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         "errors"
  12         "flag"
  13         "fmt"
  14         "io"
  15         "io/ioutil"
  16         "math"
  17         "net/http"
  18         _ "net/http/pprof"
  19         "os"
  20         "regexp"
  21         "runtime"
  22         "runtime/debug"
  23         "sort"
  24         "strconv"
  25         "strings"
  26         "sync/atomic"
  27         "unsafe"
  28
  29         "git.arvados.org/arvados.git/sdk/go/arvados"
  30         "github.com/arvados/lightning/hgvs"
  31         "github.com/james-bowman/nlp"
  32         "github.com/kshedden/gonpy"
  33         "github.com/sirupsen/logrus"
  34         log "github.com/sirupsen/logrus"
  35         "golang.org/x/crypto/blake2b"
  36         "gonum.org/v1/gonum/mat"
  37 )
  38
  39 const annotationMaxTileSpan = 100
  40
  41 type sliceNumpy struct {
  42         filter                filter
  43         threads               int
  44         chi2CaseControlColumn string
  45         chi2CaseControlFile   string
  46         chi2Cases             []bool
  47         chi2PValue            float64
  48         minCoverage           int
  49         cgnames               []string
  50         includeVariant1       bool
  51         debugTag              tagID
  52 }
  53
  54 func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  55         err := cmd.run(prog, args, stdin, stdout, stderr)
  56         if err != nil {
  57                 fmt.Fprintf(stderr, "%s\n", err)
  58                 return 1
  59         }
  60         return 0
  61 }
  62 func (cmd *sliceNumpy) run(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) error {
  63         flags := flag.NewFlagSet("", flag.ContinueOnError)
  64         flags.SetOutput(stderr)
  65         pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
  66         runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
  67         arvadosRAM := flags.Int("arvados-ram", 750000000000, "amount of memory to request for arvados container (`bytes`)")
  68         arvadosVCPUs := flags.Int("arvados-vcpus", 96, "number of VCPUs to request for arvados container")
  69         projectUUID := flags.String("project", "", "project `UUID` for output data")
  70         priority := flags.Int("priority", 500, "container request priority")
  71         inputDir := flags.String("input-dir", "./in", "input `directory`")
  72         outputDir := flags.String("output-dir", "./out", "output `directory`")
  73         ref := flags.String("ref", "", "reference name (if blank, choose last one that appears in input)")
  74         regionsFilename := flags.String("regions", "", "only output columns/annotations that intersect regions in specified bed `file`")
  75         expandRegions := flags.Int("expand-regions", 0, "expand specified regions by `N` base pairs on each side`")
  76         mergeOutput := flags.Bool("merge-output", false, "merge output into one matrix.npy and one matrix.annotations.csv")
  77         hgvsSingle := flags.Bool("single-hgvs-matrix", false, "also generate hgvs-based matrix")
  78         hgvsChunked := flags.Bool("chunked-hgvs-matrix", false, "also generate hgvs-based matrix per chromosome")
  79         onehotSingle := flags.Bool("single-onehot", false, "generate one-hot tile-based matrix")
  80         onehotChunked := flags.Bool("chunked-onehot", false, "generate one-hot tile-based matrix per input chunk")
  81         onlyPCA := flags.Bool("pca", false, "generate pca matrix")
  82         pcaComponents := flags.Int("pca-components", 4, "number of PCA components")
  83         maxPCATiles := flags.Int("max-pca-tiles", 100000, "maximum tiles to use as PCA input (filter, then drop every 2nd colum pair until below max)")
  84         debugTag := flags.Int("debug-tag", -1, "log debugging details about specified tag")
  85         flags.IntVar(&cmd.threads, "threads", 16, "number of memory-hungry assembly threads, and number of VCPUs to request for arvados container")
  86         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)")
  87         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)")
  88         flags.Float64Var(&cmd.chi2PValue, "chi2-p-value", 1, "do Χ² test and omit columns with p-value above this threshold")
  89         flags.BoolVar(&cmd.includeVariant1, "include-variant-1", false, "include most common variant when building one-hot matrix")
  90         cmd.filter.Flags(flags)
  91         err := flags.Parse(args)
  92         if err == flag.ErrHelp {
  93                 return nil
  94         } else if err != nil {
  95                 return err
  96         }
  97
  98         if *pprof != "" {
  99                 go func() {
 100                         log.Println(http.ListenAndServe(*pprof, nil))
 101                 }()
 102         }
 103
 104         if cmd.chi2PValue != 1 && (cmd.chi2CaseControlFile == "" || cmd.chi2CaseControlColumn == "") {
 105                 return fmt.Errorf("cannot use provided -chi2-p-value=%f because -chi2-case-control-file= or -chi2-case-control-column= value is empty", cmd.chi2PValue)
 106         }
 107
 108         cmd.debugTag = tagID(*debugTag)
 109
 110         if !*runlocal {
 111                 runner := arvadosContainerRunner{
 112                         Name:        "lightning slice-numpy",
 113                         Client:      arvados.NewClientFromEnv(),
 114                         ProjectUUID: *projectUUID,
 115                         RAM:         int64(*arvadosRAM),
 116                         VCPUs:       *arvadosVCPUs,
 117                         Priority:    *priority,
 118                         KeepCache:   2,
 119                         APIAccess:   true,
 120                 }
 121                 err = runner.TranslatePaths(inputDir, regionsFilename, &cmd.chi2CaseControlFile)
 122                 if err != nil {
 123                         return err
 124                 }
 125                 runner.Args = []string{"slice-numpy", "-local=true",
 126                         "-pprof=:6060",
 127                         "-input-dir=" + *inputDir,
 128                         "-output-dir=/mnt/output",
 129                         "-threads=" + fmt.Sprintf("%d", cmd.threads),
 130                         "-regions=" + *regionsFilename,
 131                         "-expand-regions=" + fmt.Sprintf("%d", *expandRegions),
 132                         "-merge-output=" + fmt.Sprintf("%v", *mergeOutput),
 133                         "-single-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsSingle),
 134                         "-chunked-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsChunked),
 135                         "-single-onehot=" + fmt.Sprintf("%v", *onehotSingle),
 136                         "-chunked-onehot=" + fmt.Sprintf("%v", *onehotChunked),
 137                         "-pca=" + fmt.Sprintf("%v", *onlyPCA),
 138                         "-pca-components=" + fmt.Sprintf("%d", *pcaComponents),
 139                         "-chi2-case-control-file=" + cmd.chi2CaseControlFile,
 140                         "-chi2-case-control-column=" + cmd.chi2CaseControlColumn,
 141                         "-chi2-p-value=" + fmt.Sprintf("%f", cmd.chi2PValue),
 142                         "-include-variant-1=" + fmt.Sprintf("%v", cmd.includeVariant1),
 143                         "-debug-tag=" + fmt.Sprintf("%d", cmd.debugTag),
 144                 }
 145                 runner.Args = append(runner.Args, cmd.filter.Args()...)
 146                 var output string
 147                 output, err = runner.Run()
 148                 if err != nil {
 149                         return err
 150                 }
 151                 fmt.Fprintln(stdout, output)
 152                 return nil
 153         }
 154
 155         infiles, err := allFiles(*inputDir, matchGobFile)
 156         if err != nil {
 157                 return err
 158         }
 159         if len(infiles) == 0 {
 160                 err = fmt.Errorf("no input files found in %s", *inputDir)
 161                 return err
 162         }
 163         sort.Strings(infiles)
 164
 165         var refseq map[string][]tileLibRef
 166         var reftiledata = make(map[tileLibRef][]byte, 11000000)
 167         in0, err := open(infiles[0])
 168         if err != nil {
 169                 return err
 170         }
 171
 172         matchGenome, err := regexp.Compile(cmd.filter.MatchGenome)
 173         if err != nil {
 174                 err = fmt.Errorf("-match-genome: invalid regexp: %q", cmd.filter.MatchGenome)
 175                 return err
 176         }
 177
 178         cmd.cgnames = nil
 179         var tagset [][]byte
 180         err = DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
 181                 if len(ent.TagSet) > 0 {
 182                         tagset = ent.TagSet
 183                 }
 184                 for _, cseq := range ent.CompactSequences {
 185                         if cseq.Name == *ref || *ref == "" {
 186                                 refseq = cseq.TileSequences
 187                         }
 188                 }
 189                 for _, cg := range ent.CompactGenomes {
 190                         if matchGenome.MatchString(cg.Name) {
 191                                 cmd.cgnames = append(cmd.cgnames, cg.Name)
 192                         }
 193                 }
 194                 for _, tv := range ent.TileVariants {
 195                         if tv.Ref {
 196                                 reftiledata[tileLibRef{tv.Tag, tv.Variant}] = tv.Sequence
 197                         }
 198                 }
 199                 return nil
 200         })
 201         if err != nil {
 202                 return err
 203         }
 204         in0.Close()
 205         if refseq == nil {
 206                 err = fmt.Errorf("%s: reference sequence not found", infiles[0])
 207                 return err
 208         }
 209         if len(tagset) == 0 {
 210                 err = fmt.Errorf("tagset not found")
 211                 return err
 212         }
 213
 214         taglib := &tagLibrary{}
 215         err = taglib.setTags(tagset)
 216         if err != nil {
 217                 return err
 218         }
 219         taglen := taglib.TagLen()
 220
 221         if len(cmd.cgnames) == 0 {
 222                 err = fmt.Errorf("no genomes found matching regexp %q", cmd.filter.MatchGenome)
 223                 return err
 224         }
 225         sort.Strings(cmd.cgnames)
 226         err = cmd.useCaseControlFiles()
 227         if err != nil {
 228                 return err
 229         }
 230         if len(cmd.cgnames) == 0 {
 231                 err = fmt.Errorf("fatal: 0 cases, 0 controls, nothing to do")
 232                 return err
 233         }
 234         if cmd.filter.MinCoverage == 1 {
 235                 // In the generic formula below, floating point
 236                 // arithmetic can effectively push the coverage
 237                 // threshold above 1.0, which is impossible/useless.
 238                 // 1.0 needs to mean exactly 100% coverage.
 239                 cmd.minCoverage = len(cmd.cgnames)
 240         } else {
 241                 cmd.minCoverage = int(math.Ceil(cmd.filter.MinCoverage * float64(len(cmd.cgnames))))
 242         }
 243
 244         {
 245                 labelsFilename := *outputDir + "/samples.csv"
 246                 log.Infof("writing labels to %s", labelsFilename)
 247                 var f *os.File
 248                 f, err = os.Create(labelsFilename)
 249                 if err != nil {
 250                         return err
 251                 }
 252                 defer f.Close()
 253                 for i, name := range cmd.cgnames {
 254                         cc := 0
 255                         if cmd.chi2Cases != nil && cmd.chi2Cases[i] {
 256                                 cc = 1
 257                         }
 258                         _, err = fmt.Fprintf(f, "%d,%q,%d\n", i, trimFilenameForLabel(name), cc)
 259                         if err != nil {
 260                                 err = fmt.Errorf("write %s: %w", labelsFilename, err)
 261                                 return err
 262                         }
 263                 }
 264                 err = f.Close()
 265                 if err != nil {
 266                         err = fmt.Errorf("close %s: %w", labelsFilename, err)
 267                         return err
 268                 }
 269         }
 270
 271         log.Info("indexing reference tiles")
 272         type reftileinfo struct {
 273                 variant  tileVariantID
 274                 seqname  string // chr1
 275                 pos      int    // distance from start of chromosome to starttag
 276                 tiledata []byte // acgtggcaa...
 277                 excluded bool   // true if excluded by regions file
 278                 nexttag  tagID  // tagID of following tile (-1 for last tag of chromosome)
 279         }
 280         isdup := map[tagID]bool{}
 281         reftile := map[tagID]*reftileinfo{}
 282         for seqname, cseq := range refseq {
 283                 pos := 0
 284                 lastreftag := tagID(-1)
 285                 for _, libref := range cseq {
 286                         if cmd.filter.MaxTag >= 0 && libref.Tag > tagID(cmd.filter.MaxTag) {
 287                                 continue
 288                         }
 289                         tiledata := reftiledata[libref]
 290                         if len(tiledata) == 0 {
 291                                 err = fmt.Errorf("missing tiledata for tag %d variant %d in %s in ref", libref.Tag, libref.Variant, seqname)
 292                                 return err
 293                         }
 294                         foundthistag := false
 295                         taglib.FindAll(tiledata[:len(tiledata)-1], func(tagid tagID, offset, _ int) {
 296                                 if !foundthistag && tagid == libref.Tag {
 297                                         foundthistag = true
 298                                         return
 299                                 }
 300                                 if dupref, ok := reftile[tagid]; ok {
 301                                         log.Printf("dropping reference tile %+v from %s @ %d, tag not unique, also found inside %+v from %s @ %d", tileLibRef{Tag: tagid, Variant: dupref.variant}, dupref.seqname, dupref.pos, libref, seqname, pos+offset+1)
 302                                         delete(reftile, tagid)
 303                                 } else {
 304                                         log.Printf("found tag %d at offset %d inside tile variant %+v on %s @ %d", tagid, offset, libref, seqname, pos+offset+1)
 305                                 }
 306                                 isdup[tagid] = true
 307                         })
 308                         if isdup[libref.Tag] {
 309                                 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
 310                         } else if reftile[libref.Tag] != nil {
 311                                 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)
 312                                 delete(reftile, libref.Tag)
 313                                 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
 314                                 isdup[libref.Tag] = true
 315                         } else {
 316                                 reftile[libref.Tag] = &reftileinfo{
 317                                         seqname:  seqname,
 318                                         variant:  libref.Variant,
 319                                         tiledata: tiledata,
 320                                         pos:      pos,
 321                                         nexttag:  -1,
 322                                 }
 323                                 if lastreftag >= 0 {
 324                                         reftile[lastreftag].nexttag = libref.Tag
 325                                 }
 326                                 lastreftag = libref.Tag
 327                         }
 328                         pos += len(tiledata) - taglen
 329                 }
 330                 log.Printf("... %s done, len %d", seqname, pos+taglen)
 331         }
 332
 333         var mask *mask
 334         if *regionsFilename != "" {
 335                 log.Printf("loading regions from %s", *regionsFilename)
 336                 mask, err = makeMask(*regionsFilename, *expandRegions)
 337                 if err != nil {
 338                         return err
 339                 }
 340                 log.Printf("before applying mask, len(reftile) == %d", len(reftile))
 341                 log.Printf("deleting reftile entries for regions outside %d intervals", mask.Len())
 342                 for _, rt := range reftile {
 343                         if !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(rt.tiledata)) {
 344                                 rt.excluded = true
 345                         }
 346                 }
 347                 log.Printf("after applying mask, len(reftile) == %d", len(reftile))
 348         }
 349
 350         type hgvsColSet map[hgvs.Variant][2][]int8
 351         encodeHGVS := throttle{Max: len(refseq)}
 352         encodeHGVSTodo := map[string]chan hgvsColSet{}
 353         tmpHGVSCols := map[string]*os.File{}
 354         if *hgvsChunked {
 355                 for seqname := range refseq {
 356                         var f *os.File
 357                         f, err = os.Create(*outputDir + "/tmp." + seqname + ".gob")
 358                         if err != nil {
 359                                 return err
 360                         }
 361                         defer os.Remove(f.Name())
 362                         bufw := bufio.NewWriterSize(f, 1<<24)
 363                         enc := gob.NewEncoder(bufw)
 364                         tmpHGVSCols[seqname] = f
 365                         todo := make(chan hgvsColSet, 128)
 366                         encodeHGVSTodo[seqname] = todo
 367                         encodeHGVS.Go(func() error {
 368                                 for colset := range todo {
 369                                         err := enc.Encode(colset)
 370                                         if err != nil {
 371                                                 encodeHGVS.Report(err)
 372                                                 for range todo {
 373                                                 }
 374                                                 return err
 375                                         }
 376                                 }
 377                                 return bufw.Flush()
 378                         })
 379                 }
 380         }
 381
 382         var toMerge [][]int16
 383         if *mergeOutput || *hgvsSingle {
 384                 toMerge = make([][]int16, len(infiles))
 385         }
 386         var onehotIndirect [][2][]uint32 // [chunkIndex][axis][index]
 387         var onehotChunkSize []uint32
 388         var onehotXrefs [][]onehotXref
 389         if *onehotSingle || *onlyPCA {
 390                 onehotIndirect = make([][2][]uint32, len(infiles))
 391                 onehotChunkSize = make([]uint32, len(infiles))
 392                 onehotXrefs = make([][]onehotXref, len(infiles))
 393         }
 394         chunkStartTag := make([]tagID, len(infiles))
 395
 396         throttleMem := throttle{Max: cmd.threads} // TODO: estimate using mem and data size
 397         throttleNumpyMem := throttle{Max: cmd.threads/2 + 1}
 398         log.Info("generating annotations and numpy matrix for each slice")
 399         var errSkip = errors.New("skip infile")
 400         var done int64
 401         for infileIdx, infile := range infiles {
 402                 infileIdx, infile := infileIdx, infile
 403                 throttleMem.Go(func() error {
 404                         seq := make(map[tagID][]TileVariant, 50000)
 405                         cgs := make(map[string]CompactGenome, len(cmd.cgnames))
 406                         f, err := open(infile)
 407                         if err != nil {
 408                                 return err
 409                         }
 410                         defer f.Close()
 411                         log.Infof("%04d: reading %s", infileIdx, infile)
 412                         err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
 413                                 for _, tv := range ent.TileVariants {
 414                                         if tv.Ref {
 415                                                 continue
 416                                         }
 417                                         // Skip tile with no
 418                                         // corresponding ref tile, if
 419                                         // mask is in play (we can't
 420                                         // determine coordinates for
 421                                         // these)
 422                                         if mask != nil && reftile[tv.Tag] == nil {
 423                                                 continue
 424                                         }
 425                                         // Skip tile whose
 426                                         // corresponding ref tile is
 427                                         // outside target regions --
 428                                         // unless it's a potential
 429                                         // spanning tile.
 430                                         if mask != nil && reftile[tv.Tag].excluded &&
 431                                                 (int(tv.Tag+1) >= len(tagset) ||
 432                                                         (bytes.HasSuffix(tv.Sequence, tagset[tv.Tag+1]) && reftile[tv.Tag+1] != nil && !reftile[tv.Tag+1].excluded)) {
 433                                                 continue
 434                                         }
 435                                         if tv.Tag == cmd.debugTag {
 436                                                 log.Printf("infile %d %s tag %d variant %d hash %x", infileIdx, infile, tv.Tag, tv.Variant, tv.Blake2b[:3])
 437                                         }
 438                                         variants := seq[tv.Tag]
 439                                         if len(variants) == 0 {
 440                                                 variants = make([]TileVariant, 100)
 441                                         }
 442                                         for len(variants) <= int(tv.Variant) {
 443                                                 variants = append(variants, TileVariant{})
 444                                         }
 445                                         variants[int(tv.Variant)] = tv
 446                                         seq[tv.Tag] = variants
 447                                 }
 448                                 for _, cg := range ent.CompactGenomes {
 449                                         if cmd.filter.MaxTag >= 0 && cg.StartTag > tagID(cmd.filter.MaxTag) {
 450                                                 return errSkip
 451                                         }
 452                                         if !matchGenome.MatchString(cg.Name) {
 453                                                 continue
 454                                         }
 455                                         // pad to full slice size
 456                                         // to avoid out-of-bounds
 457                                         // checks later
 458                                         if sliceSize := 2 * int(cg.EndTag-cg.StartTag); len(cg.Variants) < sliceSize {
 459                                                 cg.Variants = append(cg.Variants, make([]tileVariantID, sliceSize-len(cg.Variants))...)
 460                                         }
 461                                         cgs[cg.Name] = cg
 462                                 }
 463                                 return nil
 464                         })
 465                         if err == errSkip {
 466                                 return nil
 467                         } else if err != nil {
 468                                 return fmt.Errorf("%04d: DecodeLibrary(%s): err", infileIdx, infile)
 469                         }
 470                         tagstart := cgs[cmd.cgnames[0]].StartTag
 471                         tagend := cgs[cmd.cgnames[0]].EndTag
 472                         chunkStartTag[infileIdx] = tagstart
 473
 474                         // TODO: filters
 475
 476                         log.Infof("%04d: renumber/dedup variants for tags %d-%d", infileIdx, tagstart, tagend)
 477                         variantRemap := make([][]tileVariantID, tagend-tagstart)
 478                         throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
 479                         for tag, variants := range seq {
 480                                 tag, variants := tag, variants
 481                                 throttleCPU.Go(func() error {
 482                                         alleleCoverage := 0
 483                                         count := make(map[[blake2b.Size256]byte]int, len(variants))
 484
 485                                         rt := reftile[tag]
 486                                         if rt != nil {
 487                                                 count[blake2b.Sum256(rt.tiledata)] = 0
 488                                         }
 489
 490                                         for cgname, cg := range cgs {
 491                                                 idx := int(tag-tagstart) * 2
 492                                                 for allele := 0; allele < 2; allele++ {
 493                                                         v := cg.Variants[idx+allele]
 494                                                         if v > 0 && len(variants[v].Sequence) > 0 {
 495                                                                 count[variants[v].Blake2b]++
 496                                                                 alleleCoverage++
 497                                                         }
 498                                                         if v > 0 && tag == cmd.debugTag {
 499                                                                 log.Printf("tag %d cg %s allele %d tv %d hash %x count is now %d", tag, cgname, allele, v, variants[v].Blake2b[:3], count[variants[v].Blake2b])
 500                                                         }
 501                                                 }
 502                                         }
 503                                         if alleleCoverage < cmd.minCoverage*2 {
 504                                                 idx := int(tag-tagstart) * 2
 505                                                 for _, cg := range cgs {
 506                                                         cg.Variants[idx] = 0
 507                                                         cg.Variants[idx+1] = 0
 508                                                 }
 509                                                 if tag == cmd.debugTag {
 510                                                         log.Printf("tag %d alleleCoverage %d < min %d, sample data wiped", tag, alleleCoverage, cmd.minCoverage*2)
 511                                                 }
 512                                                 return nil
 513                                         }
 514
 515                                         // hash[i] will be the hash of
 516                                         // the variant(s) that should
 517                                         // be at rank i (0-based).
 518                                         hash := make([][blake2b.Size256]byte, 0, len(count))
 519                                         for b := range count {
 520                                                 hash = append(hash, b)
 521                                         }
 522                                         sort.Slice(hash, func(i, j int) bool {
 523                                                 bi, bj := &hash[i], &hash[j]
 524                                                 if ci, cj := count[*bi], count[*bj]; ci != cj {
 525                                                         return ci > cj
 526                                                 } else {
 527                                                         return bytes.Compare((*bi)[:], (*bj)[:]) < 0
 528                                                 }
 529                                         })
 530                                         // rank[b] will be the 1-based
 531                                         // new variant number for
 532                                         // variants whose hash is b.
 533                                         rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
 534                                         for i, h := range hash {
 535                                                 rank[h] = tileVariantID(i + 1)
 536                                         }
 537                                         if tag == cmd.debugTag {
 538                                                 for h, r := range rank {
 539                                                         log.Printf("tag %d rank(%x) = %v", tag, h[:3], r)
 540                                                 }
 541                                         }
 542                                         // remap[v] will be the new
 543                                         // variant number for original
 544                                         // variant number v.
 545                                         remap := make([]tileVariantID, len(variants))
 546                                         for i, tv := range variants {
 547                                                 remap[i] = rank[tv.Blake2b]
 548                                         }
 549                                         if tag == cmd.debugTag {
 550                                                 for in, out := range remap {
 551                                                         if out > 0 {
 552                                                                 log.Printf("tag %d remap %d => %d", tag, in, out)
 553                                                         }
 554                                                 }
 555                                         }
 556                                         variantRemap[tag-tagstart] = remap
 557                                         if rt != nil {
 558                                                 refrank := rank[blake2b.Sum256(rt.tiledata)]
 559                                                 if tag == cmd.debugTag {
 560                                                         log.Printf("tag %d reftile variant %d => %d", tag, rt.variant, refrank)
 561                                                 }
 562                                                 rt.variant = refrank
 563                                         }
 564                                         return nil
 565                                 })
 566                         }
 567                         throttleCPU.Wait()
 568
 569                         var onehotChunk [][]int8
 570                         var onehotXref []onehotXref
 571
 572                         var annotationsFilename string
 573                         if *onlyPCA {
 574                                 annotationsFilename = "/dev/null"
 575                         } else {
 576                                 annotationsFilename = fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
 577                                 log.Infof("%04d: writing %s", infileIdx, annotationsFilename)
 578                         }
 579                         annof, err := os.Create(annotationsFilename)
 580                         if err != nil {
 581                                 return err
 582                         }
 583                         annow := bufio.NewWriterSize(annof, 1<<20)
 584                         outcol := 0
 585                         for tag := tagstart; tag < tagend; tag++ {
 586                                 rt := reftile[tag]
 587                                 if rt == nil && mask != nil {
 588                                         // With no ref tile, we don't
 589                                         // have coordinates to say
 590                                         // this is in the desired
 591                                         // regions -- so it's not.
 592                                         // TODO: handle ref spanning
 593                                         // tile case.
 594                                         continue
 595                                 }
 596                                 if rt != nil && rt.excluded {
 597                                         // TODO: don't skip yet --
 598                                         // first check for spanning
 599                                         // tile variants that
 600                                         // intersect non-excluded ref
 601                                         // tiles.
 602                                         continue
 603                                 }
 604                                 if cmd.filter.MaxTag >= 0 && tag > tagID(cmd.filter.MaxTag) {
 605                                         break
 606                                 }
 607                                 remap := variantRemap[tag-tagstart]
 608                                 maxv := tileVariantID(0)
 609                                 for _, v := range remap {
 610                                         if maxv < v {
 611                                                 maxv = v
 612                                         }
 613                                 }
 614                                 if *onehotChunked || *onehotSingle || *onlyPCA {
 615                                         onehot, xrefs := cmd.tv2homhet(cgs, maxv, remap, tag, tagstart, seq)
 616                                         if tag == cmd.debugTag {
 617                                                 log.WithFields(logrus.Fields{
 618                                                         "onehot": onehot,
 619                                                         "xrefs":  xrefs,
 620                                                 }).Info("tv2homhet()")
 621                                         }
 622                                         onehotChunk = append(onehotChunk, onehot...)
 623                                         onehotXref = append(onehotXref, xrefs...)
 624                                 }
 625                                 if *onlyPCA {
 626                                         outcol++
 627                                         continue
 628                                 }
 629                                 if rt == nil {
 630                                         // Reference does not use any
 631                                         // variant of this tile
 632                                         //
 633                                         // TODO: diff against the
 634                                         // relevant portion of the
 635                                         // ref's spanning tile
 636                                         outcol++
 637                                         continue
 638                                 }
 639                                 fmt.Fprintf(annow, "%d,%d,%d,=,%s,%d,,,\n", tag, outcol, rt.variant, rt.seqname, rt.pos)
 640                                 variants := seq[tag]
 641                                 reftilestr := strings.ToUpper(string(rt.tiledata))
 642
 643                                 done := make([]bool, maxv+1)
 644                                 variantDiffs := make([][]hgvs.Variant, maxv+1)
 645                                 for v, tv := range variants {
 646                                         v := remap[v]
 647                                         if v == 0 || v == rt.variant || done[v] {
 648                                                 continue
 649                                         } else {
 650                                                 done[v] = true
 651                                         }
 652                                         if len(tv.Sequence) < taglen {
 653                                                 continue
 654                                         }
 655                                         // if reftilestr doesn't end
 656                                         // in the same tag as tv,
 657                                         // extend reftilestr with
 658                                         // following ref tiles until
 659                                         // it does (up to an arbitrary
 660                                         // sanity-check limit)
 661                                         reftilestr := reftilestr
 662                                         endtagstr := strings.ToUpper(string(tv.Sequence[len(tv.Sequence)-taglen:]))
 663                                         for i, rt := 0, rt; i < annotationMaxTileSpan && !strings.HasSuffix(reftilestr, endtagstr) && rt.nexttag >= 0; i++ {
 664                                                 rt = reftile[rt.nexttag]
 665                                                 if rt == nil {
 666                                                         break
 667                                                 }
 668                                                 reftilestr += strings.ToUpper(string(rt.tiledata[taglen:]))
 669                                         }
 670                                         if mask != nil && !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(reftilestr)) {
 671                                                 continue
 672                                         }
 673                                         if !strings.HasSuffix(reftilestr, endtagstr) {
 674                                                 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
 675                                                 continue
 676                                         }
 677                                         if lendiff := len(reftilestr) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
 678                                                 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
 679                                                 continue
 680                                         }
 681                                         diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
 682                                         for i := range diffs {
 683                                                 diffs[i].Position += rt.pos
 684                                         }
 685                                         for _, diff := range diffs {
 686                                                 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)
 687                                         }
 688                                         if *hgvsChunked {
 689                                                 variantDiffs[v] = diffs
 690                                         }
 691                                 }
 692                                 if *hgvsChunked {
 693                                         // We can now determine, for each HGVS
 694                                         // variant (diff) in this reftile
 695                                         // region, whether a given genome
 696                                         // phase/allele (1) has the variant, (0) has
 697                                         // =ref or a different variant in that
 698                                         // position, or (-1) is lacking
 699                                         // coverage / couldn't be diffed.
 700                                         hgvsCol := hgvsColSet{}
 701                                         for _, diffs := range variantDiffs {
 702                                                 for _, diff := range diffs {
 703                                                         if _, ok := hgvsCol[diff]; ok {
 704                                                                 continue
 705                                                         }
 706                                                         hgvsCol[diff] = [2][]int8{
 707                                                                 make([]int8, len(cmd.cgnames)),
 708                                                                 make([]int8, len(cmd.cgnames)),
 709                                                         }
 710                                                 }
 711                                         }
 712                                         for row, name := range cmd.cgnames {
 713                                                 variants := cgs[name].Variants[(tag-tagstart)*2:]
 714                                                 for ph := 0; ph < 2; ph++ {
 715                                                         v := variants[ph]
 716                                                         if int(v) >= len(remap) {
 717                                                                 v = 0
 718                                                         } else {
 719                                                                 v = remap[v]
 720                                                         }
 721                                                         if v == rt.variant {
 722                                                                 // hgvsCol[*][ph][row] is already 0
 723                                                         } else if len(variantDiffs[v]) == 0 {
 724                                                                 // lacking coverage / couldn't be diffed
 725                                                                 for _, col := range hgvsCol {
 726                                                                         col[ph][row] = -1
 727                                                                 }
 728                                                         } else {
 729                                                                 for _, diff := range variantDiffs[v] {
 730                                                                         hgvsCol[diff][ph][row] = 1
 731                                                                 }
 732                                                         }
 733                                                 }
 734                                         }
 735                                         for diff, colpair := range hgvsCol {
 736                                                 allele2homhet(colpair)
 737                                                 if !cmd.filterHGVScolpair(colpair) {
 738                                                         delete(hgvsCol, diff)
 739                                                 }
 740                                         }
 741                                         if len(hgvsCol) > 0 {
 742                                                 encodeHGVSTodo[rt.seqname] <- hgvsCol
 743                                         }
 744                                 }
 745                                 outcol++
 746                         }
 747                         err = annow.Flush()
 748                         if err != nil {
 749                                 return err
 750                         }
 751                         err = annof.Close()
 752                         if err != nil {
 753                                 return err
 754                         }
 755
 756                         if *onehotChunked {
 757                                 // transpose onehotChunk[col][row] to numpy[row*ncols+col]
 758                                 rows := len(cmd.cgnames)
 759                                 cols := len(onehotChunk)
 760                                 log.Infof("%04d: preparing onehot numpy (rows=%d, cols=%d, mem=%d)", infileIdx, rows, cols, rows*cols)
 761                                 throttleNumpyMem.Acquire()
 762                                 out := onehotcols2int8(onehotChunk)
 763                                 fnm := fmt.Sprintf("%s/onehot.%04d.npy", *outputDir, infileIdx)
 764                                 err = writeNumpyInt8(fnm, out, rows, cols)
 765                                 if err != nil {
 766                                         return err
 767                                 }
 768                                 fnm = fmt.Sprintf("%s/onehot-columns.%04d.npy", *outputDir, infileIdx)
 769                                 err = writeNumpyInt32(fnm, onehotXref2int32(onehotXref), 4, len(onehotXref))
 770                                 if err != nil {
 771                                         return err
 772                                 }
 773                                 debug.FreeOSMemory()
 774                                 throttleNumpyMem.Release()
 775                         }
 776                         if *onehotSingle || *onlyPCA {
 777                                 onehotIndirect[infileIdx] = onehotChunk2Indirect(onehotChunk)
 778                                 onehotChunkSize[infileIdx] = uint32(len(onehotChunk))
 779                                 onehotXrefs[infileIdx] = onehotXref
 780                                 n := len(onehotIndirect[infileIdx][0])
 781                                 log.Infof("%04d: keeping onehot coordinates in memory (n=%d, mem=%d)", infileIdx, n, n*8*2)
 782                         }
 783                         if !(*onehotSingle || *onehotChunked || *onlyPCA) || *mergeOutput || *hgvsSingle {
 784                                 log.Infof("%04d: preparing numpy (rows=%d, cols=%d)", infileIdx, len(cmd.cgnames), 2*outcol)
 785                                 throttleNumpyMem.Acquire()
 786                                 rows := len(cmd.cgnames)
 787                                 cols := 2 * outcol
 788                                 out := make([]int16, rows*cols)
 789                                 for row, name := range cmd.cgnames {
 790                                         outidx := row * cols
 791                                         for col, v := range cgs[name].Variants {
 792                                                 tag := tagstart + tagID(col/2)
 793                                                 if cmd.filter.MaxTag >= 0 && tag > tagID(cmd.filter.MaxTag) {
 794                                                         break
 795                                                 }
 796                                                 if rt := reftile[tag]; rt == nil || rt.excluded {
 797                                                         continue
 798                                                 }
 799                                                 if v == 0 {
 800                                                         out[outidx] = 0 // tag not found / spanning tile
 801                                                 } else if variants, ok := seq[tag]; ok && int(v) < len(variants) && len(variants[v].Sequence) > 0 {
 802                                                         out[outidx] = int16(variantRemap[tag-tagstart][v])
 803                                                 } else {
 804                                                         out[outidx] = -1 // low quality tile variant
 805                                                 }
 806                                                 if tag == cmd.debugTag {
 807                                                         log.Printf("tag %d row %d col %d outidx %d v %d out %d", tag, row, col, outidx, v, out[outidx])
 808                                                 }
 809                                                 outidx++
 810                                         }
 811                                 }
 812                                 seq = nil
 813                                 cgs = nil
 814                                 debug.FreeOSMemory()
 815                                 throttleNumpyMem.Release()
 816                                 if *mergeOutput || *hgvsSingle {
 817                                         log.Infof("%04d: matrix fragment %d rows x %d cols", infileIdx, rows, cols)
 818                                         toMerge[infileIdx] = out
 819                                 }
 820                                 if !*mergeOutput && !*onehotChunked && !*onehotSingle {
 821                                         fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
 822                                         err = writeNumpyInt16(fnm, out, rows, cols)
 823                                         if err != nil {
 824                                                 return err
 825                                         }
 826                                 }
 827                         }
 828                         debug.FreeOSMemory()
 829                         log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
 830                         return nil
 831                 })
 832         }
 833         if err = throttleMem.Wait(); err != nil {
 834                 return err
 835         }
 836
 837         if *hgvsChunked {
 838                 log.Info("flushing hgvsCols temp files")
 839                 for seqname := range refseq {
 840                         close(encodeHGVSTodo[seqname])
 841                 }
 842                 err = encodeHGVS.Wait()
 843                 if err != nil {
 844                         return err
 845                 }
 846                 for seqname := range refseq {
 847                         log.Infof("%s: reading hgvsCols from temp file", seqname)
 848                         f := tmpHGVSCols[seqname]
 849                         _, err = f.Seek(0, io.SeekStart)
 850                         if err != nil {
 851                                 return err
 852                         }
 853                         var hgvsCols hgvsColSet
 854                         dec := gob.NewDecoder(bufio.NewReaderSize(f, 1<<24))
 855                         for err == nil {
 856                                 err = dec.Decode(&hgvsCols)
 857                         }
 858                         if err != io.EOF {
 859                                 return err
 860                         }
 861                         log.Infof("%s: sorting %d hgvs variants", seqname, len(hgvsCols))
 862                         variants := make([]hgvs.Variant, 0, len(hgvsCols))
 863                         for v := range hgvsCols {
 864                                 variants = append(variants, v)
 865                         }
 866                         sort.Slice(variants, func(i, j int) bool {
 867                                 vi, vj := &variants[i], &variants[j]
 868                                 if vi.Position != vj.Position {
 869                                         return vi.Position < vj.Position
 870                                 } else if vi.Ref != vj.Ref {
 871                                         return vi.Ref < vj.Ref
 872                                 } else {
 873                                         return vi.New < vj.New
 874                                 }
 875                         })
 876                         rows := len(cmd.cgnames)
 877                         cols := len(variants) * 2
 878                         log.Infof("%s: building hgvs matrix (rows=%d, cols=%d, mem=%d)", seqname, rows, cols, rows*cols)
 879                         out := make([]int8, rows*cols)
 880                         for varIdx, variant := range variants {
 881                                 hgvsCols := hgvsCols[variant]
 882                                 for row := range cmd.cgnames {
 883                                         for ph := 0; ph < 2; ph++ {
 884                                                 out[row*cols+varIdx+ph] = hgvsCols[ph][row]
 885                                         }
 886                                 }
 887                         }
 888                         err = writeNumpyInt8(fmt.Sprintf("%s/hgvs.%s.npy", *outputDir, seqname), out, rows, cols)
 889                         if err != nil {
 890                                 return err
 891                         }
 892                         out = nil
 893
 894                         fnm := fmt.Sprintf("%s/hgvs.%s.annotations.csv", *outputDir, seqname)
 895                         log.Infof("%s: writing hgvs column labels to %s", seqname, fnm)
 896                         var hgvsLabels bytes.Buffer
 897                         for varIdx, variant := range variants {
 898                                 fmt.Fprintf(&hgvsLabels, "%d,%s:g.%s\n", varIdx, seqname, variant.String())
 899                         }
 900                         err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0666)
 901                         if err != nil {
 902                                 return err
 903                         }
 904                 }
 905         }
 906
 907         if *mergeOutput || *hgvsSingle {
 908                 var annow *bufio.Writer
 909                 var annof *os.File
 910                 if *mergeOutput {
 911                         annoFilename := fmt.Sprintf("%s/matrix.annotations.csv", *outputDir)
 912                         annof, err = os.Create(annoFilename)
 913                         if err != nil {
 914                                 return err
 915                         }
 916                         annow = bufio.NewWriterSize(annof, 1<<20)
 917                 }
 918
 919                 rows := len(cmd.cgnames)
 920                 cols := 0
 921                 for _, chunk := range toMerge {
 922                         cols += len(chunk) / rows
 923                 }
 924                 log.Infof("merging output matrix (rows=%d, cols=%d, mem=%d) and annotations", rows, cols, rows*cols*2)
 925                 var out []int16
 926                 if *mergeOutput {
 927                         out = make([]int16, rows*cols)
 928                 }
 929                 hgvsCols := map[string][2][]int16{} // hgvs -> [[g0,g1,g2,...], [g0,g1,g2,...]] (slice of genomes for each phase)
 930                 startcol := 0
 931                 for outIdx, chunk := range toMerge {
 932                         chunkcols := len(chunk) / rows
 933                         if *mergeOutput {
 934                                 for row := 0; row < rows; row++ {
 935                                         copy(out[row*cols+startcol:], chunk[row*chunkcols:(row+1)*chunkcols])
 936                                 }
 937                         }
 938                         toMerge[outIdx] = nil
 939
 940                         annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, outIdx)
 941                         log.Infof("reading %s", annotationsFilename)
 942                         buf, err := os.ReadFile(annotationsFilename)
 943                         if err != nil {
 944                                 return err
 945                         }
 946                         if *mergeOutput {
 947                                 err = os.Remove(annotationsFilename)
 948                                 if err != nil {
 949                                         return err
 950                                 }
 951                         }
 952                         for _, line := range bytes.Split(buf, []byte{'\n'}) {
 953                                 if len(line) == 0 {
 954                                         continue
 955                                 }
 956                                 fields := bytes.SplitN(line, []byte{','}, 9)
 957                                 tag, _ := strconv.Atoi(string(fields[0]))
 958                                 incol, _ := strconv.Atoi(string(fields[1]))
 959                                 tileVariant, _ := strconv.Atoi(string(fields[2]))
 960                                 hgvsID := string(fields[3])
 961                                 seqname := string(fields[4])
 962                                 pos, _ := strconv.Atoi(string(fields[5]))
 963                                 refseq := fields[6]
 964                                 if hgvsID == "" {
 965                                         // Null entry for un-diffable
 966                                         // tile variant
 967                                         continue
 968                                 }
 969                                 if hgvsID == "=" {
 970                                         // Null entry for ref tile
 971                                         continue
 972                                 }
 973                                 if mask != nil && !mask.Check(strings.TrimPrefix(seqname, "chr"), pos, pos+len(refseq)) {
 974                                         // The tile intersects one of
 975                                         // the selected regions, but
 976                                         // this particular HGVS
 977                                         // variant does not.
 978                                         continue
 979                                 }
 980                                 hgvsColPair := hgvsCols[hgvsID]
 981                                 if hgvsColPair[0] == nil {
 982                                         // values in new columns start
 983                                         // out as -1 ("no data yet")
 984                                         // or 0 ("=ref") here, may
 985                                         // change to 1 ("hgvs variant
 986                                         // present") below, either on
 987                                         // this line or a future line.
 988                                         hgvsColPair = [2][]int16{make([]int16, len(cmd.cgnames)), make([]int16, len(cmd.cgnames))}
 989                                         rt, ok := reftile[tagID(tag)]
 990                                         if !ok {
 991                                                 err = fmt.Errorf("bug: seeing annotations for tag %d, but it has no reftile entry", tag)
 992                                                 return err
 993                                         }
 994                                         for ph := 0; ph < 2; ph++ {
 995                                                 for row := 0; row < rows; row++ {
 996                                                         v := chunk[row*chunkcols+incol*2+ph]
 997                                                         if tileVariantID(v) == rt.variant {
 998                                                                 hgvsColPair[ph][row] = 0
 999                                                         } else {
1000                                                                 hgvsColPair[ph][row] = -1
1001                                                         }
1002                                                 }
1003                                         }
1004                                         hgvsCols[hgvsID] = hgvsColPair
1005                                         if annow != nil {
1006                                                 hgvsref := hgvs.Variant{
1007                                                         Position: pos,
1008                                                         Ref:      string(refseq),
1009                                                         New:      string(refseq),
1010                                                 }
1011                                                 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])
1012                                         }
1013                                 }
1014                                 if annow != nil {
1015                                         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])
1016                                 }
1017                                 for ph := 0; ph < 2; ph++ {
1018                                         for row := 0; row < rows; row++ {
1019                                                 v := chunk[row*chunkcols+incol*2+ph]
1020                                                 if int(v) == tileVariant {
1021                                                         hgvsColPair[ph][row] = 1
1022                                                 }
1023                                         }
1024                                 }
1025                         }
1026
1027                         startcol += chunkcols
1028                 }
1029                 if *mergeOutput {
1030                         err = annow.Flush()
1031                         if err != nil {
1032                                 return err
1033                         }
1034                         err = annof.Close()
1035                         if err != nil {
1036                                 return err
1037                         }
1038                         err = writeNumpyInt16(fmt.Sprintf("%s/matrix.npy", *outputDir), out, rows, cols)
1039                         if err != nil {
1040                                 return err
1041                         }
1042                 }
1043                 out = nil
1044
1045                 if *hgvsSingle {
1046                         cols = len(hgvsCols) * 2
1047                         log.Printf("building hgvs-based matrix: %d rows x %d cols", rows, cols)
1048                         out = make([]int16, rows*cols)
1049                         hgvsIDs := make([]string, 0, cols/2)
1050                         for hgvsID := range hgvsCols {
1051                                 hgvsIDs = append(hgvsIDs, hgvsID)
1052                         }
1053                         sort.Strings(hgvsIDs)
1054                         var hgvsLabels bytes.Buffer
1055                         for idx, hgvsID := range hgvsIDs {
1056                                 fmt.Fprintf(&hgvsLabels, "%d,%s\n", idx, hgvsID)
1057                                 for ph := 0; ph < 2; ph++ {
1058                                         hgvscol := hgvsCols[hgvsID][ph]
1059                                         for row, val := range hgvscol {
1060                                                 out[row*cols+idx*2+ph] = val
1061                                         }
1062                                 }
1063                         }
1064                         err = writeNumpyInt16(fmt.Sprintf("%s/hgvs.npy", *outputDir), out, rows, cols)
1065                         if err != nil {
1066                                 return err
1067                         }
1068
1069                         fnm := fmt.Sprintf("%s/hgvs.annotations.csv", *outputDir)
1070                         log.Printf("writing hgvs labels: %s", fnm)
1071                         err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0777)
1072                         if err != nil {
1073                                 return err
1074                         }
1075                 }
1076         }
1077         if *onehotSingle || *onlyPCA {
1078                 nzCount := 0
1079                 for _, part := range onehotIndirect {
1080                         nzCount += len(part[0])
1081                 }
1082                 onehot := make([]uint32, nzCount*2) // [r,r,r,...,c,c,c,...]
1083                 var xrefs []onehotXref
1084                 chunkOffset := uint32(0)
1085                 outcol := 0
1086                 for i, part := range onehotIndirect {
1087                         for i := range part[1] {
1088                                 part[1][i] += chunkOffset
1089                         }
1090                         copy(onehot[outcol:], part[0])
1091                         copy(onehot[outcol+nzCount:], part[1])
1092                         xrefs = append(xrefs, onehotXrefs[i]...)
1093
1094                         outcol += len(part[0])
1095                         chunkOffset += onehotChunkSize[i]
1096
1097                         part[0] = nil
1098                         part[1] = nil
1099                         onehotXrefs[i] = nil
1100                         debug.FreeOSMemory()
1101                 }
1102                 if *onehotSingle {
1103                         fnm := fmt.Sprintf("%s/onehot.npy", *outputDir)
1104                         err = writeNumpyUint32(fnm, onehot, 2, nzCount)
1105                         if err != nil {
1106                                 return err
1107                         }
1108                         fnm = fmt.Sprintf("%s/onehot-columns.npy", *outputDir)
1109                         err = writeNumpyInt32(fnm, onehotXref2int32(xrefs), 5, len(xrefs))
1110                         if err != nil {
1111                                 return err
1112                         }
1113                 }
1114                 if *onlyPCA {
1115                         cols := 0
1116                         for _, c := range onehot[nzCount:] {
1117                                 if int(c) >= cols {
1118                                         cols = int(c) + 1
1119                                 }
1120                         }
1121                         if cols == 0 {
1122                                 return fmt.Errorf("cannot do PCA: one-hot matrix is empty")
1123                         }
1124                         log.Printf("have %d one-hot cols", cols)
1125                         stride := 1
1126                         for cols > *maxPCATiles*2 {
1127                                 cols = cols / 2
1128                                 stride = stride * 2
1129                         }
1130                         log.Printf("creating matrix: %d rows, %d cols, stride %d", len(cmd.cgnames), cols, stride)
1131                         mtx := mat.NewDense(len(cmd.cgnames), cols, nil)
1132                         for i, c := range onehot[nzCount:] {
1133                                 if int(c/2)%stride == 0 {
1134                                         mtx.Set(int(onehot[i]), int(c/2)/stride*2+int(c)%2, 1)
1135                                 }
1136                         }
1137                         log.Print("fitting")
1138                         transformer := nlp.NewPCA(*pcaComponents)
1139                         transformer.Fit(mtx.T())
1140                         log.Printf("transforming")
1141                         pca, err := transformer.Transform(mtx.T())
1142                         if err != nil {
1143                                 return err
1144                         }
1145                         pca = pca.T()
1146                         outrows, outcols := pca.Dims()
1147                         log.Printf("copying result to numpy output array: %d rows, %d cols", outrows, outcols)
1148                         out := make([]float64, outrows*outcols)
1149                         for i := 0; i < outrows; i++ {
1150                                 for j := 0; j < outcols; j++ {
1151                                         out[i*outcols+j] = pca.At(i, j)
1152                                 }
1153                         }
1154                         fnm := fmt.Sprintf("%s/pca.npy", *outputDir)
1155                         log.Printf("writing numpy: %s", fnm)
1156                         output, err := os.OpenFile(fnm, os.O_CREATE|os.O_TRUNC|os.O_WRONLY, 0777)
1157                         if err != nil {
1158                                 return err
1159                         }
1160                         npw, err := gonpy.NewWriter(nopCloser{output})
1161                         if err != nil {
1162                                 return fmt.Errorf("gonpy.NewWriter: %w", err)
1163                         }
1164                         npw.Shape = []int{outrows, outcols}
1165                         err = npw.WriteFloat64(out)
1166                         if err != nil {
1167                                 return fmt.Errorf("WriteFloat64: %w", err)
1168                         }
1169                         err = output.Close()
1170                         if err != nil {
1171                                 return err
1172                         }
1173                         log.Print("done")
1174                 }
1175         }
1176         if !*mergeOutput && !*onehotChunked && !*onehotSingle && !*onlyPCA {
1177                 tagoffsetFilename := *outputDir + "/chunk-tag-offset.csv"
1178                 log.Infof("writing tag offsets to %s", tagoffsetFilename)
1179                 var f *os.File
1180                 f, err = os.Create(tagoffsetFilename)
1181                 if err != nil {
1182                         return err
1183                 }
1184                 defer f.Close()
1185                 for idx, offset := range chunkStartTag {
1186                         _, err = fmt.Fprintf(f, "%q,%d\n", fmt.Sprintf("matrix.%04d.npy", idx), offset)
1187                         if err != nil {
1188                                 err = fmt.Errorf("write %s: %w", tagoffsetFilename, err)
1189                                 return err
1190                         }
1191                 }
1192                 err = f.Close()
1193                 if err != nil {
1194                         err = fmt.Errorf("close %s: %w", tagoffsetFilename, err)
1195                         return err
1196                 }
1197         }
1198         return nil
1199 }
1200
1201 // Read case/control files, remove non-case/control entries from
1202 // cmd.cgnames, and build cmd.chi2Cases.
1203 func (cmd *sliceNumpy) useCaseControlFiles() error {
1204         if cmd.chi2CaseControlFile == "" {
1205                 return nil
1206         }
1207         infiles, err := allFiles(cmd.chi2CaseControlFile, nil)
1208         if err != nil {
1209                 return err
1210         }
1211         // index in cmd.cgnames => case(true) / control(false)
1212         cc := map[int]bool{}
1213         for _, infile := range infiles {
1214                 f, err := open(infile)
1215                 if err != nil {
1216                         return err
1217                 }
1218                 buf, err := io.ReadAll(f)
1219                 f.Close()
1220                 if err != nil {
1221                         return err
1222                 }
1223                 ccCol := -1
1224                 for _, tsv := range bytes.Split(buf, []byte{'\n'}) {
1225                         if len(tsv) == 0 {
1226                                 continue
1227                         }
1228                         split := strings.Split(string(tsv), "\t")
1229                         if ccCol < 0 {
1230                                 // header row
1231                                 for col, name := range split {
1232                                         if name == cmd.chi2CaseControlColumn {
1233                                                 ccCol = col
1234                                                 break
1235                                         }
1236                                 }
1237                                 if ccCol < 0 {
1238                                         return fmt.Errorf("%s: no column named %q in header row %q", infile, cmd.chi2CaseControlColumn, tsv)
1239                                 }
1240                                 continue
1241                         }
1242                         if len(split) <= ccCol {
1243                                 continue
1244                         }
1245                         pattern := split[0]
1246                         found := -1
1247                         for i, name := range cmd.cgnames {
1248                                 if strings.Contains(name, pattern) {
1249                                         if found >= 0 {
1250                                                 log.Warnf("pattern %q in %s matches multiple genome IDs (%qs, %q)", pattern, infile, cmd.cgnames[found], name)
1251                                         }
1252                                         found = i
1253                                 }
1254                         }
1255                         if found < 0 {
1256                                 log.Warnf("pattern %q in %s does not match any genome IDs", pattern, infile)
1257                                 continue
1258                         }
1259                         if split[ccCol] == "0" {
1260                                 cc[found] = false
1261                         }
1262                         if split[ccCol] == "1" {
1263                                 cc[found] = true
1264                         }
1265                 }
1266         }
1267         allnames := cmd.cgnames
1268         cmd.cgnames = nil
1269         cmd.chi2Cases = nil
1270         ncases := 0
1271         for i, name := range allnames {
1272                 if cc, ok := cc[i]; ok {
1273                         cmd.cgnames = append(cmd.cgnames, name)
1274                         cmd.chi2Cases = append(cmd.chi2Cases, cc)
1275                         if cc {
1276                                 ncases++
1277                         }
1278                 }
1279         }
1280         log.Printf("%d cases, %d controls, %d neither (dropped)", ncases, len(cmd.cgnames)-ncases, len(allnames)-len(cmd.cgnames))
1281         return nil
1282 }
1283
1284 func (cmd *sliceNumpy) filterHGVScolpair(colpair [2][]int8) bool {
1285         if cmd.chi2PValue >= 1 {
1286                 return true
1287         }
1288         col0 := make([]bool, 0, len(cmd.chi2Cases))
1289         col1 := make([]bool, 0, len(cmd.chi2Cases))
1290         cases := make([]bool, 0, len(cmd.chi2Cases))
1291         for i, c := range cmd.chi2Cases {
1292                 if colpair[0][i] < 0 {
1293                         continue
1294                 }
1295                 col0 = append(col0, colpair[0][i] != 0)
1296                 col1 = append(col1, colpair[1][i] != 0)
1297                 cases = append(cases, c)
1298         }
1299         return len(cases) >= cmd.minCoverage &&
1300                 (pvalue(col0, cases) <= cmd.chi2PValue || pvalue(col1, cases) <= cmd.chi2PValue)
1301 }
1302
1303 func writeNumpyUint32(fnm string, out []uint32, rows, cols int) error {
1304         output, err := os.Create(fnm)
1305         if err != nil {
1306                 return err
1307         }
1308         defer output.Close()
1309         bufw := bufio.NewWriterSize(output, 1<<26)
1310         npw, err := gonpy.NewWriter(nopCloser{bufw})
1311         if err != nil {
1312                 return err
1313         }
1314         log.WithFields(log.Fields{
1315                 "filename": fnm,
1316                 "rows":     rows,
1317                 "cols":     cols,
1318                 "bytes":    rows * cols * 4,
1319         }).Infof("writing numpy: %s", fnm)
1320         npw.Shape = []int{rows, cols}
1321         npw.WriteUint32(out)
1322         err = bufw.Flush()
1323         if err != nil {
1324                 return err
1325         }
1326         return output.Close()
1327 }
1328
1329 func writeNumpyInt32(fnm string, out []int32, rows, cols int) error {
1330         output, err := os.Create(fnm)
1331         if err != nil {
1332                 return err
1333         }
1334         defer output.Close()
1335         bufw := bufio.NewWriterSize(output, 1<<26)
1336         npw, err := gonpy.NewWriter(nopCloser{bufw})
1337         if err != nil {
1338                 return err
1339         }
1340         log.WithFields(log.Fields{
1341                 "filename": fnm,
1342                 "rows":     rows,
1343                 "cols":     cols,
1344                 "bytes":    rows * cols * 4,
1345         }).Infof("writing numpy: %s", fnm)
1346         npw.Shape = []int{rows, cols}
1347         npw.WriteInt32(out)
1348         err = bufw.Flush()
1349         if err != nil {
1350                 return err
1351         }
1352         return output.Close()
1353 }
1354
1355 func writeNumpyInt16(fnm string, out []int16, rows, cols int) error {
1356         output, err := os.Create(fnm)
1357         if err != nil {
1358                 return err
1359         }
1360         defer output.Close()
1361         bufw := bufio.NewWriterSize(output, 1<<26)
1362         npw, err := gonpy.NewWriter(nopCloser{bufw})
1363         if err != nil {
1364                 return err
1365         }
1366         log.WithFields(log.Fields{
1367                 "filename": fnm,
1368                 "rows":     rows,
1369                 "cols":     cols,
1370                 "bytes":    rows * cols * 2,
1371         }).Infof("writing numpy: %s", fnm)
1372         npw.Shape = []int{rows, cols}
1373         npw.WriteInt16(out)
1374         err = bufw.Flush()
1375         if err != nil {
1376                 return err
1377         }
1378         return output.Close()
1379 }
1380
1381 func writeNumpyInt8(fnm string, out []int8, rows, cols int) error {
1382         output, err := os.Create(fnm)
1383         if err != nil {
1384                 return err
1385         }
1386         defer output.Close()
1387         bufw := bufio.NewWriterSize(output, 1<<26)
1388         npw, err := gonpy.NewWriter(nopCloser{bufw})
1389         if err != nil {
1390                 return err
1391         }
1392         log.WithFields(log.Fields{
1393                 "filename": fnm,
1394                 "rows":     rows,
1395                 "cols":     cols,
1396                 "bytes":    rows * cols,
1397         }).Infof("writing numpy: %s", fnm)
1398         npw.Shape = []int{rows, cols}
1399         npw.WriteInt8(out)
1400         err = bufw.Flush()
1401         if err != nil {
1402                 return err
1403         }
1404         return output.Close()
1405 }
1406
1407 func allele2homhet(colpair [2][]int8) {
1408         a, b := colpair[0], colpair[1]
1409         for i, av := range a {
1410                 bv := b[i]
1411                 if av < 0 || bv < 0 {
1412                         // no-call
1413                         a[i], b[i] = -1, -1
1414                 } else if av > 0 && bv > 0 {
1415                         // hom
1416                         a[i], b[i] = 1, 0
1417                 } else if av > 0 || bv > 0 {
1418                         // het
1419                         a[i], b[i] = 0, 1
1420                 } else {
1421                         // ref (or a different variant in same position)
1422                         // (this is a no-op) a[i], b[i] = 0, 0
1423                 }
1424         }
1425 }
1426
1427 type onehotXref struct {
1428         tag     tagID
1429         variant tileVariantID
1430         hom     bool
1431         pvalue  float64
1432 }
1433
1434 const onehotXrefSize = unsafe.Sizeof(onehotXref{})
1435
1436 // Build onehot matrix (m[tileVariantIndex][genome] == 0 or 1) for all
1437 // variants of a single tile/tag#.
1438 //
1439 // Return nil if no tile variant passes Χ² filter.
1440 func (cmd *sliceNumpy) tv2homhet(cgs map[string]CompactGenome, maxv tileVariantID, remap []tileVariantID, tag, chunkstarttag tagID, seq map[tagID][]TileVariant) ([][]int8, []onehotXref) {
1441         if tag == cmd.debugTag {
1442                 tv := make([]tileVariantID, len(cmd.cgnames)*2)
1443                 for i, name := range cmd.cgnames {
1444                         copy(tv[i*2:(i+1)*2], cgs[name].Variants[(tag-chunkstarttag)*2:])
1445                 }
1446                 log.WithFields(logrus.Fields{
1447                         "cgs[i].Variants[tag*2+j]": tv,
1448                         "maxv":                     maxv,
1449                         "remap":                    remap,
1450                         "tag":                      tag,
1451                         "chunkstarttag":            chunkstarttag,
1452                 }).Info("tv2homhet()")
1453         }
1454         if maxv < 1 || (maxv < 2 && !cmd.includeVariant1) {
1455                 // everyone has the most common variant (of the variants we don't drop)
1456                 return nil, nil
1457         }
1458         tagoffset := tag - chunkstarttag
1459         coverage := 0
1460         for _, cg := range cgs {
1461                 alleles := 0
1462                 for _, v := range cg.Variants[tagoffset*2 : tagoffset*2+2] {
1463                         if v > 0 && int(v) < len(seq[tag]) && len(seq[tag][v].Sequence) > 0 {
1464                                 alleles++
1465                         }
1466                 }
1467                 if alleles == 2 {
1468                         coverage++
1469                 }
1470         }
1471         if coverage < cmd.minCoverage {
1472                 return nil, nil
1473         }
1474         obs := make([][]bool, (maxv+1)*2) // 2 slices (hom + het) for each variant#
1475         for i := range obs {
1476                 obs[i] = make([]bool, len(cmd.cgnames))
1477         }
1478         for cgid, name := range cmd.cgnames {
1479                 cgvars := cgs[name].Variants[tagoffset*2:]
1480                 tv0, tv1 := remap[cgvars[0]], remap[cgvars[1]]
1481                 for v := tileVariantID(1); v <= maxv; v++ {
1482                         if tv0 == v && tv1 == v {
1483                                 obs[v*2][cgid] = true
1484                         } else if tv0 == v || tv1 == v {
1485                                 obs[v*2+1][cgid] = true
1486                         }
1487                 }
1488         }
1489         var onehot [][]int8
1490         var xref []onehotXref
1491         for col := 2; col < len(obs); col++ {
1492                 // col 0,1 correspond to tile variant 0, i.e.,
1493                 // no-call; col 2,3 correspond to the most common
1494                 // variant; so we (normally) start at col 4.
1495                 if col < 4 && !cmd.includeVariant1 {
1496                         continue
1497                 }
1498                 p := pvalue(obs[col], cmd.chi2Cases)
1499                 if cmd.chi2PValue < 1 && !(p < cmd.chi2PValue) {
1500                         continue
1501                 }
1502                 onehot = append(onehot, bool2int8(obs[col]))
1503                 xref = append(xref, onehotXref{
1504                         tag:     tag,
1505                         variant: tileVariantID(col >> 1),
1506                         hom:     col&1 == 0,
1507                         pvalue:  p,
1508                 })
1509         }
1510         return onehot, xref
1511 }
1512
1513 func bool2int8(in []bool) []int8 {
1514         out := make([]int8, len(in))
1515         for i, v := range in {
1516                 if v {
1517                         out[i] = 1
1518                 }
1519         }
1520         return out
1521 }
1522
1523 // convert a []onehotXref with length N to a numpy-style []int32
1524 // matrix with N columns, one row per field of onehotXref struct.
1525 //
1526 // Hom/het row contains hom=0, het=1.
1527 //
1528 // P-value row contains 1000000x actual p-value.
1529 func onehotXref2int32(xrefs []onehotXref) []int32 {
1530         xcols := len(xrefs)
1531         xdata := make([]int32, 5*xcols)
1532         for i, xref := range xrefs {
1533                 xdata[i] = int32(xref.tag)
1534                 xdata[xcols+i] = int32(xref.variant)
1535                 if xref.hom {
1536                         xdata[xcols*2+i] = 1
1537                 }
1538                 xdata[xcols*3+i] = int32(xref.pvalue * 1000000)
1539                 xdata[xcols*4+i] = int32(-math.Log10(xref.pvalue) * 1000000)
1540         }
1541         return xdata
1542 }
1543
1544 // transpose onehot data from in[col][row] to numpy-style
1545 // out[row*cols+col].
1546 func onehotcols2int8(in [][]int8) []int8 {
1547         if len(in) == 0 {
1548                 return nil
1549         }
1550         cols := len(in)
1551         rows := len(in[0])
1552         out := make([]int8, rows*cols)
1553         for row := 0; row < rows; row++ {
1554                 outrow := out[row*cols:]
1555                 for col, incol := range in {
1556                         outrow[col] = incol[row]
1557                 }
1558         }
1559         return out
1560 }
1561
1562 // Return [2][]uint32{rowIndices, colIndices} indicating which
1563 // elements of matrixT[c][r] have non-zero values.
1564 func onehotChunk2Indirect(matrixT [][]int8) [2][]uint32 {
1565         var nz [2][]uint32
1566         for c, col := range matrixT {
1567                 for r, val := range col {
1568                         if val != 0 {
1569                                 nz[0] = append(nz[0], uint32(r))
1570                                 nz[1] = append(nz[1], uint32(c))
1571                         }
1572                 }
1573         }
1574         return nz
1575 }