVariantsF, 1<<20)
 245         mtx := sync.Mutex{}
 246
 247         throttleMem := throttle{Max: runtime.GOMAXPROCS(0)}
 248         log.Infof("reading %d slices with max concurrency %d", len(infiles), throttleMem.Max)
 249         var done int64
 250         for infileIdx, infile := range infiles {
 251                 infileIdx, infile := infileIdx, infile
 252                 throttleMem.Go(func() error {
 253                         seq := make(map[tagID][]TileVariant, 50000)
 254                         cgs := make(map[string]CompactGenome, len(cmd.cgnames))
 255                         f, err := open(infile)
 256                         if err != nil {
 257                                 return err
 258                         }
 259                         defer f.Close()
 260                         log.Infof("%04d: reading %s", infileIdx, infile)
 261                         err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
 262                                 for _, tv := range ent.TileVariants {
 263                                         if tv.Ref {
 264                                                 continue
 265                                         }
 266                                         if mask != nil && reftile[tv.Tag] == nil {
 267                                                 // Don't waste
 268                                                 // time/memory on
 269                                                 // masked-out tiles.
 270                                                 continue
 271                                         }
 272                                         variants := seq[tv.Tag]
 273                                         if len(variants) == 0 {
 274                                                 variants = make([]TileVariant, 100)
 275                                         }
 276                                         for len(variants) <= int(tv.Variant) {
 277                                                 variants = append(variants, TileVariant{})
 278                                         }
 279                                         variants[int(tv.Variant)] = tv
 280                                         seq[tv.Tag] = variants
 281                                 }
 282                                 for _, cg := range ent.CompactGenomes {
 283                                         if !matchGenome.MatchString(cg.Name) {
 284                                                 continue
 285                                         }
 286                                         // pad to full slice size
 287                                         // to avoid out-of-bounds
 288                                         // checks later
 289                                         if sliceSize := 2 * int(cg.EndTag-cg.StartTag); len(cg.Variants) < sliceSize {
 290                                                 cg.Variants = append(cg.Variants, make([]tileVariantID, sliceSize-len(cg.Variants))...)
 291                                         }
 292                                         cgs[cg.Name] = cg
 293                                 }
 294                                 return nil
 295                         })
 296                         if err != nil {
 297                                 return err
 298                         }
 299                         tagstart := cgs[cmd.cgnames[0]].StartTag
 300                         tagend := cgs[cmd.cgnames[0]].EndTag
 301
 302                         // TODO: filters
 303
 304                         log.Infof("%04d: renumber/dedup variants for tags %d-%d", infileIdx, tagstart, tagend)
 305                         variantRemap := make([][]tileVariantID, tagend-tagstart)
 306                         throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
 307                         for tag, variants := range seq {
 308                                 tag, variants := tag, variants
 309                                 throttleCPU.Go(func() error {
 310                                         count := make(map[[blake2b.Size256]byte]int, len(variants))
 311
 312                                         rt := reftile[tag]
 313                                         var rthash [blake2b.Size256]byte
 314                                         if rt != nil {
 315                                                 rthash = blake2b.Sum256(rt.tiledata)
 316                                                 count[rthash] = 0
 317                                         }
 318
 319                                         for _, cg := range cgs {
 320                                                 idx := int(tag-tagstart) * 2
 321                                                 for allele := 0; allele < 2; allele++ {
 322                                                         v := cg.Variants[idx+allele]
 323                                                         if v > 0 && len(variants[v].Sequence) > 0 {
 324                                                                 count[variants[v].Blake2b]++
 325                                                         }
 326                                                 }
 327                                         }
 328                                         // hash[i] will be the hash of
 329                                         // the variant(s) that should
 330                                         // be at rank i (0-based).
 331                                         hash := make([][blake2b.Size256]byte, 0, len(count))
 332                                         for b := range count {
 333                                                 hash = append(hash, b)
 334                                         }
 335                                         sort.Slice(hash, func(i, j int) bool {
 336                                                 bi, bj := &hash[i], &hash[j]
 337                                                 if ci, cj := count[*bi], count[*bj]; ci != cj {
 338                                                         return ci > cj
 339                                                 } else {
 340                                                         return bytes.Compare((*bi)[:], (*bj)[:]) < 0
 341                                                 }
 342                                         })
 343                                         // rank[b] will be the 1-based
 344                                         // new variant number for
 345                                         // variants whose hash is b.
 346                                         rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
 347                                         for i, h := range hash {
 348                                                 rank[h] = tileVariantID(i + 1)
 349                                         }
 350                                         // remap[v] will be the new
 351                                         // variant number for original
 352                                         // variant number v.
 353                                         remap := make([]tileVariantID, len(variants))
 354                                         for i, tv := range variants {
 355                                                 remap[i] = rank[tv.Blake2b]
 356                                         }
 357                                         variantRemap[tag-tagstart] = remap
 358                                         if rt != nil {
 359                                                 rt.variant = rank[rthash]
 360                                         }
 361                                         return nil
 362                                 })
 363                         }
 364                         throttleCPU.Wait()
 365
 366                         for tag := tagstart; tag < tagend; tag++ {
 367                                 rt, ok := reftile[tag]
 368                                 if !ok {
 369                                         // Excluded by specified
 370                                         // regions, or reference does
 371                                         // not use any variant of this
 372                                         // tile. (TODO: log this?
 373                                         // mention it in annotations?)
 374                                         continue
 375                                 }
 376                                 remap := variantRemap[tag-tagstart]
 377                                 maxv := tileVariantID(0)
 378                                 for _, v := range remap {
 379                                         if maxv < v {
 380                                                 maxv = v
 381                                         }
 382                                 }
 383                                 variants := seq[tag]
 384
 385                                 mtx.Lock()
 386                                 fmt.Fprintf(dumpVariantsW, "%d,%d,1,%s,%d,%s\n", tag, rt.variant, rt.seqname, rt.pos+1, bytes.ToUpper(rt.tiledata))
 387                                 mtx.Unlock()
 388
 389                                 done := make([]bool, maxv+1)
 390                                 for v, tv := range variants {
 391                                         v := remap[v]
 392                                         if v == 0 || v == rt.variant || done[v] {
 393                                                 continue
 394                                         } else {
 395                                                 done[v] = true
 396                                         }
 397                                         mtx.Lock()
 398                                         fmt.Fprintf(dumpVariantsW, "%d,%d,0,%s,%d,%s\n", tag, v, rt.seqname, rt.pos+1, bytes.ToUpper(tv.Sequence))
 399                                         mtx.Unlock()
 400                                 }
 401                         }
 402                         log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
 403                         return nil
 404                 })
 405         }
 406         if err = throttleMem.Wait(); err != nil {
 407                 return err
 408         }
 409         err = dumpVariantsW.Flush()
 410         if err != nil {
 411                 return err
 412         }
 413         err = dumpVariantsF.Close()
 414         if err != nil {
 415                 return err
 416         }
 417         return nil
 418 }