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         cgnames       []string
  42 }
  43
  44 func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  45         var err error
  46         defer func() {
  47                 if err != nil {
  48                         fmt.Fprintf(stderr, "%s\n", err)
  49                 }
  50         }()
  51         flags := flag.NewFlagSet("", flag.ContinueOnError)
  52         flags.SetOutput(stderr)
  53         pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
  54         runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
  55         projectUUID := flags.String("project", "", "project `UUID` for output data")
  56         priority := flags.Int("priority", 500, "container request priority")
  57         inputDir := flags.String("input-dir", "./in", "input `directory`")
  58         outputDir := flags.String("output-dir", "./out", "output `directory`")
  59         ref := flags.String("ref", "", "reference name (if blank, choose last one that appears in input)")
  60         regionsFilename := flags.String("regions", "", "only output columns/annotations that intersect regions in specified bed `file`")
  61         expandRegions := flags.Int("expand-regions", 0, "expand specified regions by `N` base pairs on each side`")
  62         mergeOutput := flags.Bool("merge-output", false, "merge output into one matrix.npy and one matrix.annotations.csv")
  63         hgvsSingle := flags.Bool("single-hgvs-matrix", false, "also generate hgvs-based matrix")
  64         hgvsChunked := flags.Bool("chunked-hgvs-matrix", false, "also generate hgvs-based matrix per chromosome")
  65         onehotChunked := flags.Bool("chunked-onehot", false, "generate one-hot tile-based matrix")
  66         flags.IntVar(&cmd.threads, "threads", 16, "number of memory-hungry assembly threads")
  67         flags.StringVar(&cmd.chi2CasesFile, "chi2-cases-file", "", "text file indicating positive cases (for Χ² test)")
  68         flags.Float64Var(&cmd.chi2PValue, "chi2-p-value", 1, "do Χ² test and omit columns with p-value above this threshold")
  69         cmd.filter.Flags(flags)
  70         err = flags.Parse(args)
  71         if err == flag.ErrHelp {
  72                 err = nil
  73                 return 0
  74         } else if err != nil {
  75                 return 2
  76         }
  77
  78         if *pprof != "" {
  79                 go func() {
  80                         log.Println(http.ListenAndServe(*pprof, nil))
  81                 }()
  82         }
  83
  84         if cmd.chi2CasesFile == "" && cmd.chi2PValue != 1 {
  85                 log.Errorf("cannot use provided -chi2-p-value=%f because -chi2-cases-file= value is empty", cmd.chi2PValue)
  86                 return 2
  87         }
  88
  89         if !*runlocal {
  90                 runner := arvadosContainerRunner{
  91                         Name:        "lightning slice-numpy",
  92                         Client:      arvados.NewClientFromEnv(),
  93                         ProjectUUID: *projectUUID,
  94                         RAM:         750000000000,
  95                         VCPUs:       96,
  96                         Priority:    *priority,
  97                         KeepCache:   2,
  98                         APIAccess:   true,
  99                 }
 100                 err = runner.TranslatePaths(inputDir, regionsFilename, &cmd.chi2CasesFile)
 101                 if err != nil {
 102                         return 1
 103                 }
 104                 runner.Args = []string{"slice-numpy", "-local=true",
 105                         "-pprof=:6060",
 106                         "-input-dir=" + *inputDir,
 107                         "-output-dir=/mnt/output",
 108                         "-threads=" + fmt.Sprintf("%d", cmd.threads),
 109                         "-regions=" + *regionsFilename,
 110                         "-expand-regions=" + fmt.Sprintf("%d", *expandRegions),
 111                         "-merge-output=" + fmt.Sprintf("%v", *mergeOutput),
 112                         "-single-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsSingle),
 113                         "-chunked-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsChunked),
 114                         "-chunked-onehot=" + fmt.Sprintf("%v", *onehotChunked),
 115                         "-chi2-cases-file=" + cmd.chi2CasesFile,
 116                         "-chi2-p-value=" + fmt.Sprintf("%f", cmd.chi2PValue),
 117                 }
 118                 runner.Args = append(runner.Args, cmd.filter.Args()...)
 119                 var output string
 120                 output, err = runner.Run()
 121                 if err != nil {
 122                         return 1
 123                 }
 124                 fmt.Fprintln(stdout, output)
 125                 return 0
 126         }
 127
 128         infiles, err := allGobFiles(*inputDir)
 129         if err != nil {
 130                 return 1
 131         }
 132         if len(infiles) == 0 {
 133                 err = fmt.Errorf("no input files found in %s", *inputDir)
 134                 return 1
 135         }
 136         sort.Strings(infiles)
 137
 138         var refseq map[string][]tileLibRef
 139         var reftiledata = make(map[tileLibRef][]byte, 11000000)
 140         in0, err := open(infiles[0])
 141         if err != nil {
 142                 return 1
 143         }
 144
 145         matchGenome, err := regexp.Compile(cmd.filter.MatchGenome)
 146         if err != nil {
 147                 err = fmt.Errorf("-match-genome: invalid regexp: %q", cmd.filter.MatchGenome)
 148                 return 1
 149         }
 150
 151         cmd.cgnames = nil
 152         taglen := -1
 153         DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
 154                 if len(ent.TagSet) > 0 {
 155                         taglen = len(ent.TagSet[0])
 156                 }
 157                 for _, cseq := range ent.CompactSequences {
 158                         if cseq.Name == *ref || *ref == "" {
 159                                 refseq = cseq.TileSequences
 160                         }
 161                 }
 162                 for _, cg := range ent.CompactGenomes {
 163                         if matchGenome.MatchString(cg.Name) {
 164                                 cmd.cgnames = append(cmd.cgnames, cg.Name)
 165                         }
 166                 }
 167                 for _, tv := range ent.TileVariants {
 168                         if tv.Ref {
 169                                 reftiledata[tileLibRef{tv.Tag, tv.Variant}] = tv.Sequence
 170                         }
 171                 }
 172                 return nil
 173         })
 174         if err != nil {
 175                 return 1
 176         }
 177         in0.Close()
 178         if refseq == nil {
 179                 err = fmt.Errorf("%s: reference sequence not found", infiles[0])
 180                 return 1
 181         }
 182         if taglen < 0 {
 183                 err = fmt.Errorf("tagset not found")
 184                 return 1
 185         }
 186         if len(cmd.cgnames) == 0 {
 187                 err = fmt.Errorf("no genomes found matching regexp %q", cmd.filter.MatchGenome)
 188                 return 1
 189         }
 190         sort.Strings(cmd.cgnames)
 191
 192         cmd.minCoverage = int(math.Ceil(cmd.filter.MinCoverage * float64(len(cmd.cgnames))))
 193
 194         if cmd.chi2CasesFile != "" {
 195                 f, err2 := open(cmd.chi2CasesFile)
 196                 if err2 != nil {
 197                         err = err2
 198                         return 1
 199                 }
 200                 buf, err2 := io.ReadAll(f)
 201                 f.Close()
 202                 if err2 != nil {
 203                         err = err2
 204                         return 1
 205                 }
 206                 cmd.chi2Cases = make([]bool, len(cmd.cgnames))
 207                 ncases := 0
 208                 for _, pattern := range bytes.Split(buf, []byte{'\n'}) {
 209                         if len(pattern) == 0 {
 210                                 continue
 211                         }
 212                         pattern := string(pattern)
 213                         idx := -1
 214                         for i, name := range cmd.cgnames {
 215                                 if !strings.Contains(name, pattern) {
 216                                         continue
 217                                 }
 218                                 cmd.chi2Cases[i] = true
 219                                 ncases++
 220                                 if idx >= 0 {
 221                                         log.Warnf("pattern %q in cases file matches multiple genome IDs: %q, %q", pattern, cmd.cgnames[idx], name)
 222                                 } else {
 223                                         idx = i
 224                                 }
 225                         }
 226                         if idx < 0 {
 227                                 log.Warnf("pattern %q in cases file does not match any genome IDs", pattern)
 228                                 continue
 229                         }
 230                 }
 231                 log.Printf("%d cases, %d controls", ncases, len(cmd.cgnames)-ncases)
 232         }
 233
 234         {
 235                 labelsFilename := *outputDir + "/labels.csv"
 236                 log.Infof("writing labels to %s", labelsFilename)
 237                 var f *os.File
 238                 f, err = os.Create(labelsFilename)
 239                 if err != nil {
 240                         return 1
 241                 }
 242                 defer f.Close()
 243                 for i, name := range cmd.cgnames {
 244                         _, err = fmt.Fprintf(f, "%d,%q\n", i, trimFilenameForLabel(name))
 245                         if err != nil {
 246                                 err = fmt.Errorf("write %s: %w", labelsFilename, err)
 247                                 return 1
 248                         }
 249                 }
 250                 err = f.Close()
 251                 if err != nil {
 252                         err = fmt.Errorf("close %s: %w", labelsFilename, err)
 253                         return 1
 254                 }
 255         }
 256
 257         log.Info("indexing reference tiles")
 258         type reftileinfo struct {
 259                 variant  tileVariantID
 260                 seqname  string // chr1
 261                 pos      int    // distance from start of chromosome to starttag
 262                 tiledata []byte // acgtggcaa...
 263         }
 264         isdup := map[tagID]bool{}
 265         reftile := map[tagID]*reftileinfo{}
 266         for seqname, cseq := range refseq {
 267                 pos := 0
 268                 for _, libref := range cseq {
 269                         tiledata := reftiledata[libref]
 270                         if len(tiledata) == 0 {
 271                                 err = fmt.Errorf("missing tiledata for tag %d variant %d in %s in ref", libref.Tag, libref.Variant, seqname)
 272                                 return 1
 273                         }
 274                         if isdup[libref.Tag] {
 275                                 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
 276                         } else if reftile[libref.Tag] != nil {
 277                                 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)
 278                                 delete(reftile, libref.Tag)
 279                                 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
 280                                 isdup[libref.Tag] = true
 281                         } else {
 282                                 reftile[libref.Tag] = &reftileinfo{
 283                                         seqname:  seqname,
 284                                         variant:  libref.Variant,
 285                                         tiledata: tiledata,
 286                                         pos:      pos,
 287                                 }
 288                         }
 289                         pos += len(tiledata) - taglen
 290                 }
 291                 log.Printf("... %s done, len %d", seqname, pos+taglen)
 292         }
 293
 294         var mask *mask
 295         if *regionsFilename != "" {
 296                 log.Printf("loading regions from %s", *regionsFilename)
 297                 mask, err = makeMask(*regionsFilename, *expandRegions)
 298                 if err != nil {
 299                         return 1
 300                 }
 301                 log.Printf("before applying mask, len(reftile) == %d", len(reftile))
 302                 log.Printf("deleting reftile entries for regions outside %d intervals", mask.Len())
 303                 for tag, rt := range reftile {
 304                         if !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(rt.tiledata)) {
 305                                 delete(reftile, tag)
 306                         }
 307                 }
 308                 log.Printf("after applying mask, len(reftile) == %d", len(reftile))
 309         }
 310
 311         type hgvsColSet map[hgvs.Variant][2][]int8
 312         encodeHGVS := throttle{Max: len(refseq)}
 313         encodeHGVSTodo := map[string]chan hgvsColSet{}
 314         tmpHGVSCols := map[string]*os.File{}
 315         if *hgvsChunked {
 316                 for seqname := range refseq {
 317                         var f *os.File
 318                         f, err = os.Create(*outputDir + "/tmp." + seqname + ".gob")
 319                         if err != nil {
 320                                 return 1
 321                         }
 322                         defer os.Remove(f.Name())
 323                         bufw := bufio.NewWriterSize(f, 1<<24)
 324                         enc := gob.NewEncoder(bufw)
 325                         tmpHGVSCols[seqname] = f
 326                         todo := make(chan hgvsColSet, 128)
 327                         encodeHGVSTodo[seqname] = todo
 328                         encodeHGVS.Go(func() error {
 329                                 for colset := range todo {
 330                                         err := enc.Encode(colset)
 331                                         if err != nil {
 332                                                 encodeHGVS.Report(err)
 333                                                 for range todo {
 334                                                 }
 335                                                 return err
 336                                         }
 337                                 }
 338                                 return bufw.Flush()
 339                         })
 340                 }
 341         }
 342
 343         var toMerge [][]int16
 344         if *mergeOutput || *hgvsSingle {
 345                 toMerge = make([][]int16, len(infiles))
 346         }
 347
 348         throttleMem := throttle{Max: cmd.threads} // TODO: estimate using mem and data size
 349         throttleNumpyMem := throttle{Max: cmd.threads/2 + 1}
 350         log.Info("generating annotations and numpy matrix for each slice")
 351         var done int64
 352         for infileIdx, infile := range infiles {
 353                 infileIdx, infile := infileIdx, infile
 354                 throttleMem.Go(func() error {
 355                         seq := make(map[tagID][]TileVariant, 50000)
 356                         cgs := make(map[string]CompactGenome, len(cmd.cgnames))
 357                         f, err := open(infile)
 358                         if err != nil {
 359                                 return err
 360                         }
 361                         defer f.Close()
 362                         log.Infof("%04d: reading %s", infileIdx, infile)
 363                         err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
 364                                 for _, tv := range ent.TileVariants {
 365                                         if tv.Ref {
 366                                                 continue
 367                                         }
 368                                         if mask != nil && reftile[tv.Tag] == nil {
 369                                                 // Don't waste
 370                                                 // time/memory on
 371                                                 // masked-out tiles.
 372                                                 continue
 373                                         }
 374                                         variants := seq[tv.Tag]
 375                                         if len(variants) == 0 {
 376                                                 variants = make([]TileVariant, 100)
 377                                         }
 378                                         for len(variants) <= int(tv.Variant) {
 379                                                 variants = append(variants, TileVariant{})
 380                                         }
 381                                         variants[int(tv.Variant)] = tv
 382                                         seq[tv.Tag] = variants
 383                                 }
 384                                 for _, cg := range ent.CompactGenomes {
 385                                         if !matchGenome.MatchString(cg.Name) {
 386                                                 continue
 387                                         }
 388                                         // pad to full slice size
 389                                         // to avoid out-of-bounds
 390                                         // checks later
 391                                         if sliceSize := 2 * int(cg.EndTag-cg.StartTag); len(cg.Variants) < sliceSize {
 392                                                 cg.Variants = append(cg.Variants, make([]tileVariantID, sliceSize-len(cg.Variants))...)
 393                                         }
 394                                         cgs[cg.Name] = cg
 395                                 }
 396                                 return nil
 397                         })
 398                         if err != nil {
 399                                 return err
 400                         }
 401                         tagstart := cgs[cmd.cgnames[0]].StartTag
 402                         tagend := cgs[cmd.cgnames[0]].EndTag
 403
 404                         // TODO: filters
 405
 406                         log.Infof("%04d: renumber/dedup variants for tags %d-%d", infileIdx, tagstart, tagend)
 407                         variantRemap := make([][]tileVariantID, tagend-tagstart)
 408                         throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
 409                         for tag, variants := range seq {
 410                                 tag, variants := tag, variants
 411                                 throttleCPU.Acquire()
 412                                 go func() {
 413                                         defer throttleCPU.Release()
 414                                         count := make(map[[blake2b.Size256]byte]int, len(variants))
 415
 416                                         rt := reftile[tag]
 417                                         if rt != nil {
 418                                                 count[blake2b.Sum256(rt.tiledata)] = 0
 419                                         }
 420
 421                                         for _, cg := range cgs {
 422                                                 idx := int(tag-tagstart) * 2
 423                                                 for allele := 0; allele < 2; allele++ {
 424                                                         v := cg.Variants[idx+allele]
 425                                                         if v > 0 && len(variants[v].Sequence) > 0 {
 426                                                                 count[variants[v].Blake2b]++
 427                                                         }
 428                                                 }
 429                                         }
 430                                         // hash[i] will be the hash of
 431                                         // the variant(s) that should
 432                                         // be at rank i (0-based).
 433                                         hash := make([][blake2b.Size256]byte, 0, len(count))
 434                                         for b := range count {
 435                                                 hash = append(hash, b)
 436                                         }
 437                                         sort.Slice(hash, func(i, j int) bool {
 438                                                 bi, bj := &hash[i], &hash[j]
 439                                                 if ci, cj := count[*bi], count[*bj]; ci != cj {
 440                                                         return ci > cj
 441                                                 } else {
 442                                                         return bytes.Compare((*bi)[:], (*bj)[:]) < 0
 443                                                 }
 444                                         })
 445                                         // rank[b] will be the 1-based
 446                                         // new variant number for
 447                                         // variants whose hash is b.
 448                                         rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
 449                                         for i, h := range hash {
 450                                                 rank[h] = tileVariantID(i + 1)
 451                                         }
 452                                         // remap[v] will be the new
 453                                         // variant number for original
 454                                         // variant number v.
 455                                         remap := make([]tileVariantID, len(variants))
 456                                         for i, tv := range variants {
 457                                                 remap[i] = rank[tv.Blake2b]
 458                                         }
 459                                         variantRemap[tag-tagstart] = remap
 460                                         if rt != nil {
 461                                                 rt.variant = rank[blake2b.Sum256(rt.tiledata)]
 462                                         }
 463                                 }()
 464                         }
 465                         throttleCPU.Wait()
 466
 467                         var onehotChunk [][]int8
 468                         var onehotXrefs []onehotXref
 469
 470                         annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
 471                         log.Infof("%04d: writing %s", infileIdx, annotationsFilename)
 472                         annof, err := os.Create(annotationsFilename)
 473                         if err != nil {
 474                                 return err
 475                         }
 476                         annow := bufio.NewWriterSize(annof, 1<<20)
 477                         outcol := 0
 478                         for tag := tagstart; tag < tagend; tag++ {
 479                                 rt, ok := reftile[tag]
 480                                 if !ok {
 481                                         if mask == nil {
 482                                                 outcol++
 483                                         }
 484                                         // Excluded by specified
 485                                         // regions, or reference does
 486                                         // not use any variant of this
 487                                         // tile. (TODO: log this?
 488                                         // mention it in annotations?)
 489                                         continue
 490                                 }
 491                                 remap := variantRemap[tag-tagstart]
 492                                 maxv := tileVariantID(0)
 493                                 for _, v := range remap {
 494                                         if maxv < v {
 495                                                 maxv = v
 496                                         }
 497                                 }
 498                                 if *onehotChunked {
 499                                         onehot, xrefs := cmd.tv2homhet(cgs, maxv, remap, tag, tagstart)
 500                                         onehotChunk = append(onehotChunk, onehot...)
 501                                         onehotXrefs = append(onehotXrefs, xrefs...)
 502                                 }
 503                                 fmt.Fprintf(annow, "%d,%d,%d,=,%s,%d,,,\n", tag, outcol, rt.variant, rt.seqname, rt.pos)
 504                                 variants := seq[tag]
 505                                 reftilestr := strings.ToUpper(string(rt.tiledata))
 506
 507                                 done := make([]bool, maxv+1)
 508                                 variantDiffs := make([][]hgvs.Variant, maxv+1)
 509                                 for v, tv := range variants {
 510                                         v := remap[v]
 511                                         if v == rt.variant || done[v] {
 512                                                 continue
 513                                         } else {
 514                                                 done[v] = true
 515                                         }
 516                                         if len(tv.Sequence) < taglen || !bytes.HasSuffix(rt.tiledata, tv.Sequence[len(tv.Sequence)-taglen:]) {
 517                                                 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
 518                                                 continue
 519                                         }
 520                                         if lendiff := len(rt.tiledata) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
 521                                                 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
 522                                                 continue
 523                                         }
 524                                         diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
 525                                         for i := range diffs {
 526                                                 diffs[i].Position += rt.pos
 527                                         }
 528                                         for _, diff := range diffs {
 529                                                 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)
 530                                         }
 531                                         if *hgvsChunked {
 532                                                 variantDiffs[v] = diffs
 533                                         }
 534                                 }
 535                                 if *hgvsChunked {
 536                                         // We can now determine, for each HGVS
 537                                         // variant (diff) in this reftile
 538                                         // region, whether a given genome
 539                                         // phase/allele (1) has the variant, (0) has
 540                                         // =ref or a different variant in that
 541                                         // position, or (-1) is lacking
 542                                         // coverage / couldn't be diffed.
 543                                         hgvsCol := hgvsColSet{}
 544                                         for _, diffs := range variantDiffs {
 545                                                 for _, diff := range diffs {
 546                                                         if _, ok := hgvsCol[diff]; ok {
 547                                                                 continue
 548                                                         }
 549                                                         hgvsCol[diff] = [2][]int8{
 550                                                                 make([]int8, len(cmd.cgnames)),
 551                                                                 make([]int8, len(cmd.cgnames)),
 552                                                         }
 553                                                 }
 554                                         }
 555                                         for row, name := range cmd.cgnames {
 556                                                 variants := cgs[name].Variants[(tag-tagstart)*2:]
 557                                                 for ph := 0; ph < 2; ph++ {
 558                                                         v := variants[ph]
 559                                                         if int(v) >= len(remap) {
 560                                                                 v = 0
 561                                                         } else {
 562                                                                 v = remap[v]
 563                                                         }
 564                                                         if v == rt.variant {
 565                                                                 // hgvsCol[*][ph][row] is already 0
 566                                                         } else if len(variantDiffs[v]) == 0 {
 567                                                                 // lacking coverage / couldn't be diffed
 568                                                                 for _, col := range hgvsCol {
 569                                                                         col[ph][row] = -1
 570                                                                 }
 571                                                         } else {
 572                                                                 for _, diff := range variantDiffs[v] {
 573                                                                         hgvsCol[diff][ph][row] = 1
 574                                                                 }
 575                                                         }
 576                                                 }
 577                                         }
 578                                         for diff, colpair := range hgvsCol {
 579                                                 allele2homhet(colpair)
 580                                                 if !cmd.filterHGVScolpair(colpair) {
 581                                                         delete(hgvsCol, diff)
 582                                                 }
 583                                         }
 584                                         if len(hgvsCol) > 0 {
 585                                                 encodeHGVSTodo[rt.seqname] <- hgvsCol
 586                                         }
 587                                 }
 588                                 outcol++
 589                         }
 590                         err = annow.Flush()
 591                         if err != nil {
 592                                 return err
 593                         }
 594                         err = annof.Close()
 595                         if err != nil {
 596                                 return err
 597                         }
 598
 599                         if *onehotChunked {
 600                                 // transpose onehotChunk[col][row] to numpy[row*ncols+col]
 601                                 rows := len(cmd.cgnames)
 602                                 cols := len(onehotChunk)
 603                                 log.Infof("%04d: preparing onehot numpy (rows=%d, cols=%d, mem=%d)", infileIdx, rows, cols, rows*cols)
 604                                 throttleNumpyMem.Acquire()
 605                                 out := make([]int8, rows*cols)
 606                                 for row := range cmd.cgnames {
 607                                         out := out[row*cols:]
 608                                         for colnum, values := range onehotChunk {
 609                                                 out[colnum] = values[row]
 610                                         }
 611                                 }
 612                                 seq = nil
 613                                 cgs = nil
 614                                 debug.FreeOSMemory()
 615                                 throttleNumpyMem.Release()
 616
 617                                 fnm := fmt.Sprintf("%s/onehot.%04d.npy", *outputDir, infileIdx)
 618                                 err = writeNumpyInt8(fnm, out, rows, cols)
 619                                 if err != nil {
 620                                         return err
 621                                 }
 622
 623                                 fnm = fmt.Sprintf("%s/onehot-columns.%04d.npy", *outputDir, infileIdx)
 624                                 xcols := len(onehotXrefs)
 625                                 xdata := make([]int32, 4*xcols)
 626                                 for i, xref := range onehotXrefs {
 627                                         xdata[i] = int32(xref.tag)
 628                                         xdata[xcols+i] = int32(xref.variant)
 629                                         if xref.het {
 630                                                 xdata[xcols*2+i] = 1
 631                                         }
 632                                         xdata[xcols*3+i] = int32(xref.pvalue * 1000000)
 633                                 }
 634                                 err = writeNumpyInt32(fnm, xdata, 4, xcols)
 635                                 if err != nil {
 636                                         return err
 637                                 }
 638                         }
 639                         if !*onehotChunked || *mergeOutput || *hgvsSingle {
 640                                 log.Infof("%04d: preparing numpy", infileIdx)
 641                                 throttleNumpyMem.Acquire()
 642                                 rows := len(cmd.cgnames)
 643                                 cols := 2 * outcol
 644                                 out := make([]int16, rows*cols)
 645                                 for row, name := range cmd.cgnames {
 646                                         out := out[row*cols:]
 647                                         outcol := 0
 648                                         for col, v := range cgs[name].Variants {
 649                                                 tag := tagstart + tagID(col/2)
 650                                                 if mask != nil && reftile[tag] == nil {
 651                                                         continue
 652                                                 }
 653                                                 if variants, ok := seq[tag]; ok && len(variants) > int(v) && len(variants[v].Sequence) > 0 {
 654                                                         out[outcol] = int16(variantRemap[tag-tagstart][v])
 655                                                 } else {
 656                                                         out[outcol] = -1
 657                                                 }
 658                                                 outcol++
 659                                         }
 660                                 }
 661                                 seq = nil
 662                                 cgs = nil
 663                                 debug.FreeOSMemory()
 664                                 throttleNumpyMem.Release()
 665                                 if *mergeOutput || *hgvsSingle {
 666                                         log.Infof("%04d: matrix fragment %d rows x %d cols", infileIdx, rows, cols)
 667                                         toMerge[infileIdx] = out
 668                                 }
 669                                 if !*mergeOutput && !*onehotChunked {
 670                                         fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
 671                                         err = writeNumpyInt16(fnm, out, rows, cols)
 672                                         if err != nil {
 673                                                 return err
 674                                         }
 675                                 }
 676                         }
 677                         debug.FreeOSMemory()
 678                         log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
 679                         return nil
 680                 })
 681         }
 682         if err = throttleMem.Wait(); err != nil {
 683                 return 1
 684         }
 685
 686         if *hgvsChunked {
 687                 log.Info("flushing hgvsCols temp files")
 688                 for seqname := range refseq {
 689                         close(encodeHGVSTodo[seqname])
 690                 }
 691                 err = encodeHGVS.Wait()
 692                 if err != nil {
 693                         return 1
 694                 }
 695                 for seqname := range refseq {
 696                         log.Infof("%s: reading hgvsCols from temp file", seqname)
 697                         f := tmpHGVSCols[seqname]
 698                         _, err = f.Seek(0, io.SeekStart)
 699                         if err != nil {
 700                                 return 1
 701                         }
 702                         var hgvsCols hgvsColSet
 703                         dec := gob.NewDecoder(bufio.NewReaderSize(f, 1<<24))
 704                         for err == nil {
 705                                 err = dec.Decode(&hgvsCols)
 706                         }
 707                         if err != io.EOF {
 708                                 return 1
 709                         }
 710                         log.Infof("%s: sorting %d hgvs variants", seqname, len(hgvsCols))
 711                         variants := make([]hgvs.Variant, 0, len(hgvsCols))
 712                         for v := range hgvsCols {
 713                                 variants = append(variants, v)
 714                         }
 715                         sort.Slice(variants, func(i, j int) bool {
 716                                 vi, vj := &variants[i], &variants[j]
 717                                 if vi.Position != vj.Position {
 718                                         return vi.Position < vj.Position
 719                                 } else if vi.Ref != vj.Ref {
 720                                         return vi.Ref < vj.Ref
 721                                 } else {
 722                                         return vi.New < vj.New
 723                                 }
 724                         })
 725                         rows := len(cmd.cgnames)
 726                         cols := len(variants) * 2
 727                         log.Infof("%s: building hgvs matrix (rows=%d, cols=%d, mem=%d)", seqname, rows, cols, rows*cols)
 728                         out := make([]int8, rows*cols)
 729                         for varIdx, variant := range variants {
 730                                 hgvsCols := hgvsCols[variant]
 731                                 for row := range cmd.cgnames {
 732                                         for ph := 0; ph < 2; ph++ {
 733                                                 out[row*cols+varIdx+ph] = hgvsCols[ph][row]
 734                                         }
 735                                 }
 736                         }
 737                         err = writeNumpyInt8(fmt.Sprintf("%s/hgvs.%s.npy", *outputDir, seqname), out, rows, cols)
 738                         if err != nil {
 739                                 return 1
 740                         }
 741                         out = nil
 742
 743                         fnm := fmt.Sprintf("%s/hgvs.%s.annotations.csv", *outputDir, seqname)
 744                         log.Infof("%s: writing hgvs column labels to %s", seqname, fnm)
 745                         var hgvsLabels bytes.Buffer
 746                         for varIdx, variant := range variants {
 747                                 fmt.Fprintf(&hgvsLabels, "%d,%s:g.%s\n", varIdx, seqname, variant.String())
 748                         }
 749                         err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0666)
 750                         if err != nil {
 751                                 return 1
 752                         }
 753                 }
 754         }
 755
 756         if *mergeOutput || *hgvsSingle {
 757                 var annow *bufio.Writer
 758                 var annof *os.File
 759                 if *mergeOutput {
 760                         annoFilename := fmt.Sprintf("%s/matrix.annotations.csv", *outputDir)
 761                         annof, err = os.Create(annoFilename)
 762                         if err != nil {
 763                                 return 1
 764                         }
 765                         annow = bufio.NewWriterSize(annof, 1<<20)
 766                 }
 767
 768                 rows := len(cmd.cgnames)
 769                 cols := 0
 770                 for _, chunk := range toMerge {
 771                         cols += len(chunk) / rows
 772                 }
 773                 log.Infof("merging output matrix (rows=%d, cols=%d, mem=%d) and annotations", rows, cols, rows*cols*2)
 774                 var out []int16
 775                 if *mergeOutput {
 776                         out = make([]int16, rows*cols)
 777                 }
 778                 hgvsCols := map[string][2][]int16{} // hgvs -> [[g0,g1,g2,...], [g0,g1,g2,...]] (slice of genomes for each phase)
 779                 startcol := 0
 780                 for outIdx, chunk := range toMerge {
 781                         chunkcols := len(chunk) / rows
 782                         if *mergeOutput {
 783                                 for row := 0; row < rows; row++ {
 784                                         copy(out[row*cols+startcol:], chunk[row*chunkcols:(row+1)*chunkcols])
 785                                 }
 786                         }
 787                         toMerge[outIdx] = nil
 788
 789                         annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, outIdx)
 790                         log.Infof("reading %s", annotationsFilename)
 791                         buf, err := os.ReadFile(annotationsFilename)
 792                         if err != nil {
 793                                 return 1
 794                         }
 795                         if *mergeOutput {
 796                                 err = os.Remove(annotationsFilename)
 797                                 if err != nil {
 798                                         return 1
 799                                 }
 800                         }
 801                         for _, line := range bytes.Split(buf, []byte{'\n'}) {
 802                                 if len(line) == 0 {
 803                                         continue
 804                                 }
 805                                 fields := bytes.SplitN(line, []byte{','}, 9)
 806                                 tag, _ := strconv.Atoi(string(fields[0]))
 807                                 incol, _ := strconv.Atoi(string(fields[1]))
 808                                 tileVariant, _ := strconv.Atoi(string(fields[2]))
 809                                 hgvsID := string(fields[3])
 810                                 seqname := string(fields[4])
 811                                 pos, _ := strconv.Atoi(string(fields[5]))
 812                                 refseq := fields[6]
 813                                 if hgvsID == "" {
 814                                         // Null entry for un-diffable
 815                                         // tile variant
 816                                         continue
 817                                 }
 818                                 if hgvsID == "=" {
 819                                         // Null entry for ref tile
 820                                         continue
 821                                 }
 822                                 if mask != nil && !mask.Check(strings.TrimPrefix(seqname, "chr"), pos, pos+len(refseq)) {
 823                                         // The tile intersects one of
 824                                         // the selected regions, but
 825                                         // this particular HGVS
 826                                         // variant does not.
 827                                         continue
 828                                 }
 829                                 hgvsColPair := hgvsCols[hgvsID]
 830                                 if hgvsColPair[0] == nil {
 831                                         // values in new columns start
 832                                         // out as -1 ("no data yet")
 833                                         // or 0 ("=ref") here, may
 834                                         // change to 1 ("hgvs variant
 835                                         // present") below, either on
 836                                         // this line or a future line.
 837                                         hgvsColPair = [2][]int16{make([]int16, len(cmd.cgnames)), make([]int16, len(cmd.cgnames))}
 838                                         rt, ok := reftile[tagID(tag)]
 839                                         if !ok {
 840                                                 err = fmt.Errorf("bug: seeing annotations for tag %d, but it has no reftile entry", tag)
 841                                                 return 1
 842                                         }
 843                                         for ph := 0; ph < 2; ph++ {
 844                                                 for row := 0; row < rows; row++ {
 845                                                         v := chunk[row*chunkcols+incol*2+ph]
 846                                                         if tileVariantID(v) == rt.variant {
 847                                                                 hgvsColPair[ph][row] = 0
 848                                                         } else {
 849                                                                 hgvsColPair[ph][row] = -1
 850                                                         }
 851                                                 }
 852                                         }
 853                                         hgvsCols[hgvsID] = hgvsColPair
 854                                         if annow != nil {
 855                                                 hgvsref := hgvs.Variant{
 856                                                         Position: pos,
 857                                                         Ref:      string(refseq),
 858                                                         New:      string(refseq),
 859                                                 }
 860                                                 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])
 861                                         }
 862                                 }
 863                                 if annow != nil {
 864                                         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])
 865                                 }
 866                                 for ph := 0; ph < 2; ph++ {
 867                                         for row := 0; row < rows; row++ {
 868                                                 v := chunk[row*chunkcols+incol*2+ph]
 869                                                 if int(v) == tileVariant {
 870                                                         hgvsColPair[ph][row] = 1
 871                                                 }
 872                                         }
 873                                 }
 874                         }
 875
 876                         startcol += chunkcols
 877                 }
 878                 if *mergeOutput {
 879                         err = annow.Flush()
 880                         if err != nil {
 881                                 return 1
 882                         }
 883                         err = annof.Close()
 884                         if err != nil {
 885                                 return 1
 886                         }
 887                         err = writeNumpyInt16(fmt.Sprintf("%s/matrix.npy", *outputDir), out, rows, cols)
 888                         if err != nil {
 889                                 return 1
 890                         }
 891                 }
 892                 out = nil
 893
 894                 if *hgvsSingle {
 895                         cols = len(hgvsCols) * 2
 896                         log.Printf("building hgvs-based matrix: %d rows x %d cols", rows, cols)
 897                         out = make([]int16, rows*cols)
 898                         hgvsIDs := make([]string, 0, cols/2)
 899                         for hgvsID := range hgvsCols {
 900                                 hgvsIDs = append(hgvsIDs, hgvsID)
 901                         }
 902                         sort.Strings(hgvsIDs)
 903                         var hgvsLabels bytes.Buffer
 904                         for idx, hgvsID := range hgvsIDs {
 905                                 fmt.Fprintf(&hgvsLabels, "%d,%s\n", idx, hgvsID)
 906                                 for ph := 0; ph < 2; ph++ {
 907                                         hgvscol := hgvsCols[hgvsID][ph]
 908                                         for row, val := range hgvscol {
 909                                                 out[row*cols+idx*2+ph] = val
 910                                         }
 911                                 }
 912                         }
 913                         err = writeNumpyInt16(fmt.Sprintf("%s/hgvs.npy", *outputDir), out, rows, cols)
 914                         if err != nil {
 915                                 return 1
 916                         }
 917
 918                         fnm := fmt.Sprintf("%s/hgvs.annotations.csv", *outputDir)
 919                         log.Printf("writing hgvs labels: %s", fnm)
 920                         err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0777)
 921                         if err != nil {
 922                                 return 1
 923                         }
 924                 }
 925         }
 926         return 0
 927 }
 928
 929 func (cmd *sliceNumpy) filterHGVScolpair(colpair [2][]int8) bool {
 930         if cmd.chi2PValue >= 1 {
 931                 return true
 932         }
 933         col0 := make([]bool, 0, len(cmd.chi2Cases))
 934         col1 := make([]bool, 0, len(cmd.chi2Cases))
 935         cases := make([]bool, 0, len(cmd.chi2Cases))
 936         for i, c := range cmd.chi2Cases {
 937                 if colpair[0][i] < 0 {
 938                         continue
 939                 }
 940                 col0 = append(col0, colpair[0][i] != 0)
 941                 col1 = append(col1, colpair[1][i] != 0)
 942                 cases = append(cases, c)
 943         }
 944         return len(cases) >= cmd.minCoverage &&
 945                 (pvalue(cases, col0) <= cmd.chi2PValue || pvalue(cases, col1) <= cmd.chi2PValue)
 946 }
 947
 948 func writeNumpyInt32(fnm string, out []int32, rows, cols int) error {
 949         output, err := os.Create(fnm)
 950         if err != nil {
 951                 return err
 952         }
 953         defer output.Close()
 954         bufw := bufio.NewWriterSize(output, 1<<26)
 955         npw, err := gonpy.NewWriter(nopCloser{bufw})
 956         if err != nil {
 957                 return err
 958         }
 959         log.WithFields(log.Fields{
 960                 "filename": fnm,
 961                 "rows":     rows,
 962                 "cols":     cols,
 963                 "bytes":    rows * cols * 4,
 964         }).Infof("writing numpy: %s", fnm)
 965         npw.Shape = []int{rows, cols}
 966         npw.WriteInt32(out)
 967         err = bufw.Flush()
 968         if err != nil {
 969                 return err
 970         }
 971         return output.Close()
 972 }
 973
 974 func writeNumpyInt16(fnm string, out []int16, rows, cols int) error {
 975         output, err := os.Create(fnm)
 976         if err != nil {
 977                 return err
 978         }
 979         defer output.Close()
 980         bufw := bufio.NewWriterSize(output, 1<<26)
 981         npw, err := gonpy.NewWriter(nopCloser{bufw})
 982         if err != nil {
 983                 return err
 984         }
 985         log.WithFields(log.Fields{
 986                 "filename": fnm,
 987                 "rows":     rows,
 988                 "cols":     cols,
 989                 "bytes":    rows * cols * 2,
 990         }).Infof("writing numpy: %s", fnm)
 991         npw.Shape = []int{rows, cols}
 992         npw.WriteInt16(out)
 993         err = bufw.Flush()
 994         if err != nil {
 995                 return err
 996         }
 997         return output.Close()
 998 }
 999
1000 func writeNumpyInt8(fnm string, out []int8, rows, cols int) error {
1001         output, err := os.Create(fnm)
1002         if err != nil {
1003                 return err
1004         }
1005         defer output.Close()
1006         bufw := bufio.NewWriterSize(output, 1<<26)
1007         npw, err := gonpy.NewWriter(nopCloser{bufw})
1008         if err != nil {
1009                 return err
1010         }
1011         log.WithFields(log.Fields{
1012                 "filename": fnm,
1013                 "rows":     rows,
1014                 "cols":     cols,
1015                 "bytes":    rows * cols,
1016         }).Infof("writing numpy: %s", fnm)
1017         npw.Shape = []int{rows, cols}
1018         npw.WriteInt8(out)
1019         err = bufw.Flush()
1020         if err != nil {
1021                 return err
1022         }
1023         return output.Close()
1024 }
1025
1026 func allele2homhet(colpair [2][]int8) {
1027         a, b := colpair[0], colpair[1]
1028         for i, av := range a {
1029                 bv := b[i]
1030                 if av < 0 || bv < 0 {
1031                         // no-call
1032                         a[i], b[i] = -1, -1
1033                 } else if av > 0 && bv > 0 {
1034                         // hom
1035                         a[i], b[i] = 1, 0
1036                 } else if av > 0 || bv > 0 {
1037                         // het
1038                         a[i], b[i] = 0, 1
1039                 } else {
1040                         // ref (or a different variant in same position)
1041                         // (this is a no-op) a[i], b[i] = 0, 0
1042                 }
1043         }
1044 }
1045
1046 type onehotXref struct {
1047         tag     tagID
1048         variant tileVariantID
1049         het     bool
1050         pvalue  float64
1051 }
1052
1053 // Build onehot matrix (m[variant*2+isHet][genome] == 0 or 1) for all
1054 // variants of a single tile/tag#.
1055 //
1056 // Return nil if no tile variant passes Χ² filter.
1057 func (cmd *sliceNumpy) tv2homhet(cgs map[string]CompactGenome, maxv tileVariantID, remap []tileVariantID, tag, chunkstarttag tagID) ([][]int8, []onehotXref) {
1058         if maxv < 2 {
1059                 // everyone has the most common variant
1060                 return nil, nil
1061         }
1062         tagoffset := tag - chunkstarttag
1063         coverage := 0
1064         for _, cg := range cgs {
1065                 if cg.Variants[tagoffset*2] > 0 && cg.Variants[tagoffset*2+1] > 0 {
1066                         coverage++
1067                 }
1068         }
1069         if coverage < cmd.minCoverage {
1070                 return nil, nil
1071         }
1072         obs := make([][]bool, (maxv+1)*2) // 2 slices (hom + het) for each variant#
1073         for i := range obs {
1074                 obs[i] = make([]bool, len(cmd.cgnames))
1075         }
1076         for cgid, name := range cmd.cgnames {
1077                 cgvars := cgs[name].Variants
1078                 for v := tileVariantID(2); v <= maxv; v++ {
1079                         if remap[cgvars[tagoffset*2]] == v && remap[cgvars[tagoffset*2+1]] == v {
1080                                 obs[v*2][cgid] = true
1081                         } else if remap[cgvars[tagoffset*2]] == v || remap[cgvars[tagoffset*2+1]] == v {
1082                                 obs[v*2+1][cgid] = true
1083                         }
1084                 }
1085         }
1086         var onehot [][]int8
1087         var xref []onehotXref
1088         for homcol := 4; homcol < len(obs); homcol += 2 {
1089                 p := [2]float64{
1090                         pvalue(cmd.chi2Cases, obs[homcol]),
1091                         pvalue(cmd.chi2Cases, obs[homcol+1]),
1092                 }
1093                 if cmd.chi2PValue < 1 && !(p[0] < cmd.chi2PValue || p[1] < cmd.chi2PValue) {
1094                         continue
1095                 }
1096                 for het := 0; het < 2; het++ {
1097                         onehot = append(onehot, bool2int8(obs[homcol+het]))
1098                         xref = append(xref, onehotXref{
1099                                 tag:     tag,
1100                                 variant: tileVariantID(homcol / 2),
1101                                 het:     het == 1,
1102                                 pvalue:  p[het],
1103                         })
1104                 }
1105         }
1106         return onehot, xref
1107 }
1108
1109 func bool2int8(in []bool) []int8 {
1110         out := make([]int8, len(in))
1111         for i, v := range in {
1112                 if v {
1113                         out[i] = 1
1114                 }
1115         }
1116         return out
1117 }