slicenumpy.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         "encoding/gob"
  11         "flag"
  12         "fmt"
  13         "io"
  14         "io/ioutil"
  15         "math"
  16         "net/http"
  17         _ "net/http/pprof"
  18         "os"
  19         "regexp"
  20         "runtime"
  21         "runtime/debug"
  22         "sort"
  23         "strconv"
  24         "strings"
  25         "sync/atomic"
  26
  27         "git.arvados.org/arvados.git/sdk/go/arvados"
  28         "github.com/arvados/lightning/hgvs"
  29         "github.com/kshedden/gonpy"
  30         log "github.com/sirupsen/logrus"
  31         "golang.org/x/crypto/blake2b"
  32 )
  33
  34 type sliceNumpy struct {
  35         filter        filter
  36         threads       int
  37         chi2CasesFile string
  38         chi2Cases     []bool
  39         chi2PValue    float64
  40         minCoverage   int
  41 }
  42
  43 func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  44         var err error
  45         defer func() {
  46                 if err != nil {
  47                         fmt.Fprintf(stderr, "%s\n", err)
  48                 }
  49         }()
  50         flags := flag.NewFlagSet("", flag.ContinueOnError)
  51         flags.SetOutput(stderr)
  52         pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
  53         runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
  54         projectUUID := flags.String("project", "", "project `UUID` for output data")
  55         priority := flags.Int("priority", 500, "container request priority")
  56         inputDir := flags.String("input-dir", "./in", "input `directory`")
  57         outputDir := flags.String("output-dir", "./out", "output `directory`")
  58         ref := flags.String("ref", "", "reference name (if blank, choose last one that appears in input)")
  59         regionsFilename := flags.String("regions", "", "only output columns/annotations that intersect regions in specified bed `file`")
  60         expandRegions := flags.Int("expand-regions", 0, "expand specified regions by `N` base pairs on each side`")
  61         mergeOutput := flags.Bool("merge-output", false, "merge output into one matrix.npy and one matrix.annotations.csv")
  62         hgvsSingle := flags.Bool("single-hgvs-matrix", false, "also generate hgvs-based matrix")
  63         hgvsChunked := flags.Bool("chunked-hgvs-matrix", false, "also generate hgvs-based matrix per chromosome")
  64         flags.IntVar(&cmd.threads, "threads", 16, "number of memory-hungry assembly threads")
  65         flags.StringVar(&cmd.chi2CasesFile, "chi2-cases-file", "", "text file indicating positive cases (for Χ² test)")
  66         flags.Float64Var(&cmd.chi2PValue, "chi2-p-value", 1, "do Χ² test and omit columns with p-value above this threshold")
  67         cmd.filter.Flags(flags)
  68         err = flags.Parse(args)
  69         if err == flag.ErrHelp {
  70                 err = nil
  71                 return 0
  72         } else if err != nil {
  73                 return 2
  74         }
  75
  76         if *pprof != "" {
  77                 go func() {
  78                         log.Println(http.ListenAndServe(*pprof, nil))
  79                 }()
  80         }
  81
  82         if cmd.chi2CasesFile == "" && cmd.chi2PValue != 1 {
  83                 log.Errorf("cannot use provided -chi2-p-value=%f because -chi2-cases-file= value is empty", cmd.chi2PValue)
  84                 return 2
  85         }
  86
  87         if !*runlocal {
  88                 runner := arvadosContainerRunner{
  89                         Name:        "lightning slice-numpy",
  90                         Client:      arvados.NewClientFromEnv(),
  91                         ProjectUUID: *projectUUID,
  92                         RAM:         750000000000,
  93                         VCPUs:       96,
  94                         Priority:    *priority,
  95                         KeepCache:   2,
  96                         APIAccess:   true,
  97                 }
  98                 err = runner.TranslatePaths(inputDir, regionsFilename, &cmd.chi2CasesFile)
  99                 if err != nil {
 100                         return 1
 101                 }
 102                 runner.Args = []string{"slice-numpy", "-local=true",
 103                         "-pprof=:6060",
 104                         "-input-dir=" + *inputDir,
 105                         "-output-dir=/mnt/output",
 106                         "-threads=" + fmt.Sprintf("%d", cmd.threads),
 107                         "-regions=" + *regionsFilename,
 108                         "-expand-regions=" + fmt.Sprintf("%d", *expandRegions),
 109                         "-merge-output=" + fmt.Sprintf("%v", *mergeOutput),
 110                         "-single-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsSingle),
 111                         "-chunked-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsChunked),
 112                         "-chi2-cases-file=" + cmd.chi2CasesFile,
 113                         "-chi2-p-value=" + fmt.Sprintf("%f", cmd.chi2PValue),
 114                 }
 115                 runner.Args = append(runner.Args, cmd.filter.Args()...)
 116                 var output string
 117                 output, err = runner.Run()
 118                 if err != nil {
 119                         return 1
 120                 }
 121                 fmt.Fprintln(stdout, output)
 122                 return 0
 123         }
 124
 125         infiles, err := allGobFiles(*inputDir)
 126         if err != nil {
 127                 return 1
 128         }
 129         if len(infiles) == 0 {
 130                 err = fmt.Errorf("no input files found in %s", *inputDir)
 131                 return 1
 132         }
 133         sort.Strings(infiles)
 134
 135         var cgnames []string
 136         var refseq map[string][]tileLibRef
 137         var reftiledata = make(map[tileLibRef][]byte, 11000000)
 138         in0, err := open(infiles[0])
 139         if err != nil {
 140                 return 1
 141         }
 142
 143         matchGenome, err := regexp.Compile(cmd.filter.MatchGenome)
 144         if err != nil {
 145                 err = fmt.Errorf("-match-genome: invalid regexp: %q", cmd.filter.MatchGenome)
 146                 return 1
 147         }
 148
 149         taglen := -1
 150         DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
 151                 if len(ent.TagSet) > 0 {
 152                         taglen = len(ent.TagSet[0])
 153                 }
 154                 for _, cseq := range ent.CompactSequences {
 155                         if cseq.Name == *ref || *ref == "" {
 156                                 refseq = cseq.TileSequences
 157                         }
 158                 }
 159                 for _, cg := range ent.CompactGenomes {
 160                         if matchGenome.MatchString(cg.Name) {
 161                                 cgnames = append(cgnames, cg.Name)
 162                         }
 163                 }
 164                 for _, tv := range ent.TileVariants {
 165                         if tv.Ref {
 166                                 reftiledata[tileLibRef{tv.Tag, tv.Variant}] = tv.Sequence
 167                         }
 168                 }
 169                 return nil
 170         })
 171         if err != nil {
 172                 return 1
 173         }
 174         in0.Close()
 175         if refseq == nil {
 176                 err = fmt.Errorf("%s: reference sequence not found", infiles[0])
 177                 return 1
 178         }
 179         if taglen < 0 {
 180                 err = fmt.Errorf("tagset not found")
 181                 return 1
 182         }
 183         if len(cgnames) == 0 {
 184                 err = fmt.Errorf("no genomes found matching regexp %q", cmd.filter.MatchGenome)
 185                 return 1
 186         }
 187         sort.Strings(cgnames)
 188
 189         cmd.minCoverage = int(math.Ceil(cmd.filter.MinCoverage * float64(len(cgnames))))
 190
 191         if cmd.chi2CasesFile != "" {
 192                 f, err2 := open(cmd.chi2CasesFile)
 193                 if err2 != nil {
 194                         err = err2
 195                         return 1
 196                 }
 197                 buf, err2 := io.ReadAll(f)
 198                 f.Close()
 199                 if err2 != nil {
 200                         err = err2
 201                         return 1
 202                 }
 203                 cmd.chi2Cases = make([]bool, len(cgnames))
 204                 ncases := 0
 205                 for _, pattern := range bytes.Split(buf, []byte{'\n'}) {
 206                         if len(pattern) == 0 {
 207                                 continue
 208                         }
 209                         pattern := string(pattern)
 210                         idx := -1
 211                         for i, name := range cgnames {
 212                                 if !strings.Contains(name, pattern) {
 213                                         continue
 214                                 }
 215                                 cmd.chi2Cases[i] = true
 216                                 ncases++
 217                                 if idx >= 0 {
 218                                         log.Warnf("pattern %q in cases file matches multiple genome IDs: %q, %q", pattern, cgnames[idx], name)
 219                                 } else {
 220                                         idx = i
 221                                 }
 222                         }
 223                         if idx < 0 {
 224                                 log.Warnf("pattern %q in cases file does not match any genome IDs", pattern)
 225                                 continue
 226                         }
 227                 }
 228                 log.Printf("%d cases, %d controls", ncases, len(cgnames)-ncases)
 229         }
 230
 231         {
 232                 labelsFilename := *outputDir + "/labels.csv"
 233                 log.Infof("writing labels to %s", labelsFilename)
 234                 var f *os.File
 235                 f, err = os.Create(labelsFilename)
 236                 if err != nil {
 237                         return 1
 238                 }
 239                 defer f.Close()
 240                 for i, name := range cgnames {
 241                         _, err = fmt.Fprintf(f, "%d,%q\n", i, trimFilenameForLabel(name))
 242                         if err != nil {
 243                                 err = fmt.Errorf("write %s: %w", labelsFilename, err)
 244                                 return 1
 245                         }
 246                 }
 247                 err = f.Close()
 248                 if err != nil {
 249                         err = fmt.Errorf("close %s: %w", labelsFilename, err)
 250                         return 1
 251                 }
 252         }
 253
 254         log.Info("indexing reference tiles")
 255         type reftileinfo struct {
 256                 variant  tileVariantID
 257                 seqname  string // chr1
 258                 pos      int    // distance from start of chromosome to starttag
 259                 tiledata []byte // acgtggcaa...
 260         }
 261         isdup := map[tagID]bool{}
 262         reftile := map[tagID]*reftileinfo{}
 263         for seqname, cseq := range refseq {
 264                 pos := 0
 265                 for _, libref := range cseq {
 266                         tiledata := reftiledata[libref]
 267                         if len(tiledata) == 0 {
 268                                 err = fmt.Errorf("missing tiledata for tag %d variant %d in %s in ref", libref.Tag, libref.Variant, seqname)
 269                                 return 1
 270                         }
 271                         if isdup[libref.Tag] {
 272                                 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
 273                         } else if reftile[libref.Tag] != nil {
 274                                 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)
 275                                 delete(reftile, libref.Tag)
 276                                 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
 277                                 isdup[libref.Tag] = true
 278                         } else {
 279                                 reftile[libref.Tag] = &reftileinfo{
 280                                         seqname:  seqname,
 281                                         variant:  libref.Variant,
 282                                         tiledata: tiledata,
 283                                         pos:      pos,
 284                                 }
 285                         }
 286                         pos += len(tiledata) - taglen
 287                 }
 288                 log.Printf("... %s done, len %d", seqname, pos+taglen)
 289         }
 290
 291         var mask *mask
 292         if *regionsFilename != "" {
 293                 log.Printf("loading regions from %s", *regionsFilename)
 294                 mask, err = makeMask(*regionsFilename, *expandRegions)
 295                 if err != nil {
 296                         return 1
 297                 }
 298                 log.Printf("before applying mask, len(reftile) == %d", len(reftile))
 299                 log.Printf("deleting reftile entries for regions outside %d intervals", mask.Len())
 300                 for tag, rt := range reftile {
 301                         if !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(rt.tiledata)) {
 302                                 delete(reftile, tag)
 303                         }
 304                 }
 305                 log.Printf("after applying mask, len(reftile) == %d", len(reftile))
 306         }
 307
 308         type hgvsColSet map[hgvs.Variant][2][]int8
 309         encodeHGVS := throttle{Max: len(refseq)}
 310         encodeHGVSTodo := map[string]chan hgvsColSet{}
 311         tmpHGVSCols := map[string]*os.File{}
 312         if *hgvsChunked {
 313                 for seqname := range refseq {
 314                         var f *os.File
 315                         f, err = os.Create(*outputDir + "/tmp." + seqname + ".gob")
 316                         if err != nil {
 317                                 return 1
 318                         }
 319                         defer os.Remove(f.Name())
 320                         bufw := bufio.NewWriterSize(f, 1<<24)
 321                         enc := gob.NewEncoder(bufw)
 322                         tmpHGVSCols[seqname] = f
 323                         todo := make(chan hgvsColSet, 128)
 324                         encodeHGVSTodo[seqname] = todo
 325                         encodeHGVS.Go(func() error {
 326                                 for colset := range todo {
 327                                         err := enc.Encode(colset)
 328                                         if err != nil {
 329                                                 encodeHGVS.Report(err)
 330                                                 for range todo {
 331                                                 }
 332                                                 return err
 333                                         }
 334                                 }
 335                                 return bufw.Flush()
 336                         })
 337                 }
 338         }
 339
 340         var toMerge [][]int16
 341         if *mergeOutput || *hgvsSingle {
 342                 toMerge = make([][]int16, len(infiles))
 343         }
 344
 345         throttleMem := throttle{Max: cmd.threads} // TODO: estimate using mem and data size
 346         throttleNumpyMem := throttle{Max: cmd.threads/2 + 1}
 347         log.Info("generating annotations and numpy matrix for each slice")
 348         var done int64
 349         for infileIdx, infile := range infiles {
 350                 infileIdx, infile := infileIdx, infile
 351                 throttleMem.Go(func() error {
 352                         seq := make(map[tagID][]TileVariant, 50000)
 353                         cgs := make(map[string]CompactGenome, len(cgnames))
 354                         f, err := open(infile)
 355                         if err != nil {
 356                                 return err
 357                         }
 358                         defer f.Close()
 359                         log.Infof("%04d: reading %s", infileIdx, infile)
 360                         err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
 361                                 for _, tv := range ent.TileVariants {
 362                                         if tv.Ref {
 363                                                 continue
 364                                         }
 365                                         if mask != nil && reftile[tv.Tag] == nil {
 366                                                 // Don't waste
 367                                                 // time/memory on
 368                                                 // masked-out tiles.
 369                                                 continue
 370                                         }
 371                                         variants := seq[tv.Tag]
 372                                         if len(variants) == 0 {
 373                                                 variants = make([]TileVariant, 100)
 374                                         }
 375                                         for len(variants) <= int(tv.Variant) {
 376                                                 variants = append(variants, TileVariant{})
 377                                         }
 378                                         variants[int(tv.Variant)] = tv
 379                                         seq[tv.Tag] = variants
 380                                 }
 381                                 for _, cg := range ent.CompactGenomes {
 382                                         if !matchGenome.MatchString(cg.Name) {
 383                                                 continue
 384                                         }
 385                                         // pad to full slice size
 386                                         // to avoid out-of-bounds
 387                                         // checks later
 388                                         if sliceSize := 2 * int(cg.EndTag-cg.StartTag); len(cg.Variants) < sliceSize {
 389                                                 cg.Variants = append(cg.Variants, make([]tileVariantID, sliceSize-len(cg.Variants))...)
 390                                         }
 391                                         cgs[cg.Name] = cg
 392                                 }
 393                                 return nil
 394                         })
 395                         if err != nil {
 396                                 return err
 397                         }
 398                         tagstart := cgs[cgnames[0]].StartTag
 399                         tagend := cgs[cgnames[0]].EndTag
 400
 401                         // TODO: filters
 402
 403                         log.Infof("%04d: renumber/dedup variants for tags %d-%d", infileIdx, tagstart, tagend)
 404                         variantRemap := make([][]tileVariantID, tagend-tagstart)
 405                         throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
 406                         for tag, variants := range seq {
 407                                 tag, variants := tag, variants
 408                                 throttleCPU.Acquire()
 409                                 go func() {
 410                                         defer throttleCPU.Release()
 411                                         count := make(map[[blake2b.Size256]byte]int, len(variants))
 412
 413                                         rt := reftile[tag]
 414                                         if rt != nil {
 415                                                 count[blake2b.Sum256(rt.tiledata)] = 0
 416                                         }
 417
 418                                         for _, cg := range cgs {
 419                                                 idx := int(tag-tagstart) * 2
 420                                                 for allele := 0; allele < 2; allele++ {
 421                                                         v := cg.Variants[idx+allele]
 422                                                         if v > 0 && len(variants[v].Sequence) > 0 {
 423                                                                 count[variants[v].Blake2b]++
 424                                                         }
 425                                                 }
 426                                         }
 427                                         // hash[i] will be the hash of
 428                                         // the variant(s) that should
 429                                         // be at rank i (0-based).
 430                                         hash := make([][blake2b.Size256]byte, 0, len(count))
 431                                         for b := range count {
 432                                                 hash = append(hash, b)
 433                                         }
 434                                         sort.Slice(hash, func(i, j int) bool {
 435                                                 bi, bj := &hash[i], &hash[j]
 436                                                 if ci, cj := count[*bi], count[*bj]; ci != cj {
 437                                                         return ci > cj
 438                                                 } else {
 439                                                         return bytes.Compare((*bi)[:], (*bj)[:]) < 0
 440                                                 }
 441                                         })
 442                                         // rank[b] will be the 1-based
 443                                         // new variant number for
 444                                         // variants whose hash is b.
 445                                         rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
 446                                         for i, h := range hash {
 447                                                 rank[h] = tileVariantID(i + 1)
 448                                         }
 449                                         // remap[v] will be the new
 450                                         // variant number for original
 451                                         // variant number v.
 452                                         remap := make([]tileVariantID, len(variants))
 453                                         for i, tv := range variants {
 454                                                 remap[i] = rank[tv.Blake2b]
 455                                         }
 456                                         variantRemap[tag-tagstart] = remap
 457                                         if rt != nil {
 458                                                 rt.variant = rank[blake2b.Sum256(rt.tiledata)]
 459                                         }
 460                                 }()
 461                         }
 462                         throttleCPU.Wait()
 463
 464                         annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
 465                         log.Infof("%04d: writing %s", infileIdx, annotationsFilename)
 466                         annof, err := os.Create(annotationsFilename)
 467                         if err != nil {
 468                                 return err
 469                         }
 470                         annow := bufio.NewWriterSize(annof, 1<<20)
 471                         outcol := 0
 472                         for tag := tagstart; tag < tagend; tag++ {
 473                                 rt, ok := reftile[tag]
 474                                 if !ok {
 475                                         if mask == nil {
 476                                                 outcol++
 477                                         }
 478                                         // Excluded by specified
 479                                         // regions, or reference does
 480                                         // not use any variant of this
 481                                         // tile. (TODO: log this?
 482                                         // mention it in annotations?)
 483                                         continue
 484                                 }
 485                                 fmt.Fprintf(annow, "%d,%d,%d,=,%s,%d,,,\n", tag, outcol, rt.variant, rt.seqname, rt.pos)
 486                                 variants := seq[tag]
 487                                 reftilestr := strings.ToUpper(string(rt.tiledata))
 488                                 remap := variantRemap[tag-tagstart]
 489                                 maxv := tileVariantID(0)
 490                                 for _, v := range remap {
 491                                         if maxv < v {
 492                                                 maxv = v
 493                                         }
 494                                 }
 495                                 done := make([]bool, maxv+1)
 496                                 variantDiffs := make([][]hgvs.Variant, maxv+1)
 497                                 for v, tv := range variants {
 498                                         v := remap[v]
 499                                         if v == rt.variant || done[v] {
 500                                                 continue
 501                                         } else {
 502                                                 done[v] = true
 503                                         }
 504                                         if len(tv.Sequence) < taglen || !bytes.HasSuffix(rt.tiledata, tv.Sequence[len(tv.Sequence)-taglen:]) {
 505                                                 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
 506                                                 continue
 507                                         }
 508                                         if lendiff := len(rt.tiledata) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
 509                                                 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
 510                                                 continue
 511                                         }
 512                                         diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
 513                                         for i := range diffs {
 514                                                 diffs[i].Position += rt.pos
 515                                         }
 516                                         for _, diff := range diffs {
 517                                                 fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s,%s,%d,%s,%s,%s\n", tag, outcol, v, rt.seqname, diff.String(), rt.seqname, diff.Position, diff.Ref, diff.New, diff.Left)
 518                                         }
 519                                         if *hgvsChunked {
 520                                                 variantDiffs[v] = diffs
 521                                         }
 522                                 }
 523                                 if *hgvsChunked {
 524                                         // We can now determine, for each HGVS
 525                                         // variant (diff) in this reftile
 526                                         // region, whether a given genome
 527                                         // phase/allele (1) has the variant, (0) has
 528                                         // =ref or a different variant in that
 529                                         // position, or (-1) is lacking
 530                                         // coverage / couldn't be diffed.
 531                                         hgvsCol := hgvsColSet{}
 532                                         for _, diffs := range variantDiffs {
 533                                                 for _, diff := range diffs {
 534                                                         if _, ok := hgvsCol[diff]; ok {
 535                                                                 continue
 536                                                         }
 537                                                         hgvsCol[diff] = [2][]int8{
 538                                                                 make([]int8, len(cgnames)),
 539                                                                 make([]int8, len(cgnames)),
 540                                                         }
 541                                                 }
 542                                         }
 543                                         for row, name := range cgnames {
 544                                                 variants := cgs[name].Variants[(tag-tagstart)*2:]
 545                                                 for ph := 0; ph < 2; ph++ {
 546                                                         v := variants[ph]
 547                                                         if int(v) >= len(remap) {
 548                                                                 v = 0
 549                                                         } else {
 550                                                                 v = remap[v]
 551                                                         }
 552                                                         if v == rt.variant {
 553                                                                 // hgvsCol[*][ph][row] is already 0
 554                                                         } else if len(variantDiffs[v]) == 0 {
 555                                                                 // lacking coverage / couldn't be diffed
 556                                                                 for _, col := range hgvsCol {
 557                                                                         col[ph][row] = -1
 558                                                                 }
 559                                                         } else {
 560                                                                 for _, diff := range variantDiffs[v] {
 561                                                                         hgvsCol[diff][ph][row] = 1
 562                                                                 }
 563                                                         }
 564                                                 }
 565                                         }
 566                                         for diff, colpair := range hgvsCol {
 567                                                 allele2homhet(colpair)
 568                                                 if !cmd.filterHGVScolpair(colpair) {
 569                                                         delete(hgvsCol, diff)
 570                                                 }
 571                                         }
 572                                         if len(hgvsCol) > 0 {
 573                                                 encodeHGVSTodo[rt.seqname] <- hgvsCol
 574                                         }
 575                                 }
 576                                 outcol++
 577                         }
 578                         err = annow.Flush()
 579                         if err != nil {
 580                                 return err
 581                         }
 582                         err = annof.Close()
 583                         if err != nil {
 584                                 return err
 585                         }
 586
 587                         log.Infof("%04d: preparing numpy", infileIdx)
 588                         throttleNumpyMem.Acquire()
 589                         rows := len(cgnames)
 590                         cols := 2 * outcol
 591                         out := make([]int16, rows*cols)
 592                         for row, name := range cgnames {
 593                                 out := out[row*cols:]
 594                                 outcol := 0
 595                                 for col, v := range cgs[name].Variants {
 596                                         tag := tagstart + tagID(col/2)
 597                                         if mask != nil && reftile[tag] == nil {
 598                                                 continue
 599                                         }
 600                                         if variants, ok := seq[tag]; ok && len(variants) > int(v) && len(variants[v].Sequence) > 0 {
 601                                                 out[outcol] = int16(variantRemap[tag-tagstart][v])
 602                                         } else {
 603                                                 out[outcol] = -1
 604                                         }
 605                                         outcol++
 606                                 }
 607                         }
 608                         seq = nil
 609                         cgs = nil
 610                         debug.FreeOSMemory()
 611                         throttleNumpyMem.Release()
 612
 613                         if *mergeOutput || *hgvsSingle {
 614                                 log.Infof("%04d: matrix fragment %d rows x %d cols", infileIdx, rows, cols)
 615                                 toMerge[infileIdx] = out
 616                         }
 617                         if !*mergeOutput {
 618                                 fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
 619                                 err = writeNumpyInt16(fnm, out, rows, cols)
 620                                 if err != nil {
 621                                         return err
 622                                 }
 623                                 debug.FreeOSMemory()
 624                         }
 625                         log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
 626                         return nil
 627                 })
 628         }
 629         if err = throttleMem.Wait(); err != nil {
 630                 return 1
 631         }
 632
 633         if *hgvsChunked {
 634                 log.Info("flushing hgvsCols temp files")
 635                 for seqname := range refseq {
 636                         close(encodeHGVSTodo[seqname])
 637                 }
 638                 err = encodeHGVS.Wait()
 639                 if err != nil {
 640                         return 1
 641                 }
 642                 for seqname := range refseq {
 643                         log.Infof("%s: reading hgvsCols from temp file", seqname)
 644                         f := tmpHGVSCols[seqname]
 645                         _, err = f.Seek(0, io.SeekStart)
 646                         if err != nil {
 647                                 return 1
 648                         }
 649                         var hgvsCols hgvsColSet
 650                         dec := gob.NewDecoder(bufio.NewReaderSize(f, 1<<24))
 651                         for err == nil {
 652                                 err = dec.Decode(&hgvsCols)
 653                         }
 654                         if err != io.EOF {
 655                                 return 1
 656                         }
 657                         log.Infof("%s: sorting %d hgvs variants", seqname, len(hgvsCols))
 658                         variants := make([]hgvs.Variant, 0, len(hgvsCols))
 659                         for v := range hgvsCols {
 660                                 variants = append(variants, v)
 661                         }
 662                         sort.Slice(variants, func(i, j int) bool {
 663                                 vi, vj := &variants[i], &variants[j]
 664                                 if vi.Position != vj.Position {
 665                                         return vi.Position < vj.Position
 666                                 } else if vi.Ref != vj.Ref {
 667                                         return vi.Ref < vj.Ref
 668                                 } else {
 669                                         return vi.New < vj.New
 670                                 }
 671                         })
 672                         rows := len(cgnames)
 673                         cols := len(variants) * 2
 674                         log.Infof("%s: building hgvs matrix (rows=%d, cols=%d, mem=%d)", seqname, rows, cols, rows*cols)
 675                         out := make([]int8, rows*cols)
 676                         for varIdx, variant := range variants {
 677                                 hgvsCols := hgvsCols[variant]
 678                                 for row := range cgnames {
 679                                         for ph := 0; ph < 2; ph++ {
 680                                                 out[row*cols+varIdx+ph] = hgvsCols[ph][row]
 681                                         }
 682                                 }
 683                         }
 684                         err = writeNumpyInt8(fmt.Sprintf("%s/hgvs.%s.npy", *outputDir, seqname), out, rows, cols)
 685                         if err != nil {
 686                                 return 1
 687                         }
 688                         out = nil
 689
 690                         fnm := fmt.Sprintf("%s/hgvs.%s.annotations.csv", *outputDir, seqname)
 691                         log.Infof("%s: writing hgvs column labels to %s", seqname, fnm)
 692                         var hgvsLabels bytes.Buffer
 693                         for varIdx, variant := range variants {
 694                                 fmt.Fprintf(&hgvsLabels, "%d,%s:g.%s\n", varIdx, seqname, variant.String())
 695                         }
 696                         err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0666)
 697                         if err != nil {
 698                                 return 1
 699                         }
 700                 }
 701         }
 702
 703         if *mergeOutput || *hgvsSingle {
 704                 var annow *bufio.Writer
 705                 var annof *os.File
 706                 if *mergeOutput {
 707                         annoFilename := fmt.Sprintf("%s/matrix.annotations.csv", *outputDir)
 708                         annof, err = os.Create(annoFilename)
 709                         if err != nil {
 710                                 return 1
 711                         }
 712                         annow = bufio.NewWriterSize(annof, 1<<20)
 713                 }
 714
 715                 rows := len(cgnames)
 716                 cols := 0
 717                 for _, chunk := range toMerge {
 718                         cols += len(chunk) / rows
 719                 }
 720                 log.Infof("merging output matrix (rows=%d, cols=%d, mem=%d) and annotations", rows, cols, rows*cols*2)
 721                 var out []int16
 722                 if *mergeOutput {
 723                         out = make([]int16, rows*cols)
 724                 }
 725                 hgvsCols := map[string][2][]int16{} // hgvs -> [[g0,g1,g2,...], [g0,g1,g2,...]] (slice of genomes for each phase)
 726                 startcol := 0
 727                 for outIdx, chunk := range toMerge {
 728                         chunkcols := len(chunk) / rows
 729                         if *mergeOutput {
 730                                 for row := 0; row < rows; row++ {
 731                                         copy(out[row*cols+startcol:], chunk[row*chunkcols:(row+1)*chunkcols])
 732                                 }
 733                         }
 734                         toMerge[outIdx] = nil
 735
 736                         annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, outIdx)
 737                         log.Infof("reading %s", annotationsFilename)
 738                         buf, err := os.ReadFile(annotationsFilename)
 739                         if err != nil {
 740                                 return 1
 741                         }
 742                         if *mergeOutput {
 743                                 err = os.Remove(annotationsFilename)
 744                                 if err != nil {
 745                                         return 1
 746                                 }
 747                         }
 748                         for _, line := range bytes.Split(buf, []byte{'\n'}) {
 749                                 if len(line) == 0 {
 750                                         continue
 751                                 }
 752                                 fields := bytes.SplitN(line, []byte{','}, 9)
 753                                 tag, _ := strconv.Atoi(string(fields[0]))
 754                                 incol, _ := strconv.Atoi(string(fields[1]))
 755                                 tileVariant, _ := strconv.Atoi(string(fields[2]))
 756                                 hgvsID := string(fields[3])
 757                                 seqname := string(fields[4])
 758                                 pos, _ := strconv.Atoi(string(fields[5]))
 759                                 refseq := fields[6]
 760                                 if hgvsID == "" {
 761                                         // Null entry for un-diffable
 762                                         // tile variant
 763                                         continue
 764                                 }
 765                                 if hgvsID == "=" {
 766                                         // Null entry for ref tile
 767                                         continue
 768                                 }
 769                                 if mask != nil && !mask.Check(strings.TrimPrefix(seqname, "chr"), pos, pos+len(refseq)) {
 770                                         // The tile intersects one of
 771                                         // the selected regions, but
 772                                         // this particular HGVS
 773                                         // variant does not.
 774                                         continue
 775                                 }
 776                                 hgvsColPair := hgvsCols[hgvsID]
 777                                 if hgvsColPair[0] == nil {
 778                                         // values in new columns start
 779                                         // out as -1 ("no data yet")
 780                                         // or 0 ("=ref") here, may
 781                                         // change to 1 ("hgvs variant
 782                                         // present") below, either on
 783                                         // this line or a future line.
 784                                         hgvsColPair = [2][]int16{make([]int16, len(cgnames)), make([]int16, len(cgnames))}
 785                                         rt, ok := reftile[tagID(tag)]
 786                                         if !ok {
 787                                                 err = fmt.Errorf("bug: seeing annotations for tag %d, but it has no reftile entry", tag)
 788                                                 return 1
 789                                         }
 790                                         for ph := 0; ph < 2; ph++ {
 791                                                 for row := 0; row < rows; row++ {
 792                                                         v := chunk[row*chunkcols+incol*2+ph]
 793                                                         if tileVariantID(v) == rt.variant {
 794                                                                 hgvsColPair[ph][row] = 0
 795                                                         } else {
 796                                                                 hgvsColPair[ph][row] = -1
 797                                                         }
 798                                                 }
 799                                         }
 800                                         hgvsCols[hgvsID] = hgvsColPair
 801                                         if annow != nil {
 802                                                 hgvsref := hgvs.Variant{
 803                                                         Position: pos,
 804                                                         Ref:      string(refseq),
 805                                                         New:      string(refseq),
 806                                                 }
 807                                                 fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s,%s,%d,%s,%s,%s\n", tag, incol+startcol/2, rt.variant, seqname, hgvsref.String(), seqname, pos, refseq, refseq, fields[8])
 808                                         }
 809                                 }
 810                                 if annow != nil {
 811                                         fmt.Fprintf(annow, "%d,%d,%d,%s,%s,%d,%s,%s,%s\n", tag, incol+startcol/2, tileVariant, hgvsID, seqname, pos, refseq, fields[7], fields[8])
 812                                 }
 813                                 for ph := 0; ph < 2; ph++ {
 814                                         for row := 0; row < rows; row++ {
 815                                                 v := chunk[row*chunkcols+incol*2+ph]
 816                                                 if int(v) == tileVariant {
 817                                                         hgvsColPair[ph][row] = 1
 818                                                 }
 819                                         }
 820                                 }
 821                         }
 822
 823                         startcol += chunkcols
 824                 }
 825                 if *mergeOutput {
 826                         err = annow.Flush()
 827                         if err != nil {
 828                                 return 1
 829                         }
 830                         err = annof.Close()
 831                         if err != nil {
 832                                 return 1
 833                         }
 834                         err = writeNumpyInt16(fmt.Sprintf("%s/matrix.npy", *outputDir), out, rows, cols)
 835                         if err != nil {
 836                                 return 1
 837                         }
 838                 }
 839                 out = nil
 840
 841                 if *hgvsSingle {
 842                         cols = len(hgvsCols) * 2
 843                         log.Printf("building hgvs-based matrix: %d rows x %d cols", rows, cols)
 844                         out = make([]int16, rows*cols)
 845                         hgvsIDs := make([]string, 0, cols/2)
 846                         for hgvsID := range hgvsCols {
 847                                 hgvsIDs = append(hgvsIDs, hgvsID)
 848                         }
 849                         sort.Strings(hgvsIDs)
 850                         var hgvsLabels bytes.Buffer
 851                         for idx, hgvsID := range hgvsIDs {
 852                                 fmt.Fprintf(&hgvsLabels, "%d,%s\n", idx, hgvsID)
 853                                 for ph := 0; ph < 2; ph++ {
 854                                         hgvscol := hgvsCols[hgvsID][ph]
 855                                         for row, val := range hgvscol {
 856                                                 out[row*cols+idx*2+ph] = val
 857                                         }
 858                                 }
 859                         }
 860                         err = writeNumpyInt16(fmt.Sprintf("%s/hgvs.npy", *outputDir), out, rows, cols)
 861                         if err != nil {
 862                                 return 1
 863                         }
 864
 865                         fnm := fmt.Sprintf("%s/hgvs.annotations.csv", *outputDir)
 866                         log.Printf("writing hgvs labels: %s", fnm)
 867                         err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0777)
 868                         if err != nil {
 869                                 return 1
 870                         }
 871                 }
 872         }
 873         return 0
 874 }
 875
 876 func (cmd *sliceNumpy) filterHGVScolpair(colpair [2][]int8) bool {
 877         if cmd.chi2PValue >= 1 {
 878                 return true
 879         }
 880         col0 := make([]bool, 0, len(cmd.chi2Cases))
 881         col1 := make([]bool, 0, len(cmd.chi2Cases))
 882         cases := make([]bool, 0, len(cmd.chi2Cases))
 883         for i, c := range cmd.chi2Cases {
 884                 if colpair[0][i] < 0 {
 885                         continue
 886                 }
 887                 col0 = append(col0, colpair[0][i] != 0)
 888                 col1 = append(col1, colpair[1][i] != 0)
 889                 cases = append(cases, c)
 890         }
 891         return len(cases) >= cmd.minCoverage &&
 892                 (pvalue(cases, col0) <= cmd.chi2PValue || pvalue(cases, col1) <= cmd.chi2PValue)
 893 }
 894
 895 func writeNumpyInt16(fnm string, out []int16, rows, cols int) error {
 896         output, err := os.Create(fnm)
 897         if err != nil {
 898                 return err
 899         }
 900         defer output.Close()
 901         bufw := bufio.NewWriterSize(output, 1<<26)
 902         npw, err := gonpy.NewWriter(nopCloser{bufw})
 903         if err != nil {
 904                 return err
 905         }
 906         log.WithFields(log.Fields{
 907                 "filename": fnm,
 908                 "rows":     rows,
 909                 "cols":     cols,
 910         }).Infof("writing numpy: %s", fnm)
 911         npw.Shape = []int{rows, cols}
 912         npw.WriteInt16(out)
 913         err = bufw.Flush()
 914         if err != nil {
 915                 return err
 916         }
 917         return output.Close()
 918 }
 919
 920 func writeNumpyInt8(fnm string, out []int8, rows, cols int) error {
 921         output, err := os.Create(fnm)
 922         if err != nil {
 923                 return err
 924         }
 925         defer output.Close()
 926         bufw := bufio.NewWriterSize(output, 1<<26)
 927         npw, err := gonpy.NewWriter(nopCloser{bufw})
 928         if err != nil {
 929                 return err
 930         }
 931         log.WithFields(log.Fields{
 932                 "filename": fnm,
 933                 "rows":     rows,
 934                 "cols":     cols,
 935         }).Infof("writing numpy: %s", fnm)
 936         npw.Shape = []int{rows, cols}
 937         npw.WriteInt8(out)
 938         err = bufw.Flush()
 939         if err != nil {
 940                 return err
 941         }
 942         return output.Close()
 943 }
 944
 945 func allele2homhet(colpair [2][]int8) {
 946         a, b := colpair[0], colpair[1]
 947         for i, av := range a {
 948                 bv := b[i]
 949                 if av < 0 || bv < 0 {
 950                         // no-call
 951                         a[i], b[i] = -1, -1
 952                 } else if av > 0 && bv > 0 {
 953                         // hom
 954                         a[i], b[i] = 1, 0
 955                 } else if av > 0 || bv > 0 {
 956                         // het
 957                         a[i], b[i] = 0, 1
 958                 } else {
 959                         // ref (or a different variant in same position)
 960                         // (this is a no-op) a[i], b[i] = 0, 0
 961                 }
 962         }
 963 }