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         chi2CaseControlColumn string
  38         chi2CaseControlFile   string
  39         chi2Cases             []bool
  40         chi2PValue            float64
  41         minCoverage           int
  42         cgnames               []string
  43 }
  44
  45 func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  46         var err error
  47         defer func() {
  48                 if err != nil {
  49                         fmt.Fprintf(stderr, "%s\n", err)
  50                 }
  51         }()
  52         flags := flag.NewFlagSet("", flag.ContinueOnError)
  53         flags.SetOutput(stderr)
  54         pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
  55         runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
  56         projectUUID := flags.String("project", "", "project `UUID` for output data")
  57         priority := flags.Int("priority", 500, "container request priority")
  58         inputDir := flags.String("input-dir", "./in", "input `directory`")
  59         outputDir := flags.String("output-dir", "./out", "output `directory`")
  60         ref := flags.String("ref", "", "reference name (if blank, choose last one that appears in input)")
  61         regionsFilename := flags.String("regions", "", "only output columns/annotations that intersect regions in specified bed `file`")
  62         expandRegions := flags.Int("expand-regions", 0, "expand specified regions by `N` base pairs on each side`")
  63         mergeOutput := flags.Bool("merge-output", false, "merge output into one matrix.npy and one matrix.annotations.csv")
  64         hgvsSingle := flags.Bool("single-hgvs-matrix", false, "also generate hgvs-based matrix")
  65         hgvsChunked := flags.Bool("chunked-hgvs-matrix", false, "also generate hgvs-based matrix per chromosome")
  66         onehotChunked := flags.Bool("chunked-onehot", false, "generate one-hot tile-based matrix")
  67         flags.IntVar(&cmd.threads, "threads", 16, "number of memory-hungry assembly threads")
  68         flags.StringVar(&cmd.chi2CaseControlFile, "chi2-case-control-file", "", "tsv file or directory indicating cases and controls for Χ² test (if directory, all .tsv files will be read)")
  69         flags.StringVar(&cmd.chi2CaseControlColumn, "chi2-case-control-column", "", "name of case/control column in case-control files for Χ² test (value must be 0 for control, 1 for case)")
  70         flags.Float64Var(&cmd.chi2PValue, "chi2-p-value", 1, "do Χ² test and omit columns with p-value above this threshold")
  71         cmd.filter.Flags(flags)
  72         err = flags.Parse(args)
  73         if err == flag.ErrHelp {
  74                 err = nil
  75                 return 0
  76         } else if err != nil {
  77                 return 2
  78         }
  79
  80         if *pprof != "" {
  81                 go func() {
  82                         log.Println(http.ListenAndServe(*pprof, nil))
  83                 }()
  84         }
  85
  86         if cmd.chi2PValue != 1 && (cmd.chi2CaseControlFile == "" || cmd.chi2CaseControlColumn == "") {
  87                 log.Errorf("cannot use provided -chi2-p-value=%f because -chi2-case-control-file= or -chi2-case-control-column= value is empty", cmd.chi2PValue)
  88                 return 2
  89         }
  90
  91         if !*runlocal {
  92                 runner := arvadosContainerRunner{
  93                         Name:        "lightning slice-numpy",
  94                         Client:      arvados.NewClientFromEnv(),
  95                         ProjectUUID: *projectUUID,
  96                         RAM:         750000000000,
  97                         VCPUs:       96,
  98                         Priority:    *priority,
  99                         KeepCache:   2,
 100                         APIAccess:   true,
 101                 }
 102                 err = runner.TranslatePaths(inputDir, regionsFilename, &cmd.chi2CaseControlFile)
 103                 if err != nil {
 104                         return 1
 105                 }
 106                 runner.Args = []string{"slice-numpy", "-local=true",
 107                         "-pprof=:6060",
 108                         "-input-dir=" + *inputDir,
 109                         "-output-dir=/mnt/output",
 110                         "-threads=" + fmt.Sprintf("%d", cmd.threads),
 111                         "-regions=" + *regionsFilename,
 112                         "-expand-regions=" + fmt.Sprintf("%d", *expandRegions),
 113                         "-merge-output=" + fmt.Sprintf("%v", *mergeOutput),
 114                         "-single-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsSingle),
 115                         "-chunked-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsChunked),
 116                         "-chunked-onehot=" + fmt.Sprintf("%v", *onehotChunked),
 117                         "-chi2-case-control-file=" + cmd.chi2CaseControlFile,
 118                         "-chi2-case-control-column=" + cmd.chi2CaseControlColumn,
 119                         "-chi2-p-value=" + fmt.Sprintf("%f", cmd.chi2PValue),
 120                 }
 121                 runner.Args = append(runner.Args, cmd.filter.Args()...)
 122                 var output string
 123                 output, err = runner.Run()
 124                 if err != nil {
 125                         return 1
 126                 }
 127                 fmt.Fprintln(stdout, output)
 128                 return 0
 129         }
 130
 131         infiles, err := allFiles(*inputDir, matchGobFile)
 132         if err != nil {
 133                 return 1
 134         }
 135         if len(infiles) == 0 {
 136                 err = fmt.Errorf("no input files found in %s", *inputDir)
 137                 return 1
 138         }
 139         sort.Strings(infiles)
 140
 141         var refseq map[string][]tileLibRef
 142         var reftiledata = make(map[tileLibRef][]byte, 11000000)
 143         in0, err := open(infiles[0])
 144         if err != nil {
 145                 return 1
 146         }
 147
 148         matchGenome, err := regexp.Compile(cmd.filter.MatchGenome)
 149         if err != nil {
 150                 err = fmt.Errorf("-match-genome: invalid regexp: %q", cmd.filter.MatchGenome)
 151                 return 1
 152         }
 153
 154         cmd.cgnames = nil
 155         taglen := -1
 156         DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
 157                 if len(ent.TagSet) > 0 {
 158                         taglen = len(ent.TagSet[0])
 159                 }
 160                 for _, cseq := range ent.CompactSequences {
 161                         if cseq.Name == *ref || *ref == "" {
 162                                 refseq = cseq.TileSequences
 163                         }
 164                 }
 165                 for _, cg := range ent.CompactGenomes {
 166                         if matchGenome.MatchString(cg.Name) {
 167                                 cmd.cgnames = append(cmd.cgnames, cg.Name)
 168                         }
 169                 }
 170                 for _, tv := range ent.TileVariants {
 171                         if tv.Ref {
 172                                 reftiledata[tileLibRef{tv.Tag, tv.Variant}] = tv.Sequence
 173                         }
 174                 }
 175                 return nil
 176         })
 177         if err != nil {
 178                 return 1
 179         }
 180         in0.Close()
 181         if refseq == nil {
 182                 err = fmt.Errorf("%s: reference sequence not found", infiles[0])
 183                 return 1
 184         }
 185         if taglen < 0 {
 186                 err = fmt.Errorf("tagset not found")
 187                 return 1
 188         }
 189         if len(cmd.cgnames) == 0 {
 190                 err = fmt.Errorf("no genomes found matching regexp %q", cmd.filter.MatchGenome)
 191                 return 1
 192         }
 193         sort.Strings(cmd.cgnames)
 194         err = cmd.useCaseControlFiles()
 195         if err != nil {
 196                 return 1
 197         }
 198         cmd.minCoverage = int(math.Ceil(cmd.filter.MinCoverage * float64(len(cmd.cgnames))))
 199
 200         {
 201                 labelsFilename := *outputDir + "/samples.csv"
 202                 log.Infof("writing labels to %s", labelsFilename)
 203                 var f *os.File
 204                 f, err = os.Create(labelsFilename)
 205                 if err != nil {
 206                         return 1
 207                 }
 208                 defer f.Close()
 209                 for i, name := range cmd.cgnames {
 210                         cc := 0
 211                         if cmd.chi2Cases != nil && cmd.chi2Cases[i] {
 212                                 cc = 1
 213                         }
 214                         _, err = fmt.Fprintf(f, "%d,%q,%d\n", i, trimFilenameForLabel(name), cc)
 215                         if err != nil {
 216                                 err = fmt.Errorf("write %s: %w", labelsFilename, err)
 217                                 return 1
 218                         }
 219                 }
 220                 err = f.Close()
 221                 if err != nil {
 222                         err = fmt.Errorf("close %s: %w", labelsFilename, err)
 223                         return 1
 224                 }
 225         }
 226
 227         log.Info("indexing reference tiles")
 228         type reftileinfo struct {
 229                 variant  tileVariantID
 230                 seqname  string // chr1
 231                 pos      int    // distance from start of chromosome to starttag
 232                 tiledata []byte // acgtggcaa...
 233         }
 234         isdup := map[tagID]bool{}
 235         reftile := map[tagID]*reftileinfo{}
 236         for seqname, cseq := range refseq {
 237                 pos := 0
 238                 for _, libref := range cseq {
 239                         tiledata := reftiledata[libref]
 240                         if len(tiledata) == 0 {
 241                                 err = fmt.Errorf("missing tiledata for tag %d variant %d in %s in ref", libref.Tag, libref.Variant, seqname)
 242                                 return 1
 243                         }
 244                         if isdup[libref.Tag] {
 245                                 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
 246                         } else if reftile[libref.Tag] != nil {
 247                                 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)
 248                                 delete(reftile, libref.Tag)
 249                                 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
 250                                 isdup[libref.Tag] = true
 251                         } else {
 252                                 reftile[libref.Tag] = &reftileinfo{
 253                                         seqname:  seqname,
 254                                         variant:  libref.Variant,
 255                                         tiledata: tiledata,
 256                                         pos:      pos,
 257                                 }
 258                         }
 259                         pos += len(tiledata) - taglen
 260                 }
 261                 log.Printf("... %s done, len %d", seqname, pos+taglen)
 262         }
 263
 264         var mask *mask
 265         if *regionsFilename != "" {
 266                 log.Printf("loading regions from %s", *regionsFilename)
 267                 mask, err = makeMask(*regionsFilename, *expandRegions)
 268                 if err != nil {
 269                         return 1
 270                 }
 271                 log.Printf("before applying mask, len(reftile) == %d", len(reftile))
 272                 log.Printf("deleting reftile entries for regions outside %d intervals", mask.Len())
 273                 for tag, rt := range reftile {
 274                         if !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(rt.tiledata)) {
 275                                 delete(reftile, tag)
 276                         }
 277                 }
 278                 log.Printf("after applying mask, len(reftile) == %d", len(reftile))
 279         }
 280
 281         type hgvsColSet map[hgvs.Variant][2][]int8
 282         encodeHGVS := throttle{Max: len(refseq)}
 283         encodeHGVSTodo := map[string]chan hgvsColSet{}
 284         tmpHGVSCols := map[string]*os.File{}
 285         if *hgvsChunked {
 286                 for seqname := range refseq {
 287                         var f *os.File
 288                         f, err = os.Create(*outputDir + "/tmp." + seqname + ".gob")
 289                         if err != nil {
 290                                 return 1
 291                         }
 292                         defer os.Remove(f.Name())
 293                         bufw := bufio.NewWriterSize(f, 1<<24)
 294                         enc := gob.NewEncoder(bufw)
 295                         tmpHGVSCols[seqname] = f
 296                         todo := make(chan hgvsColSet, 128)
 297                         encodeHGVSTodo[seqname] = todo
 298                         encodeHGVS.Go(func() error {
 299                                 for colset := range todo {
 300                                         err := enc.Encode(colset)
 301                                         if err != nil {
 302                                                 encodeHGVS.Report(err)
 303                                                 for range todo {
 304                                                 }
 305                                                 return err
 306                                         }
 307                                 }
 308                                 return bufw.Flush()
 309                         })
 310                 }
 311         }
 312
 313         var toMerge [][]int16
 314         if *mergeOutput || *hgvsSingle {
 315                 toMerge = make([][]int16, len(infiles))
 316         }
 317
 318         throttleMem := throttle{Max: cmd.threads} // TODO: estimate using mem and data size
 319         throttleNumpyMem := throttle{Max: cmd.threads/2 + 1}
 320         log.Info("generating annotations and numpy matrix for each slice")
 321         var done int64
 322         for infileIdx, infile := range infiles {
 323                 infileIdx, infile := infileIdx, infile
 324                 throttleMem.Go(func() error {
 325                         seq := make(map[tagID][]TileVariant, 50000)
 326                         cgs := make(map[string]CompactGenome, len(cmd.cgnames))
 327                         f, err := open(infile)
 328                         if err != nil {
 329                                 return err
 330                         }
 331                         defer f.Close()
 332                         log.Infof("%04d: reading %s", infileIdx, infile)
 333                         err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
 334                                 for _, tv := range ent.TileVariants {
 335                                         if tv.Ref {
 336                                                 continue
 337                                         }
 338                                         if mask != nil && reftile[tv.Tag] == nil {
 339                                                 // Don't waste
 340                                                 // time/memory on
 341                                                 // masked-out tiles.
 342                                                 continue
 343                                         }
 344                                         variants := seq[tv.Tag]
 345                                         if len(variants) == 0 {
 346                                                 variants = make([]TileVariant, 100)
 347                                         }
 348                                         for len(variants) <= int(tv.Variant) {
 349                                                 variants = append(variants, TileVariant{})
 350                                         }
 351                                         variants[int(tv.Variant)] = tv
 352                                         seq[tv.Tag] = variants
 353                                 }
 354                                 for _, cg := range ent.CompactGenomes {
 355                                         if !matchGenome.MatchString(cg.Name) {
 356                                                 continue
 357                                         }
 358                                         // pad to full slice size
 359                                         // to avoid out-of-bounds
 360                                         // checks later
 361                                         if sliceSize := 2 * int(cg.EndTag-cg.StartTag); len(cg.Variants) < sliceSize {
 362                                                 cg.Variants = append(cg.Variants, make([]tileVariantID, sliceSize-len(cg.Variants))...)
 363                                         }
 364                                         cgs[cg.Name] = cg
 365                                 }
 366                                 return nil
 367                         })
 368                         if err != nil {
 369                                 return err
 370                         }
 371                         tagstart := cgs[cmd.cgnames[0]].StartTag
 372                         tagend := cgs[cmd.cgnames[0]].EndTag
 373
 374                         // TODO: filters
 375
 376                         log.Infof("%04d: renumber/dedup variants for tags %d-%d", infileIdx, tagstart, tagend)
 377                         variantRemap := make([][]tileVariantID, tagend-tagstart)
 378                         throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
 379                         for tag, variants := range seq {
 380                                 tag, variants := tag, variants
 381                                 throttleCPU.Acquire()
 382                                 go func() {
 383                                         defer throttleCPU.Release()
 384                                         count := make(map[[blake2b.Size256]byte]int, len(variants))
 385
 386                                         rt := reftile[tag]
 387                                         if rt != nil {
 388                                                 count[blake2b.Sum256(rt.tiledata)] = 0
 389                                         }
 390
 391                                         for _, cg := range cgs {
 392                                                 idx := int(tag-tagstart) * 2
 393                                                 for allele := 0; allele < 2; allele++ {
 394                                                         v := cg.Variants[idx+allele]
 395                                                         if v > 0 && len(variants[v].Sequence) > 0 {
 396                                                                 count[variants[v].Blake2b]++
 397                                                         }
 398                                                 }
 399                                         }
 400                                         // hash[i] will be the hash of
 401                                         // the variant(s) that should
 402                                         // be at rank i (0-based).
 403                                         hash := make([][blake2b.Size256]byte, 0, len(count))
 404                                         for b := range count {
 405                                                 hash = append(hash, b)
 406                                         }
 407                                         sort.Slice(hash, func(i, j int) bool {
 408                                                 bi, bj := &hash[i], &hash[j]
 409                                                 if ci, cj := count[*bi], count[*bj]; ci != cj {
 410                                                         return ci > cj
 411                                                 } else {
 412                                                         return bytes.Compare((*bi)[:], (*bj)[:]) < 0
 413                                                 }
 414                                         })
 415                                         // rank[b] will be the 1-based
 416                                         // new variant number for
 417                                         // variants whose hash is b.
 418                                         rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
 419                                         for i, h := range hash {
 420                                                 rank[h] = tileVariantID(i + 1)
 421                                         }
 422                                         // remap[v] will be the new
 423                                         // variant number for original
 424                                         // variant number v.
 425                                         remap := make([]tileVariantID, len(variants))
 426                                         for i, tv := range variants {
 427                                                 remap[i] = rank[tv.Blake2b]
 428                                         }
 429                                         variantRemap[tag-tagstart] = remap
 430                                         if rt != nil {
 431                                                 rt.variant = rank[blake2b.Sum256(rt.tiledata)]
 432                                         }
 433                                 }()
 434                         }
 435                         throttleCPU.Wait()
 436
 437                         var onehotChunk [][]int8
 438                         var onehotXrefs []onehotXref
 439
 440                         annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
 441                         log.Infof("%04d: writing %s", infileIdx, annotationsFilename)
 442                         annof, err := os.Create(annotationsFilename)
 443                         if err != nil {
 444                                 return err
 445                         }
 446                         annow := bufio.NewWriterSize(annof, 1<<20)
 447                         outcol := 0
 448                         for tag := tagstart; tag < tagend; tag++ {
 449                                 rt, ok := reftile[tag]
 450                                 if !ok {
 451                                         if mask == nil {
 452                                                 outcol++
 453                                         }
 454                                         // Excluded by specified
 455                                         // regions, or reference does
 456                                         // not use any variant of this
 457                                         // tile. (TODO: log this?
 458                                         // mention it in annotations?)
 459                                         continue
 460                                 }
 461                                 remap := variantRemap[tag-tagstart]
 462                                 maxv := tileVariantID(0)
 463                                 for _, v := range remap {
 464                                         if maxv < v {
 465                                                 maxv = v
 466                                         }
 467                                 }
 468                                 if *onehotChunked {
 469                                         onehot, xrefs := cmd.tv2homhet(cgs, maxv, remap, tag, tagstart)
 470                                         onehotChunk = append(onehotChunk, onehot...)
 471                                         onehotXrefs = append(onehotXrefs, xrefs...)
 472                                 }
 473                                 fmt.Fprintf(annow, "%d,%d,%d,=,%s,%d,,,\n", tag, outcol, rt.variant, rt.seqname, rt.pos)
 474                                 variants := seq[tag]
 475                                 reftilestr := strings.ToUpper(string(rt.tiledata))
 476
 477                                 done := make([]bool, maxv+1)
 478                                 variantDiffs := make([][]hgvs.Variant, maxv+1)
 479                                 for v, tv := range variants {
 480                                         v := remap[v]
 481                                         if v == rt.variant || done[v] {
 482                                                 continue
 483                                         } else {
 484                                                 done[v] = true
 485                                         }
 486                                         if len(tv.Sequence) < taglen || !bytes.HasSuffix(rt.tiledata, tv.Sequence[len(tv.Sequence)-taglen:]) {
 487                                                 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
 488                                                 continue
 489                                         }
 490                                         if lendiff := len(rt.tiledata) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
 491                                                 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
 492                                                 continue
 493                                         }
 494                                         diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
 495                                         for i := range diffs {
 496                                                 diffs[i].Position += rt.pos
 497                                         }
 498                                         for _, diff := range diffs {
 499                                                 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)
 500                                         }
 501                                         if *hgvsChunked {
 502                                                 variantDiffs[v] = diffs
 503                                         }
 504                                 }
 505                                 if *hgvsChunked {
 506                                         // We can now determine, for each HGVS
 507                                         // variant (diff) in this reftile
 508                                         // region, whether a given genome
 509                                         // phase/allele (1) has the variant, (0) has
 510                                         // =ref or a different variant in that
 511                                         // position, or (-1) is lacking
 512                                         // coverage / couldn't be diffed.
 513                                         hgvsCol := hgvsColSet{}
 514                                         for _, diffs := range variantDiffs {
 515                                                 for _, diff := range diffs {
 516                                                         if _, ok := hgvsCol[diff]; ok {
 517                                                                 continue
 518                                                         }
 519                                                         hgvsCol[diff] = [2][]int8{
 520                                                                 make([]int8, len(cmd.cgnames)),
 521                                                                 make([]int8, len(cmd.cgnames)),
 522                                                         }
 523                                                 }
 524                                         }
 525                                         for row, name := range cmd.cgnames {
 526                                                 variants := cgs[name].Variants[(tag-tagstart)*2:]
 527                                                 for ph := 0; ph < 2; ph++ {
 528                                                         v := variants[ph]
 529                                                         if int(v) >= len(remap) {
 530                                                                 v = 0
 531                                                         } else {
 532                                                                 v = remap[v]
 533                                                         }
 534                                                         if v == rt.variant {
 535                                                                 // hgvsCol[*][ph][row] is already 0
 536                                                         } else if len(variantDiffs[v]) == 0 {
 537                                                                 // lacking coverage / couldn't be diffed
 538                                                                 for _, col := range hgvsCol {
 539                                                                         col[ph][row] = -1
 540                                                                 }
 541                                                         } else {
 542                                                                 for _, diff := range variantDiffs[v] {
 543                                                                         hgvsCol[diff][ph][row] = 1
 544                                                                 }
 545                                                         }
 546                                                 }
 547                                         }
 548                                         for diff, colpair := range hgvsCol {
 549                                                 allele2homhet(colpair)
 550                                                 if !cmd.filterHGVScolpair(colpair) {
 551                                                         delete(hgvsCol, diff)
 552                                                 }
 553                                         }
 554                                         if len(hgvsCol) > 0 {
 555                                                 encodeHGVSTodo[rt.seqname] <- hgvsCol
 556                                         }
 557                                 }
 558                                 outcol++
 559                         }
 560                         err = annow.Flush()
 561                         if err != nil {
 562                                 return err
 563                         }
 564                         err = annof.Close()
 565                         if err != nil {
 566                                 return err
 567                         }
 568
 569                         if *onehotChunked {
 570                                 // transpose onehotChunk[col][row] to numpy[row*ncols+col]
 571                                 rows := len(cmd.cgnames)
 572                                 cols := len(onehotChunk)
 573                                 log.Infof("%04d: preparing onehot numpy (rows=%d, cols=%d, mem=%d)", infileIdx, rows, cols, rows*cols)
 574                                 throttleNumpyMem.Acquire()
 575                                 out := make([]int8, rows*cols)
 576                                 for row := range cmd.cgnames {
 577                                         out := out[row*cols:]
 578                                         for colnum, values := range onehotChunk {
 579                                                 out[colnum] = values[row]
 580                                         }
 581                                 }
 582                                 seq = nil
 583                                 cgs = nil
 584                                 debug.FreeOSMemory()
 585                                 throttleNumpyMem.Release()
 586
 587                                 fnm := fmt.Sprintf("%s/onehot.%04d.npy", *outputDir, infileIdx)
 588                                 err = writeNumpyInt8(fnm, out, rows, cols)
 589                                 if err != nil {
 590                                         return err
 591                                 }
 592
 593                                 fnm = fmt.Sprintf("%s/onehot-columns.%04d.npy", *outputDir, infileIdx)
 594                                 xcols := len(onehotXrefs)
 595                                 xdata := make([]int32, 4*xcols)
 596                                 for i, xref := range onehotXrefs {
 597                                         xdata[i] = int32(xref.tag)
 598                                         xdata[xcols+i] = int32(xref.variant)
 599                                         if xref.het {
 600                                                 xdata[xcols*2+i] = 1
 601                                         }
 602                                         xdata[xcols*3+i] = int32(xref.pvalue * 1000000)
 603                                 }
 604                                 err = writeNumpyInt32(fnm, xdata, 4, xcols)
 605                                 if err != nil {
 606                                         return err
 607                                 }
 608                         }
 609                         if !*onehotChunked || *mergeOutput || *hgvsSingle {
 610                                 log.Infof("%04d: preparing numpy", infileIdx)
 611                                 throttleNumpyMem.Acquire()
 612                                 rows := len(cmd.cgnames)
 613                                 cols := 2 * outcol
 614                                 out := make([]int16, rows*cols)
 615                                 for row, name := range cmd.cgnames {
 616                                         out := out[row*cols:]
 617                                         outcol := 0
 618                                         for col, v := range cgs[name].Variants {
 619                                                 tag := tagstart + tagID(col/2)
 620                                                 if mask != nil && reftile[tag] == nil {
 621                                                         continue
 622                                                 }
 623                                                 if variants, ok := seq[tag]; ok && len(variants) > int(v) && len(variants[v].Sequence) > 0 {
 624                                                         out[outcol] = int16(variantRemap[tag-tagstart][v])
 625                                                 } else {
 626                                                         out[outcol] = -1
 627                                                 }
 628                                                 outcol++
 629                                         }
 630                                 }
 631                                 seq = nil
 632                                 cgs = nil
 633                                 debug.FreeOSMemory()
 634                                 throttleNumpyMem.Release()
 635                                 if *mergeOutput || *hgvsSingle {
 636                                         log.Infof("%04d: matrix fragment %d rows x %d cols", infileIdx, rows, cols)
 637                                         toMerge[infileIdx] = out
 638                                 }
 639                                 if !*mergeOutput && !*onehotChunked {
 640                                         fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
 641                                         err = writeNumpyInt16(fnm, out, rows, cols)
 642                                         if err != nil {
 643                                                 return err
 644                                         }
 645                                 }
 646                         }
 647                         debug.FreeOSMemory()
 648                         log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
 649                         return nil
 650                 })
 651         }
 652         if err = throttleMem.Wait(); err != nil {
 653                 return 1
 654         }
 655
 656         if *hgvsChunked {
 657                 log.Info("flushing hgvsCols temp files")
 658                 for seqname := range refseq {
 659                         close(encodeHGVSTodo[seqname])
 660                 }
 661                 err = encodeHGVS.Wait()
 662                 if err != nil {
 663                         return 1
 664                 }
 665                 for seqname := range refseq {
 666                         log.Infof("%s: reading hgvsCols from temp file", seqname)
 667                         f := tmpHGVSCols[seqname]
 668                         _, err = f.Seek(0, io.SeekStart)
 669                         if err != nil {
 670                                 return 1
 671                         }
 672                         var hgvsCols hgvsColSet
 673                         dec := gob.NewDecoder(bufio.NewReaderSize(f, 1<<24))
 674                         for err == nil {
 675                                 err = dec.Decode(&hgvsCols)
 676                         }
 677                         if err != io.EOF {
 678                                 return 1
 679                         }
 680                         log.Infof("%s: sorting %d hgvs variants", seqname, len(hgvsCols))
 681                         variants := make([]hgvs.Variant, 0, len(hgvsCols))
 682                         for v := range hgvsCols {
 683                                 variants = append(variants, v)
 684                         }
 685                         sort.Slice(variants, func(i, j int) bool {
 686                                 vi, vj := &variants[i], &variants[j]
 687                                 if vi.Position != vj.Position {
 688                                         return vi.Position < vj.Position
 689                                 } else if vi.Ref != vj.Ref {
 690                                         return vi.Ref < vj.Ref
 691                                 } else {
 692                                         return vi.New < vj.New
 693                                 }
 694                         })
 695                         rows := len(cmd.cgnames)
 696                         cols := len(variants) * 2
 697                         log.Infof("%s: building hgvs matrix (rows=%d, cols=%d, mem=%d)", seqname, rows, cols, rows*cols)
 698                         out := make([]int8, rows*cols)
 699                         for varIdx, variant := range variants {
 700                                 hgvsCols := hgvsCols[variant]
 701                                 for row := range cmd.cgnames {
 702                                         for ph := 0; ph < 2; ph++ {
 703                                                 out[row*cols+varIdx+ph] = hgvsCols[ph][row]
 704                                         }
 705                                 }
 706                         }
 707                         err = writeNumpyInt8(fmt.Sprintf("%s/hgvs.%s.npy", *outputDir, seqname), out, rows, cols)
 708                         if err != nil {
 709                                 return 1
 710                         }
 711                         out = nil
 712
 713                         fnm := fmt.Sprintf("%s/hgvs.%s.annotations.csv", *outputDir, seqname)
 714                         log.Infof("%s: writing hgvs column labels to %s", seqname, fnm)
 715                         var hgvsLabels bytes.Buffer
 716                         for varIdx, variant := range variants {
 717                                 fmt.Fprintf(&hgvsLabels, "%d,%s:g.%s\n", varIdx, seqname, variant.String())
 718                         }
 719                         err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0666)
 720                         if err != nil {
 721                                 return 1
 722                         }
 723                 }
 724         }
 725
 726         if *mergeOutput || *hgvsSingle {
 727                 var annow *bufio.Writer
 728                 var annof *os.File
 729                 if *mergeOutput {
 730                         annoFilename := fmt.Sprintf("%s/matrix.annotations.csv", *outputDir)
 731                         annof, err = os.Create(annoFilename)
 732                         if err != nil {
 733                                 return 1
 734                         }
 735                         annow = bufio.NewWriterSize(annof, 1<<20)
 736                 }
 737
 738                 rows := len(cmd.cgnames)
 739                 cols := 0
 740                 for _, chunk := range toMerge {
 741                         cols += len(chunk) / rows
 742                 }
 743                 log.Infof("merging output matrix (rows=%d, cols=%d, mem=%d) and annotations", rows, cols, rows*cols*2)
 744                 var out []int16
 745                 if *mergeOutput {
 746                         out = make([]int16, rows*cols)
 747                 }
 748                 hgvsCols := map[string][2][]int16{} // hgvs -> [[g0,g1,g2,...], [g0,g1,g2,...]] (slice of genomes for each phase)
 749                 startcol := 0
 750                 for outIdx, chunk := range toMerge {
 751                         chunkcols := len(chunk) / rows
 752                         if *mergeOutput {
 753                                 for row := 0; row < rows; row++ {
 754                                         copy(out[row*cols+startcol:], chunk[row*chunkcols:(row+1)*chunkcols])
 755                                 }
 756                         }
 757                         toMerge[outIdx] = nil
 758
 759                         annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, outIdx)
 760                         log.Infof("reading %s", annotationsFilename)
 761                         buf, err := os.ReadFile(annotationsFilename)
 762                         if err != nil {
 763                                 return 1
 764                         }
 765                         if *mergeOutput {
 766                                 err = os.Remove(annotationsFilename)
 767                                 if err != nil {
 768                                         return 1
 769                                 }
 770                         }
 771                         for _, line := range bytes.Split(buf, []byte{'\n'}) {
 772                                 if len(line) == 0 {
 773                                         continue
 774                                 }
 775                                 fields := bytes.SplitN(line, []byte{','}, 9)
 776                                 tag, _ := strconv.Atoi(string(fields[0]))
 777                                 incol, _ := strconv.Atoi(string(fields[1]))
 778                                 tileVariant, _ := strconv.Atoi(string(fields[2]))
 779                                 hgvsID := string(fields[3])
 780                                 seqname := string(fields[4])
 781                                 pos, _ := strconv.Atoi(string(fields[5]))
 782                                 refseq := fields[6]
 783                                 if hgvsID == "" {
 784                                         // Null entry for un-diffable
 785                                         // tile variant
 786                                         continue
 787                                 }
 788                                 if hgvsID == "=" {
 789                                         // Null entry for ref tile
 790                                         continue
 791                                 }
 792                                 if mask != nil && !mask.Check(strings.TrimPrefix(seqname, "chr"), pos, pos+len(refseq)) {
 793                                         // The tile intersects one of
 794                                         // the selected regions, but
 795                                         // this particular HGVS
 796                                         // variant does not.
 797                                         continue
 798                                 }
 799                                 hgvsColPair := hgvsCols[hgvsID]
 800                                 if hgvsColPair[0] == nil {
 801                                         // values in new columns start
 802                                         // out as -1 ("no data yet")
 803                                         // or 0 ("=ref") here, may
 804                                         // change to 1 ("hgvs variant
 805                                         // present") below, either on
 806                                         // this line or a future line.
 807                                         hgvsColPair = [2][]int16{make([]int16, len(cmd.cgnames)), make([]int16, len(cmd.cgnames))}
 808                                         rt, ok := reftile[tagID(tag)]
 809                                         if !ok {
 810                                                 err = fmt.Errorf("bug: seeing annotations for tag %d, but it has no reftile entry", tag)
 811                                                 return 1
 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 tileVariantID(v) == rt.variant {
 817                                                                 hgvsColPair[ph][row] = 0
 818                                                         } else {
 819                                                                 hgvsColPair[ph][row] = -1
 820                                                         }
 821                                                 }
 822                                         }
 823                                         hgvsCols[hgvsID] = hgvsColPair
 824                                         if annow != nil {
 825                                                 hgvsref := hgvs.Variant{
 826                                                         Position: pos,
 827                                                         Ref:      string(refseq),
 828                                                         New:      string(refseq),
 829                                                 }
 830                                                 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])
 831                                         }
 832                                 }
 833                                 if annow != nil {
 834                                         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])
 835                                 }
 836                                 for ph := 0; ph < 2; ph++ {
 837                                         for row := 0; row < rows; row++ {
 838                                                 v := chunk[row*chunkcols+incol*2+ph]
 839                                                 if int(v) == tileVariant {
 840                                                         hgvsColPair[ph][row] = 1
 841                                                 }
 842                                         }
 843                                 }
 844                         }
 845
 846                         startcol += chunkcols
 847                 }
 848                 if *mergeOutput {
 849                         err = annow.Flush()
 850                         if err != nil {
 851                                 return 1
 852                         }
 853                         err = annof.Close()
 854                         if err != nil {
 855                                 return 1
 856                         }
 857                         err = writeNumpyInt16(fmt.Sprintf("%s/matrix.npy", *outputDir), out, rows, cols)
 858                         if err != nil {
 859                                 return 1
 860                         }
 861                 }
 862                 out = nil
 863
 864                 if *hgvsSingle {
 865                         cols = len(hgvsCols) * 2
 866                         log.Printf("building hgvs-based matrix: %d rows x %d cols", rows, cols)
 867                         out = make([]int16, rows*cols)
 868                         hgvsIDs := make([]string, 0, cols/2)
 869                         for hgvsID := range hgvsCols {
 870                                 hgvsIDs = append(hgvsIDs, hgvsID)
 871                         }
 872                         sort.Strings(hgvsIDs)
 873                         var hgvsLabels bytes.Buffer
 874                         for idx, hgvsID := range hgvsIDs {
 875                                 fmt.Fprintf(&hgvsLabels, "%d,%s\n", idx, hgvsID)
 876                                 for ph := 0; ph < 2; ph++ {
 877                                         hgvscol := hgvsCols[hgvsID][ph]
 878                                         for row, val := range hgvscol {
 879                                                 out[row*cols+idx*2+ph] = val
 880                                         }
 881                                 }
 882                         }
 883                         err = writeNumpyInt16(fmt.Sprintf("%s/hgvs.npy", *outputDir), out, rows, cols)
 884                         if err != nil {
 885                                 return 1
 886                         }
 887
 888                         fnm := fmt.Sprintf("%s/hgvs.annotations.csv", *outputDir)
 889                         log.Printf("writing hgvs labels: %s", fnm)
 890                         err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0777)
 891                         if err != nil {
 892                                 return 1
 893                         }
 894                 }
 895         }
 896         return 0
 897 }
 898
 899 // Read case/control files, remove non-case/control entries from
 900 // cmd.cgnames, and build cmd.chi2Cases.
 901 func (cmd *sliceNumpy) useCaseControlFiles() error {
 902         if cmd.chi2CaseControlFile == "" {
 903                 return nil
 904         }
 905         infiles, err := allFiles(cmd.chi2CaseControlFile, nil)
 906         if err != nil {
 907                 return err
 908         }
 909         // index in cmd.cgnames => case(true) / control(false)
 910         cc := map[int]bool{}
 911         for _, infile := range infiles {
 912                 f, err := open(infile)
 913                 if err != nil {
 914                         return err
 915                 }
 916                 buf, err := io.ReadAll(f)
 917                 f.Close()
 918                 if err != nil {
 919                         return err
 920                 }
 921                 ccCol := -1
 922                 for _, tsv := range bytes.Split(buf, []byte{'\n'}) {
 923                         if len(tsv) == 0 {
 924                                 continue
 925                         }
 926                         split := strings.Split(string(tsv), "\t")
 927                         if ccCol < 0 {
 928                                 // header row
 929                                 for col, name := range split {
 930                                         if name == cmd.chi2CaseControlColumn {
 931                                                 ccCol = col
 932                                                 break
 933                                         }
 934                                 }
 935                                 if ccCol < 0 {
 936                                         return fmt.Errorf("%s: no column named %q in header row %q", infile, cmd.chi2CaseControlColumn, tsv)
 937                                 }
 938                                 continue
 939                         }
 940                         if len(split) <= ccCol {
 941                                 continue
 942                         }
 943                         pattern := split[0]
 944                         found := -1
 945                         for i, name := range cmd.cgnames {
 946                                 if strings.Contains(name, pattern) {
 947                                         if found >= 0 {
 948                                                 log.Warnf("pattern %q in %s matches multiple genome IDs (%qs, %q)", pattern, infile, cmd.cgnames[found], name)
 949                                         }
 950                                         found = i
 951                                 }
 952                         }
 953                         if found < 0 {
 954                                 log.Warnf("pattern %q in %s does not match any genome IDs", pattern, infile)
 955                                 continue
 956                         }
 957                         if split[ccCol] == "0" {
 958                                 cc[found] = false
 959                         }
 960                         if split[ccCol] == "1" {
 961                                 cc[found] = true
 962                         }
 963                 }
 964         }
 965         allnames := cmd.cgnames
 966         cmd.cgnames = nil
 967         cmd.chi2Cases = nil
 968         ncases := 0
 969         for i, name := range allnames {
 970                 if cc, ok := cc[i]; ok {
 971                         cmd.cgnames = append(cmd.cgnames, name)
 972                         cmd.chi2Cases = append(cmd.chi2Cases, cc)
 973                         if cc {
 974                                 ncases++
 975                         }
 976                 }
 977         }
 978         log.Printf("%d cases, %d controls, %d neither (dropped)", ncases, len(cmd.cgnames)-ncases, len(allnames)-len(cmd.cgnames))
 979         return nil
 980 }
 981
 982 func (cmd *sliceNumpy) filterHGVScolpair(colpair [2][]int8) bool {
 983         if cmd.chi2PValue >= 1 {
 984                 return true
 985         }
 986         col0 := make([]bool, 0, len(cmd.chi2Cases))
 987         col1 := make([]bool, 0, len(cmd.chi2Cases))
 988         cases := make([]bool, 0, len(cmd.chi2Cases))
 989         for i, c := range cmd.chi2Cases {
 990                 if colpair[0][i] < 0 {
 991                         continue
 992                 }
 993                 col0 = append(col0, colpair[0][i] != 0)
 994                 col1 = append(col1, colpair[1][i] != 0)
 995                 cases = append(cases, c)
 996         }
 997         return len(cases) >= cmd.minCoverage &&
 998                 (pvalue(cases, col0) <= cmd.chi2PValue || pvalue(cases, col1) <= cmd.chi2PValue)
 999 }
1000
1001 func writeNumpyInt32(fnm string, out []int32, rows, cols int) error {
1002         output, err := os.Create(fnm)
1003         if err != nil {
1004                 return err
1005         }
1006         defer output.Close()
1007         bufw := bufio.NewWriterSize(output, 1<<26)
1008         npw, err := gonpy.NewWriter(nopCloser{bufw})
1009         if err != nil {
1010                 return err
1011         }
1012         log.WithFields(log.Fields{
1013                 "filename": fnm,
1014                 "rows":     rows,
1015                 "cols":     cols,
1016                 "bytes":    rows * cols * 4,
1017         }).Infof("writing numpy: %s", fnm)
1018         npw.Shape = []int{rows, cols}
1019         npw.WriteInt32(out)
1020         err = bufw.Flush()
1021         if err != nil {
1022                 return err
1023         }
1024         return output.Close()
1025 }
1026
1027 func writeNumpyInt16(fnm string, out []int16, rows, cols int) error {
1028         output, err := os.Create(fnm)
1029         if err != nil {
1030                 return err
1031         }
1032         defer output.Close()
1033         bufw := bufio.NewWriterSize(output, 1<<26)
1034         npw, err := gonpy.NewWriter(nopCloser{bufw})
1035         if err != nil {
1036                 return err
1037         }
1038         log.WithFields(log.Fields{
1039                 "filename": fnm,
1040                 "rows":     rows,
1041                 "cols":     cols,
1042                 "bytes":    rows * cols * 2,
1043         }).Infof("writing numpy: %s", fnm)
1044         npw.Shape = []int{rows, cols}
1045         npw.WriteInt16(out)
1046         err = bufw.Flush()
1047         if err != nil {
1048                 return err
1049         }
1050         return output.Close()
1051 }
1052
1053 func writeNumpyInt8(fnm string, out []int8, rows, cols int) error {
1054         output, err := os.Create(fnm)
1055         if err != nil {
1056                 return err
1057         }
1058         defer output.Close()
1059         bufw := bufio.NewWriterSize(output, 1<<26)
1060         npw, err := gonpy.NewWriter(nopCloser{bufw})
1061         if err != nil {
1062                 return err
1063         }
1064         log.WithFields(log.Fields{
1065                 "filename": fnm,
1066                 "rows":     rows,
1067                 "cols":     cols,
1068                 "bytes":    rows * cols,
1069         }).Infof("writing numpy: %s", fnm)
1070         npw.Shape = []int{rows, cols}
1071         npw.WriteInt8(out)
1072         err = bufw.Flush()
1073         if err != nil {
1074                 return err
1075         }
1076         return output.Close()
1077 }
1078
1079 func allele2homhet(colpair [2][]int8) {
1080         a, b := colpair[0], colpair[1]
1081         for i, av := range a {
1082                 bv := b[i]
1083                 if av < 0 || bv < 0 {
1084                         // no-call
1085                         a[i], b[i] = -1, -1
1086                 } else if av > 0 && bv > 0 {
1087                         // hom
1088                         a[i], b[i] = 1, 0
1089                 } else if av > 0 || bv > 0 {
1090                         // het
1091                         a[i], b[i] = 0, 1
1092                 } else {
1093                         // ref (or a different variant in same position)
1094                         // (this is a no-op) a[i], b[i] = 0, 0
1095                 }
1096         }
1097 }
1098
1099 type onehotXref struct {
1100         tag     tagID
1101         variant tileVariantID
1102         het     bool
1103         pvalue  float64
1104 }
1105
1106 // Build onehot matrix (m[variant*2+isHet][genome] == 0 or 1) for all
1107 // variants of a single tile/tag#.
1108 //
1109 // Return nil if no tile variant passes Χ² filter.
1110 func (cmd *sliceNumpy) tv2homhet(cgs map[string]CompactGenome, maxv tileVariantID, remap []tileVariantID, tag, chunkstarttag tagID) ([][]int8, []onehotXref) {
1111         if maxv < 2 {
1112                 // everyone has the most common variant
1113                 return nil, nil
1114         }
1115         tagoffset := tag - chunkstarttag
1116         coverage := 0
1117         for _, cg := range cgs {
1118                 if cg.Variants[tagoffset*2] > 0 && cg.Variants[tagoffset*2+1] > 0 {
1119                         coverage++
1120                 }
1121         }
1122         if coverage < cmd.minCoverage {
1123                 return nil, nil
1124         }
1125         obs := make([][]bool, (maxv+1)*2) // 2 slices (hom + het) for each variant#
1126         for i := range obs {
1127                 obs[i] = make([]bool, len(cmd.cgnames))
1128         }
1129         for cgid, name := range cmd.cgnames {
1130                 cgvars := cgs[name].Variants
1131                 for v := tileVariantID(2); v <= maxv; v++ {
1132                         if remap[cgvars[tagoffset*2]] == v && remap[cgvars[tagoffset*2+1]] == v {
1133                                 obs[v*2][cgid] = true
1134                         } else if remap[cgvars[tagoffset*2]] == v || remap[cgvars[tagoffset*2+1]] == v {
1135                                 obs[v*2+1][cgid] = true
1136                         }
1137                 }
1138         }
1139         var onehot [][]int8
1140         var xref []onehotXref
1141         for homcol := 4; homcol < len(obs); homcol += 2 {
1142                 p := [2]float64{
1143                         pvalue(cmd.chi2Cases, obs[homcol]),
1144                         pvalue(cmd.chi2Cases, obs[homcol+1]),
1145                 }
1146                 if cmd.chi2PValue < 1 && !(p[0] < cmd.chi2PValue || p[1] < cmd.chi2PValue) {
1147                         continue
1148                 }
1149                 for het := 0; het < 2; het++ {
1150                         onehot = append(onehot, bool2int8(obs[homcol+het]))
1151                         xref = append(xref, onehotXref{
1152                                 tag:     tag,
1153                                 variant: tileVariantID(homcol / 2),
1154                                 het:     het == 1,
1155                                 pvalue:  p[het],
1156                         })
1157                 }
1158         }
1159         return onehot, xref
1160 }
1161
1162 func bool2int8(in []bool) []int8 {
1163         out := make([]int8, len(in))
1164         for i, v := range in {
1165                 if v {
1166                         out[i] = 1
1167                 }
1168         }
1169         return out
1170 }