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", 0, "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                         "-max-pca-tiles=" + fmt.Sprintf("%d", *maxPCATiles),
 140                         "-chi2-case-control-file=" + cmd.chi2CaseControlFile,
 141                         "-chi2-case-control-column=" + cmd.chi2CaseControlColumn,
 142                         "-chi2-p-value=" + fmt.Sprintf("%f", cmd.chi2PValue),
 143                         "-include-variant-1=" + fmt.Sprintf("%v", cmd.includeVariant1),
 144                         "-debug-tag=" + fmt.Sprintf("%d", cmd.debugTag),
 145                 }
 146                 runner.Args = append(runner.Args, cmd.filter.Args()...)
 147                 var output string
 148                 output, err = runner.Run()
 149                 if err != nil {
 150                         return err
 151                 }
 152                 fmt.Fprintln(stdout, output)
 153                 return nil
 154         }
 155
 156         infiles, err := allFiles(*inputDir, matchGobFile)
 157         if err != nil {
 158                 return err
 159         }
 160         if len(infiles) == 0 {
 161                 err = fmt.Errorf("no input files found in %s", *inputDir)
 162                 return err
 163         }
 164         sort.Strings(infiles)
 165
 166         var refseq map[string][]tileLibRef
 167         var reftiledata = make(map[tileLibRef][]byte, 11000000)
 168         in0, err := open(infiles[0])
 169         if err != nil {
 170                 return err
 171         }
 172
 173         matchGenome, err := regexp.Compile(cmd.filter.MatchGenome)
 174         if err != nil {
 175                 err = fmt.Errorf("-match-genome: invalid regexp: %q", cmd.filter.MatchGenome)
 176                 return err
 177         }
 178
 179         cmd.cgnames = nil
 180         var tagset [][]byte
 181         err = DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
 182                 if len(ent.TagSet) > 0 {
 183                         tagset = ent.TagSet
 184                 }
 185                 for _, cseq := range ent.CompactSequences {
 186                         if cseq.Name == *ref || *ref == "" {
 187                                 refseq = cseq.TileSequences
 188                         }
 189                 }
 190                 for _, cg := range ent.CompactGenomes {
 191                         if matchGenome.MatchString(cg.Name) {
 192                                 cmd.cgnames = append(cmd.cgnames, cg.Name)
 193                         }
 194                 }
 195                 for _, tv := range ent.TileVariants {
 196                         if tv.Ref {
 197                                 reftiledata[tileLibRef{tv.Tag, tv.Variant}] = tv.Sequence
 198                         }
 199                 }
 200                 return nil
 201         })
 202         if err != nil {
 203                 return err
 204         }
 205         in0.Close()
 206         if refseq == nil {
 207                 err = fmt.Errorf("%s: reference sequence not found", infiles[0])
 208                 return err
 209         }
 210         if len(tagset) == 0 {
 211                 err = fmt.Errorf("tagset not found")
 212                 return err
 213         }
 214
 215         taglib := &tagLibrary{}
 216         err = taglib.setTags(tagset)
 217         if err != nil {
 218                 return err
 219         }
 220         taglen := taglib.TagLen()
 221
 222         if len(cmd.cgnames) == 0 {
 223                 err = fmt.Errorf("no genomes found matching regexp %q", cmd.filter.MatchGenome)
 224                 return err
 225         }
 226         sort.Strings(cmd.cgnames)
 227         err = cmd.useCaseControlFiles()
 228         if err != nil {
 229                 return err
 230         }
 231         if len(cmd.cgnames) == 0 {
 232                 err = fmt.Errorf("fatal: 0 cases, 0 controls, nothing to do")
 233                 return err
 234         }
 235         if cmd.filter.MinCoverage == 1 {
 236                 // In the generic formula below, floating point
 237                 // arithmetic can effectively push the coverage
 238                 // threshold above 1.0, which is impossible/useless.
 239                 // 1.0 needs to mean exactly 100% coverage.
 240                 cmd.minCoverage = len(cmd.cgnames)
 241         } else {
 242                 cmd.minCoverage = int(math.Ceil(cmd.filter.MinCoverage * float64(len(cmd.cgnames))))
 243         }
 244
 245         {
 246                 labelsFilename := *outputDir + "/samples.csv"
 247                 log.Infof("writing labels to %s", labelsFilename)
 248                 var f *os.File
 249                 f, err = os.Create(labelsFilename)
 250                 if err != nil {
 251                         return err
 252                 }
 253                 defer f.Close()
 254                 for i, name := range cmd.cgnames {
 255                         cc := 0
 256                         if cmd.chi2Cases != nil && cmd.chi2Cases[i] {
 257                                 cc = 1
 258                         }
 259                         _, err = fmt.Fprintf(f, "%d,%q,%d\n", i, trimFilenameForLabel(name), cc)
 260                         if err != nil {
 261                                 err = fmt.Errorf("write %s: %w", labelsFilename, err)
 262                                 return err
 263                         }
 264                 }
 265                 err = f.Close()
 266                 if err != nil {
 267                         err = fmt.Errorf("close %s: %w", labelsFilename, err)
 268                         return err
 269                 }
 270         }
 271
 272         log.Info("indexing reference tiles")
 273         type reftileinfo struct {
 274                 variant  tileVariantID
 275                 seqname  string // chr1
 276                 pos      int    // distance from start of chromosome to starttag
 277                 tiledata []byte // acgtggcaa...
 278                 excluded bool   // true if excluded by regions file
 279                 nexttag  tagID  // tagID of following tile (-1 for last tag of chromosome)
 280         }
 281         isdup := map[tagID]bool{}
 282         reftile := map[tagID]*reftileinfo{}
 283         for seqname, cseq := range refseq {
 284                 pos := 0
 285                 lastreftag := tagID(-1)
 286                 for _, libref := range cseq {
 287                         if cmd.filter.MaxTag >= 0 && libref.Tag > tagID(cmd.filter.MaxTag) {
 288                                 continue
 289                         }
 290                         tiledata := reftiledata[libref]
 291                         if len(tiledata) == 0 {
 292                                 err = fmt.Errorf("missing tiledata for tag %d variant %d in %s in ref", libref.Tag, libref.Variant, seqname)
 293                                 return err
 294                         }
 295                         foundthistag := false
 296                         taglib.FindAll(tiledata[:len(tiledata)-1], func(tagid tagID, offset, _ int) {
 297                                 if !foundthistag && tagid == libref.Tag {
 298                                         foundthistag = true
 299                                         return
 300                                 }
 301                                 if dupref, ok := reftile[tagid]; ok {
 302                                         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)
 303                                         delete(reftile, tagid)
 304                                 } else {
 305                                         log.Printf("found tag %d at offset %d inside tile variant %+v on %s @ %d", tagid, offset, libref, seqname, pos+offset+1)
 306                                 }
 307                                 isdup[tagid] = true
 308                         })
 309                         if isdup[libref.Tag] {
 310                                 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
 311                         } else if reftile[libref.Tag] != nil {
 312                                 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)
 313                                 delete(reftile, libref.Tag)
 314                                 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
 315                                 isdup[libref.Tag] = true
 316                         } else {
 317                                 reftile[libref.Tag] = &reftileinfo{
 318                                         seqname:  seqname,
 319                                         variant:  libref.Variant,
 320                                         tiledata: tiledata,
 321                                         pos:      pos,
 322                                         nexttag:  -1,
 323                                 }
 324                                 if lastreftag >= 0 {
 325                                         reftile[lastreftag].nexttag = libref.Tag
 326                                 }
 327                                 lastreftag = libref.Tag
 328                         }
 329                         pos += len(tiledata) - taglen
 330                 }
 331                 log.Printf("... %s done, len %d", seqname, pos+taglen)
 332         }
 333
 334         var mask *mask
 335         if *regionsFilename != "" {
 336                 log.Printf("loading regions from %s", *regionsFilename)
 337                 mask, err = makeMask(*regionsFilename, *expandRegions)
 338                 if err != nil {
 339                         return err
 340                 }
 341                 log.Printf("before applying mask, len(reftile) == %d", len(reftile))
 342                 log.Printf("deleting reftile entries for regions outside %d intervals", mask.Len())
 343                 for _, rt := range reftile {
 344                         if !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(rt.tiledata)) {
 345                                 rt.excluded = true
 346                         }
 347                 }
 348                 log.Printf("after applying mask, len(reftile) == %d", len(reftile))
 349         }
 350
 351         type hgvsColSet map[hgvs.Variant][2][]int8
 352         encodeHGVS := throttle{Max: len(refseq)}
 353         encodeHGVSTodo := map[string]chan hgvsColSet{}
 354         tmpHGVSCols := map[string]*os.File{}
 355         if *hgvsChunked {
 356                 for seqname := range refseq {
 357                         var f *os.File
 358                         f, err = os.Create(*outputDir + "/tmp." + seqname + ".gob")
 359                         if err != nil {
 360                                 return err
 361                         }
 362                         defer os.Remove(f.Name())
 363                         bufw := bufio.NewWriterSize(f, 1<<24)
 364                         enc := gob.NewEncoder(bufw)
 365                         tmpHGVSCols[seqname] = f
 366                         todo := make(chan hgvsColSet, 128)
 367                         encodeHGVSTodo[seqname] = todo
 368                         encodeHGVS.Go(func() error {
 369                                 for colset := range todo {
 370                                         err := enc.Encode(colset)
 371                                         if err != nil {
 372                                                 encodeHGVS.Report(err)
 373                                                 for range todo {
 374                                                 }
 375                                                 return err
 376                                         }
 377                                 }
 378                                 return bufw.Flush()
 379                         })
 380                 }
 381         }
 382
 383         var toMerge [][]int16
 384         if *mergeOutput || *hgvsSingle {
 385                 toMerge = make([][]int16, len(infiles))
 386         }
 387         var onehotIndirect [][2][]uint32 // [chunkIndex][axis][index]
 388         var onehotChunkSize []uint32
 389         var onehotXrefs [][]onehotXref
 390         if *onehotSingle || *onlyPCA {
 391                 onehotIndirect = make([][2][]uint32, len(infiles))
 392                 onehotChunkSize = make([]uint32, len(infiles))
 393                 onehotXrefs = make([][]onehotXref, len(infiles))
 394         }
 395         chunkStartTag := make([]tagID, len(infiles))
 396
 397         throttleMem := throttle{Max: cmd.threads} // TODO: estimate using mem and data size
 398         throttleNumpyMem := throttle{Max: cmd.threads/2 + 1}
 399         log.Info("generating annotations and numpy matrix for each slice")
 400         var errSkip = errors.New("skip infile")
 401         var done int64
 402         for infileIdx, infile := range infiles {
 403                 infileIdx, infile := infileIdx, infile
 404                 throttleMem.Go(func() error {
 405                         seq := make(map[tagID][]TileVariant, 50000)
 406                         cgs := make(map[string]CompactGenome, len(cmd.cgnames))
 407                         f, err := open(infile)
 408                         if err != nil {
 409                                 return err
 410                         }
 411                         defer f.Close()
 412                         log.Infof("%04d: reading %s", infileIdx, infile)
 413                         err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
 414                                 for _, tv := range ent.TileVariants {
 415                                         if tv.Ref {
 416                                                 continue
 417                                         }
 418                                         // Skip tile with no
 419                                         // corresponding ref tile, if
 420                                         // mask is in play (we can't
 421                                         // determine coordinates for
 422                                         // these)
 423                                         if mask != nil && reftile[tv.Tag] == nil {
 424                                                 continue
 425                                         }
 426                                         // Skip tile whose
 427                                         // corresponding ref tile is
 428                                         // outside target regions --
 429                                         // unless it's a potential
 430                                         // spanning tile.
 431                                         if mask != nil && reftile[tv.Tag].excluded &&
 432                                                 (int(tv.Tag+1) >= len(tagset) ||
 433                                                         (bytes.HasSuffix(tv.Sequence, tagset[tv.Tag+1]) && reftile[tv.Tag+1] != nil && !reftile[tv.Tag+1].excluded)) {
 434                                                 continue
 435                                         }
 436                                         if tv.Tag == cmd.debugTag {
 437                                                 log.Printf("infile %d %s tag %d variant %d hash %x", infileIdx, infile, tv.Tag, tv.Variant, tv.Blake2b[:3])
 438                                         }
 439                                         variants := seq[tv.Tag]
 440                                         if len(variants) == 0 {
 441                                                 variants = make([]TileVariant, 100)
 442                                         }
 443                                         for len(variants) <= int(tv.Variant) {
 444                                                 variants = append(variants, TileVariant{})
 445                                         }
 446                                         variants[int(tv.Variant)] = tv
 447                                         seq[tv.Tag] = variants
 448                                 }
 449                                 for _, cg := range ent.CompactGenomes {
 450                                         if cmd.filter.MaxTag >= 0 && cg.StartTag > tagID(cmd.filter.MaxTag) {
 451                                                 return errSkip
 452                                         }
 453                                         if !matchGenome.MatchString(cg.Name) {
 454                                                 continue
 455                                         }
 456                                         // pad to full slice size
 457                                         // to avoid out-of-bounds
 458                                         // checks later
 459                                         if sliceSize := 2 * int(cg.EndTag-cg.StartTag); len(cg.Variants) < sliceSize {
 460                                                 cg.Variants = append(cg.Variants, make([]tileVariantID, sliceSize-len(cg.Variants))...)
 461                                         }
 462                                         cgs[cg.Name] = cg
 463                                 }
 464                                 return nil
 465                         })
 466                         if err == errSkip {
 467                                 return nil
 468                         } else if err != nil {
 469                                 return fmt.Errorf("%04d: DecodeLibrary(%s): err", infileIdx, infile)
 470                         }
 471                         tagstart := cgs[cmd.cgnames[0]].StartTag
 472                         tagend := cgs[cmd.cgnames[0]].EndTag
 473                         chunkStartTag[infileIdx] = tagstart
 474
 475                         // TODO: filters
 476
 477                         log.Infof("%04d: renumber/dedup variants for tags %d-%d", infileIdx, tagstart, tagend)
 478                         variantRemap := make([][]tileVariantID, tagend-tagstart)
 479                         throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
 480                         for tag, variants := range seq {
 481                                 tag, variants := tag, variants
 482                                 throttleCPU.Go(func() error {
 483                                         alleleCoverage := 0
 484                                         count := make(map[[blake2b.Size256]byte]int, len(variants))
 485
 486                                         rt := reftile[tag]
 487                                         if rt != nil {
 488                                                 count[blake2b.Sum256(rt.tiledata)] = 0
 489                                         }
 490
 491                                         for cgname, cg := range cgs {
 492                                                 idx := int(tag-tagstart) * 2
 493                                                 for allele := 0; allele < 2; allele++ {
 494                                                         v := cg.Variants[idx+allele]
 495                                                         if v > 0 && len(variants[v].Sequence) > 0 {
 496                                                                 count[variants[v].Blake2b]++
 497                                                                 alleleCoverage++
 498                                                         }
 499                                                         if v > 0 && tag == cmd.debugTag {
 500                                                                 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])
 501                                                         }
 502                                                 }
 503                                         }
 504                                         if alleleCoverage < cmd.minCoverage*2 {
 505                                                 idx := int(tag-tagstart) * 2
 506                                                 for _, cg := range cgs {
 507                                                         cg.Variants[idx] = 0
 508                                                         cg.Variants[idx+1] = 0
 509                                                 }
 510                                                 if tag == cmd.debugTag {
 511                                                         log.Printf("tag %d alleleCoverage %d < min %d, sample data wiped", tag, alleleCoverage, cmd.minCoverage*2)
 512                                                 }
 513                                                 return nil
 514                                         }
 515
 516                                         // hash[i] will be the hash of
 517                                         // the variant(s) that should
 518                                         // be at rank i (0-based).
 519                                         hash := make([][blake2b.Size256]byte, 0, len(count))
 520                                         for b := range count {
 521                                                 hash = append(hash, b)
 522                                         }
 523                                         sort.Slice(hash, func(i, j int) bool {
 524                                                 bi, bj := &hash[i], &hash[j]
 525                                                 if ci, cj := count[*bi], count[*bj]; ci != cj {
 526                                                         return ci > cj
 527                                                 } else {
 528                                                         return bytes.Compare((*bi)[:], (*bj)[:]) < 0
 529                                                 }
 530                                         })
 531                                         // rank[b] will be the 1-based
 532                                         // new variant number for
 533                                         // variants whose hash is b.
 534                                         rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
 535                                         for i, h := range hash {
 536                                                 rank[h] = tileVariantID(i + 1)
 537                                         }
 538                                         if tag == cmd.debugTag {
 539                                                 for h, r := range rank {
 540                                                         log.Printf("tag %d rank(%x) = %v", tag, h[:3], r)
 541                                                 }
 542                                         }
 543                                         // remap[v] will be the new
 544                                         // variant number for original
 545                                         // variant number v.
 546                                         remap := make([]tileVariantID, len(variants))
 547                                         for i, tv := range variants {
 548                                                 remap[i] = rank[tv.Blake2b]
 549                                         }
 550                                         if tag == cmd.debugTag {
 551                                                 for in, out := range remap {
 552                                                         if out > 0 {
 553                                                                 log.Printf("tag %d remap %d => %d", tag, in, out)
 554                                                         }
 555                                                 }
 556                                         }
 557                                         variantRemap[tag-tagstart] = remap
 558                                         if rt != nil {
 559                                                 refrank := rank[blake2b.Sum256(rt.tiledata)]
 560                                                 if tag == cmd.debugTag {
 561                                                         log.Printf("tag %d reftile variant %d => %d", tag, rt.variant, refrank)
 562                                                 }
 563                                                 rt.variant = refrank
 564                                         }
 565                                         return nil
 566                                 })
 567                         }
 568                         throttleCPU.Wait()
 569
 570                         var onehotChunk [][]int8
 571                         var onehotXref []onehotXref
 572
 573                         var annotationsFilename string
 574                         if *onlyPCA {
 575                                 annotationsFilename = "/dev/null"
 576                         } else {
 577                                 annotationsFilename = fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
 578                                 log.Infof("%04d: writing %s", infileIdx, annotationsFilename)
 579                         }
 580                         annof, err := os.Create(annotationsFilename)
 581                         if err != nil {
 582                                 return err
 583                         }
 584                         annow := bufio.NewWriterSize(annof, 1<<20)
 585                         outcol := 0
 586                         for tag := tagstart; tag < tagend; tag++ {
 587                                 rt := reftile[tag]
 588                                 if rt == nil && mask != nil {
 589                                         // With no ref tile, we don't
 590                                         // have coordinates to say
 591                                         // this is in the desired
 592                                         // regions -- so it's not.
 593                                         // TODO: handle ref spanning
 594                                         // tile case.
 595                                         continue
 596                                 }
 597                                 if rt != nil && rt.excluded {
 598                                         // TODO: don't skip yet --
 599                                         // first check for spanning
 600                                         // tile variants that
 601                                         // intersect non-excluded ref
 602                                         // tiles.
 603                                         continue
 604                                 }
 605                                 if cmd.filter.MaxTag >= 0 && tag > tagID(cmd.filter.MaxTag) {
 606                                         break
 607                                 }
 608                                 remap := variantRemap[tag-tagstart]
 609                                 maxv := tileVariantID(0)
 610                                 for _, v := range remap {
 611                                         if maxv < v {
 612                                                 maxv = v
 613                                         }
 614                                 }
 615                                 if *onehotChunked || *onehotSingle || *onlyPCA {
 616                                         onehot, xrefs := cmd.tv2homhet(cgs, maxv, remap, tag, tagstart, seq)
 617                                         if tag == cmd.debugTag {
 618                                                 log.WithFields(logrus.Fields{
 619                                                         "onehot": onehot,
 620                                                         "xrefs":  xrefs,
 621                                                 }).Info("tv2homhet()")
 622                                         }
 623                                         onehotChunk = append(onehotChunk, onehot...)
 624                                         onehotXref = append(onehotXref, xrefs...)
 625                                 }
 626                                 if *onlyPCA {
 627                                         outcol++
 628                                         continue
 629                                 }
 630                                 if rt == nil {
 631                                         // Reference does not use any
 632                                         // variant of this tile
 633                                         //
 634                                         // TODO: diff against the
 635                                         // relevant portion of the
 636                                         // ref's spanning tile
 637                                         outcol++
 638                                         continue
 639                                 }
 640                                 fmt.Fprintf(annow, "%d,%d,%d,=,%s,%d,,,\n", tag, outcol, rt.variant, rt.seqname, rt.pos)
 641                                 variants := seq[tag]
 642                                 reftilestr := strings.ToUpper(string(rt.tiledata))
 643
 644                                 done := make([]bool, maxv+1)
 645                                 variantDiffs := make([][]hgvs.Variant, maxv+1)
 646                                 for v, tv := range variants {
 647                                         v := remap[v]
 648                                         if v == 0 || v == rt.variant || done[v] {
 649                                                 continue
 650                                         } else {
 651                                                 done[v] = true
 652                                         }
 653                                         if len(tv.Sequence) < taglen {
 654                                                 continue
 655                                         }
 656                                         // if reftilestr doesn't end
 657                                         // in the same tag as tv,
 658                                         // extend reftilestr with
 659                                         // following ref tiles until
 660                                         // it does (up to an arbitrary
 661                                         // sanity-check limit)
 662                                         reftilestr := reftilestr
 663                                         endtagstr := strings.ToUpper(string(tv.Sequence[len(tv.Sequence)-taglen:]))
 664                                         for i, rt := 0, rt; i < annotationMaxTileSpan && !strings.HasSuffix(reftilestr, endtagstr) && rt.nexttag >= 0; i++ {
 665                                                 rt = reftile[rt.nexttag]
 666                                                 if rt == nil {
 667                                                         break
 668                                                 }
 669                                                 reftilestr += strings.ToUpper(string(rt.tiledata[taglen:]))
 670                                         }
 671                                         if mask != nil && !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(reftilestr)) {
 672                                                 continue
 673                                         }
 674                                         if !strings.HasSuffix(reftilestr, endtagstr) {
 675                                                 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
 676                                                 continue
 677                                         }
 678                                         if lendiff := len(reftilestr) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
 679                                                 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
 680                                                 continue
 681                                         }
 682                                         diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
 683                                         for i := range diffs {
 684                                                 diffs[i].Position += rt.pos
 685                                         }
 686                                         for _, diff := range diffs {
 687                                                 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)
 688                                         }
 689                                         if *hgvsChunked {
 690                                                 variantDiffs[v] = diffs
 691                                         }
 692                                 }
 693                                 if *hgvsChunked {
 694                                         // We can now determine, for each HGVS
 695                                         // variant (diff) in this reftile
 696                                         // region, whether a given genome
 697                                         // phase/allele (1) has the variant, (0) has
 698                                         // =ref or a different variant in that
 699                                         // position, or (-1) is lacking
 700                                         // coverage / couldn't be diffed.
 701                                         hgvsCol := hgvsColSet{}
 702                                         for _, diffs := range variantDiffs {
 703                                                 for _, diff := range diffs {
 704                                                         if _, ok := hgvsCol[diff]; ok {
 705                                                                 continue
 706                                                         }
 707                                                         hgvsCol[diff] = [2][]int8{
 708                                                                 make([]int8, len(cmd.cgnames)),
 709                                                                 make([]int8, len(cmd.cgnames)),
 710                                                         }
 711                                                 }
 712                                         }
 713                                         for row, name := range cmd.cgnames {
 714                                                 variants := cgs[name].Variants[(tag-tagstart)*2:]
 715                                                 for ph := 0; ph < 2; ph++ {
 716                                                         v := variants[ph]
 717                                                         if int(v) >= len(remap) {
 718                                                                 v = 0
 719                                                         } else {
 720                                                                 v = remap[v]
 721                                                         }
 722                                                         if v == rt.variant {
 723                                                                 // hgvsCol[*][ph][row] is already 0
 724                                                         } else if len(variantDiffs[v]) == 0 {
 725                                                                 // lacking coverage / couldn't be diffed
 726                                                                 for _, col := range hgvsCol {
 727                                                                         col[ph][row] = -1
 728                                                                 }
 729                                                         } else {
 730                                                                 for _, diff := range variantDiffs[v] {
 731                                                                         hgvsCol[diff][ph][row] = 1
 732                                                                 }
 733                                                         }
 734                                                 }
 735                                         }
 736                                         for diff, colpair := range hgvsCol {
 737                                                 allele2homhet(colpair)
 738                                                 if !cmd.filterHGVScolpair(colpair) {
 739                                                         delete(hgvsCol, diff)
 740                                                 }
 741                                         }
 742                                         if len(hgvsCol) > 0 {
 743                                                 encodeHGVSTodo[rt.seqname] <- hgvsCol
 744                                         }
 745                                 }
 746                                 outcol++
 747                         }
 748                         err = annow.Flush()
 749                         if err != nil {
 750                                 return err
 751                         }
 752                         err = annof.Close()
 753                         if err != nil {
 754                                 return err
 755                         }
 756
 757                         if *onehotChunked {
 758                                 // transpose onehotChunk[col][row] to numpy[row*ncols+col]
 759                                 rows := len(cmd.cgnames)
 760                                 cols := len(onehotChunk)
 761                                 log.Infof("%04d: preparing onehot numpy (rows=%d, cols=%d, mem=%d)", infileIdx, rows, cols, rows*cols)
 762                                 throttleNumpyMem.Acquire()
 763                                 out := onehotcols2int8(onehotChunk)
 764                                 fnm := fmt.Sprintf("%s/onehot.%04d.npy", *outputDir, infileIdx)
 765                                 err = writeNumpyInt8(fnm, out, rows, cols)
 766                                 if err != nil {
 767                                         return err
 768                                 }
 769                                 fnm = fmt.Sprintf("%s/onehot-columns.%04d.npy", *outputDir, infileIdx)
 770                                 err = writeNumpyInt32(fnm, onehotXref2int32(onehotXref), 4, len(onehotXref))
 771                                 if err != nil {
 772                                         return err
 773                                 }
 774                                 debug.FreeOSMemory()
 775                                 throttleNumpyMem.Release()
 776                         }
 777                         if *onehotSingle || *onlyPCA {
 778                                 onehotIndirect[infileIdx] = onehotChunk2Indirect(onehotChunk)
 779                                 onehotChunkSize[infileIdx] = uint32(len(onehotChunk))
 780                                 onehotXrefs[infileIdx] = onehotXref
 781                                 n := len(onehotIndirect[infileIdx][0])
 782                                 log.Infof("%04d: keeping onehot coordinates in memory (n=%d, mem=%d)", infileIdx, n, n*8*2)
 783                         }
 784                         if !(*onehotSingle || *onehotChunked || *onlyPCA) || *mergeOutput || *hgvsSingle {
 785                                 log.Infof("%04d: preparing numpy (rows=%d, cols=%d)", infileIdx, len(cmd.cgnames), 2*outcol)
 786                                 throttleNumpyMem.Acquire()
 787                                 rows := len(cmd.cgnames)
 788                                 cols := 2 * outcol
 789                                 out := make([]int16, rows*cols)
 790                                 for row, name := range cmd.cgnames {
 791                                         outidx := row * cols
 792                                         for col, v := range cgs[name].Variants {
 793                                                 tag := tagstart + tagID(col/2)
 794                                                 if cmd.filter.MaxTag >= 0 && tag > tagID(cmd.filter.MaxTag) {
 795                                                         break
 796                                                 }
 797                                                 if rt := reftile[tag]; rt == nil || rt.excluded {
 798                                                         continue
 799                                                 }
 800                                                 if v == 0 {
 801                                                         out[outidx] = 0 // tag not found / spanning tile
 802                                                 } else if variants, ok := seq[tag]; ok && int(v) < len(variants) && len(variants[v].Sequence) > 0 {
 803                                                         out[outidx] = int16(variantRemap[tag-tagstart][v])
 804                                                 } else {
 805                                                         out[outidx] = -1 // low quality tile variant
 806                                                 }
 807                                                 if tag == cmd.debugTag {
 808                                                         log.Printf("tag %d row %d col %d outidx %d v %d out %d", tag, row, col, outidx, v, out[outidx])
 809                                                 }
 810                                                 outidx++
 811                                         }
 812                                 }
 813                                 seq = nil
 814                                 cgs = nil
 815                                 debug.FreeOSMemory()
 816                                 throttleNumpyMem.Release()
 817                                 if *mergeOutput || *hgvsSingle {
 818                                         log.Infof("%04d: matrix fragment %d rows x %d cols", infileIdx, rows, cols)
 819                                         toMerge[infileIdx] = out
 820                                 }
 821                                 if !*mergeOutput && !*onehotChunked && !*onehotSingle {
 822                                         fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
 823                                         err = writeNumpyInt16(fnm, out, rows, cols)
 824                                         if err != nil {
 825                                                 return err
 826                                         }
 827                                 }
 828                         }
 829                         debug.FreeOSMemory()
 830                         log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
 831                         return nil
 832                 })
 833         }
 834         if err = throttleMem.Wait(); err != nil {
 835                 return err
 836         }
 837
 838         if *hgvsChunked {
 839                 log.Info("flushing hgvsCols temp files")
 840                 for seqname := range refseq {
 841                         close(encodeHGVSTodo[seqname])
 842                 }
 843                 err = encodeHGVS.Wait()
 844                 if err != nil {
 845                         return err
 846                 }
 847                 for seqname := range refseq {
 848                         log.Infof("%s: reading hgvsCols from temp file", seqname)
 849                         f := tmpHGVSCols[seqname]
 850                         _, err = f.Seek(0, io.SeekStart)
 851                         if err != nil {
 852                                 return err
 853                         }
 854                         var hgvsCols hgvsColSet
 855                         dec := gob.NewDecoder(bufio.NewReaderSize(f, 1<<24))
 856                         for err == nil {
 857                                 err = dec.Decode(&hgvsCols)
 858                         }
 859                         if err != io.EOF {
 860                                 return err
 861                         }
 862                         log.Infof("%s: sorting %d hgvs variants", seqname, len(hgvsCols))
 863                         variants := make([]hgvs.Variant, 0, len(hgvsCols))
 864                         for v := range hgvsCols {
 865                                 variants = append(variants, v)
 866                         }
 867                         sort.Slice(variants, func(i, j int) bool {
 868                                 vi, vj := &variants[i], &variants[j]
 869                                 if vi.Position != vj.Position {
 870                                         return vi.Position < vj.Position
 871                                 } else if vi.Ref != vj.Ref {
 872                                         return vi.Ref < vj.Ref
 873                                 } else {
 874                                         return vi.New < vj.New
 875                                 }
 876                         })
 877                         rows := len(cmd.cgnames)
 878                         cols := len(variants) * 2
 879                         log.Infof("%s: building hgvs matrix (rows=%d, cols=%d, mem=%d)", seqname, rows, cols, rows*cols)
 880                         out := make([]int8, rows*cols)
 881                         for varIdx, variant := range variants {
 882                                 hgvsCols := hgvsCols[variant]
 883                                 for row := range cmd.cgnames {
 884                                         for ph := 0; ph < 2; ph++ {
 885                                                 out[row*cols+varIdx+ph] = hgvsCols[ph][row]
 886                                         }
 887                                 }
 888                         }
 889                         err = writeNumpyInt8(fmt.Sprintf("%s/hgvs.%s.npy", *outputDir, seqname), out, rows, cols)
 890                         if err != nil {
 891                                 return err
 892                         }
 893                         out = nil
 894
 895                         fnm := fmt.Sprintf("%s/hgvs.%s.annotations.csv", *outputDir, seqname)
 896                         log.Infof("%s: writing hgvs column labels to %s", seqname, fnm)
 897                         var hgvsLabels bytes.Buffer
 898                         for varIdx, variant := range variants {
 899                                 fmt.Fprintf(&hgvsLabels, "%d,%s:g.%s\n", varIdx, seqname, variant.String())
 900                         }
 901                         err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0666)
 902                         if err != nil {
 903                                 return err
 904                         }
 905                 }
 906         }
 907
 908         if *mergeOutput || *hgvsSingle {
 909                 var annow *bufio.Writer
 910                 var annof *os.File
 911                 if *mergeOutput {
 912                         annoFilename := fmt.Sprintf("%s/matrix.annotations.csv", *outputDir)
 913                         annof, err = os.Create(annoFilename)
 914                         if err != nil {
 915                                 return err
 916                         }
 917                         annow = bufio.NewWriterSize(annof, 1<<20)
 918                 }
 919
 920                 rows := len(cmd.cgnames)
 921                 cols := 0
 922                 for _, chunk := range toMerge {
 923                         cols += len(chunk) / rows
 924                 }
 925                 log.Infof("merging output matrix (rows=%d, cols=%d, mem=%d) and annotations", rows, cols, rows*cols*2)
 926                 var out []int16
 927                 if *mergeOutput {
 928                         out = make([]int16, rows*cols)
 929                 }
 930                 hgvsCols := map[string][2][]int16{} // hgvs -> [[g0,g1,g2,...], [g0,g1,g2,...]] (slice of genomes for each phase)
 931                 startcol := 0
 932                 for outIdx, chunk := range toMerge {
 933                         chunkcols := len(chunk) / rows
 934                         if *mergeOutput {
 935                                 for row := 0; row < rows; row++ {
 936                                         copy(out[row*cols+startcol:], chunk[row*chunkcols:(row+1)*chunkcols])
 937                                 }
 938                         }
 939                         toMerge[outIdx] = nil
 940
 941                         annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, outIdx)
 942                         log.Infof("reading %s", annotationsFilename)
 943                         buf, err := os.ReadFile(annotationsFilename)
 944                         if err != nil {
 945                                 return err
 946                         }
 947                         if *mergeOutput {
 948                                 err = os.Remove(annotationsFilename)
 949                                 if err != nil {
 950                                         return err
 951                                 }
 952                         }
 953                         for _, line := range bytes.Split(buf, []byte{'\n'}) {
 954                                 if len(line) == 0 {
 955                                         continue
 956                                 }
 957                                 fields := bytes.SplitN(line, []byte{','}, 9)
 958                                 tag, _ := strconv.Atoi(string(fields[0]))
 959                                 incol, _ := strconv.Atoi(string(fields[1]))
 960                                 tileVariant, _ := strconv.Atoi(string(fields[2]))
 961                                 hgvsID := string(fields[3])
 962                                 seqname := string(fields[4])
 963                                 pos, _ := strconv.Atoi(string(fields[5]))
 964                                 refseq := fields[6]
 965                                 if hgvsID == "" {
 966                                         // Null entry for un-diffable
 967                                         // tile variant
 968                                         continue
 969                                 }
 970                                 if hgvsID == "=" {
 971                                         // Null entry for ref tile
 972                                         continue
 973                                 }
 974                                 if mask != nil && !mask.Check(strings.TrimPrefix(seqname, "chr"), pos, pos+len(refseq)) {
 975                                         // The tile intersects one of
 976                                         // the selected regions, but
 977                                         // this particular HGVS
 978                                         // variant does not.
 979                                         continue
 980                                 }
 981                                 hgvsColPair := hgvsCols[hgvsID]
 982                                 if hgvsColPair[0] == nil {
 983                                         // values in new columns start
 984                                         // out as -1 ("no data yet")
 985                                         // or 0 ("=ref") here, may
 986                                         // change to 1 ("hgvs variant
 987                                         // present") below, either on
 988                                         // this line or a future line.
 989                                         hgvsColPair = [2][]int16{make([]int16, len(cmd.cgnames)), make([]int16, len(cmd.cgnames))}
 990                                         rt, ok := reftile[tagID(tag)]
 991                                         if !ok {
 992                                                 err = fmt.Errorf("bug: seeing annotations for tag %d, but it has no reftile entry", tag)
 993                                                 return err
 994                                         }
 995                                         for ph := 0; ph < 2; ph++ {
 996                                                 for row := 0; row < rows; row++ {
 997                                                         v := chunk[row*chunkcols+incol*2+ph]
 998                                                         if tileVariantID(v) == rt.variant {
 999                                                                 hgvsColPair[ph][row] = 0
1000                                                         } else {
1001                                                                 hgvsColPair[ph][row] = -1
1002                                                         }
1003                                                 }
1004                                         }
1005                                         hgvsCols[hgvsID] = hgvsColPair
1006                                         if annow != nil {
1007                                                 hgvsref := hgvs.Variant{
1008                                                         Position: pos,
1009                                                         Ref:      string(refseq),
1010                                                         New:      string(refseq),
1011                                                 }
1012                                                 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])
1013                                         }
1014                                 }
1015                                 if annow != nil {
1016                                         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])
1017                                 }
1018                                 for ph := 0; ph < 2; ph++ {
1019                                         for row := 0; row < rows; row++ {
1020                                                 v := chunk[row*chunkcols+incol*2+ph]
1021                                                 if int(v) == tileVariant {
1022                                                         hgvsColPair[ph][row] = 1
1023                                                 }
1024                                         }
1025                                 }
1026                         }
1027
1028                         startcol += chunkcols
1029                 }
1030                 if *mergeOutput {
1031                         err = annow.Flush()
1032                         if err != nil {
1033                                 return err
1034                         }
1035                         err = annof.Close()
1036                         if err != nil {
1037                                 return err
1038                         }
1039                         err = writeNumpyInt16(fmt.Sprintf("%s/matrix.npy", *outputDir), out, rows, cols)
1040                         if err != nil {
1041                                 return err
1042                         }
1043                 }
1044                 out = nil
1045
1046                 if *hgvsSingle {
1047                         cols = len(hgvsCols) * 2
1048                         log.Printf("building hgvs-based matrix: %d rows x %d cols", rows, cols)
1049                         out = make([]int16, rows*cols)
1050                         hgvsIDs := make([]string, 0, cols/2)
1051                         for hgvsID := range hgvsCols {
1052                                 hgvsIDs = append(hgvsIDs, hgvsID)
1053                         }
1054                         sort.Strings(hgvsIDs)
1055                         var hgvsLabels bytes.Buffer
1056                         for idx, hgvsID := range hgvsIDs {
1057                                 fmt.Fprintf(&hgvsLabels, "%d,%s\n", idx, hgvsID)
1058                                 for ph := 0; ph < 2; ph++ {
1059                                         hgvscol := hgvsCols[hgvsID][ph]
1060                                         for row, val := range hgvscol {
1061                                                 out[row*cols+idx*2+ph] = val
1062                                         }
1063                                 }
1064                         }
1065                         err = writeNumpyInt16(fmt.Sprintf("%s/hgvs.npy", *outputDir), out, rows, cols)
1066                         if err != nil {
1067                                 return err
1068                         }
1069
1070                         fnm := fmt.Sprintf("%s/hgvs.annotations.csv", *outputDir)
1071                         log.Printf("writing hgvs labels: %s", fnm)
1072                         err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0777)
1073                         if err != nil {
1074                                 return err
1075                         }
1076                 }
1077         }
1078         if *onehotSingle || *onlyPCA {
1079                 nzCount := 0
1080                 for _, part := range onehotIndirect {
1081                         nzCount += len(part[0])
1082                 }
1083                 onehot := make([]uint32, nzCount*2) // [r,r,r,...,c,c,c,...]
1084                 var xrefs []onehotXref
1085                 chunkOffset := uint32(0)
1086                 outcol := 0
1087                 for i, part := range onehotIndirect {
1088                         for i := range part[1] {
1089                                 part[1][i] += chunkOffset
1090                         }
1091                         copy(onehot[outcol:], part[0])
1092                         copy(onehot[outcol+nzCount:], part[1])
1093                         xrefs = append(xrefs, onehotXrefs[i]...)
1094
1095                         outcol += len(part[0])
1096                         chunkOffset += onehotChunkSize[i]
1097
1098                         part[0] = nil
1099                         part[1] = nil
1100                         onehotXrefs[i] = nil
1101                         debug.FreeOSMemory()
1102                 }
1103                 if *onehotSingle {
1104                         fnm := fmt.Sprintf("%s/onehot.npy", *outputDir)
1105                         err = writeNumpyUint32(fnm, onehot, 2, nzCount)
1106                         if err != nil {
1107                                 return err
1108                         }
1109                         fnm = fmt.Sprintf("%s/onehot-columns.npy", *outputDir)
1110                         err = writeNumpyInt32(fnm, onehotXref2int32(xrefs), 5, len(xrefs))
1111                         if err != nil {
1112                                 return err
1113                         }
1114                 }
1115                 if *onlyPCA {
1116                         cols := 0
1117                         for _, c := range onehot[nzCount:] {
1118                                 if int(c) >= cols {
1119                                         cols = int(c) + 1
1120                                 }
1121                         }
1122                         if cols == 0 {
1123                                 return fmt.Errorf("cannot do PCA: one-hot matrix is empty")
1124                         }
1125                         log.Printf("have %d one-hot cols", cols)
1126                         stride := 1
1127                         for *maxPCATiles > 0 && cols > *maxPCATiles*2 {
1128                                 cols = cols / 2
1129                                 stride = stride * 2
1130                         }
1131                         log.Printf("creating matrix: %d rows, %d cols, stride %d", len(cmd.cgnames), cols, stride)
1132                         mtx := mat.NewDense(len(cmd.cgnames), cols, nil)
1133                         for i, c := range onehot[nzCount:] {
1134                                 if int(c/2)%stride == 0 {
1135                                         mtx.Set(int(onehot[i]), int(c/2)/stride*2+int(c)%2, 1)
1136                                 }
1137                         }
1138                         log.Print("fitting")
1139                         transformer := nlp.NewPCA(*pcaComponents)
1140                         transformer.Fit(mtx.T())
1141                         log.Printf("transforming")
1142                         pca, err := transformer.Transform(mtx.T())
1143                         if err != nil {
1144                                 return err
1145                         }
1146                         pca = pca.T()
1147                         outrows, outcols := pca.Dims()
1148                         log.Printf("copying result to numpy output array: %d rows, %d cols", outrows, outcols)
1149                         out := make([]float64, outrows*outcols)
1150                         for i := 0; i < outrows; i++ {
1151                                 for j := 0; j < outcols; j++ {
1152                                         out[i*outcols+j] = pca.At(i, j)
1153                                 }
1154                         }
1155                         fnm := fmt.Sprintf("%s/pca.npy", *outputDir)
1156                         log.Printf("writing numpy: %s", fnm)
1157                         output, err := os.OpenFile(fnm, os.O_CREATE|os.O_TRUNC|os.O_WRONLY, 0777)
1158                         if err != nil {
1159                                 return err
1160                         }
1161                         npw, err := gonpy.NewWriter(nopCloser{output})
1162                         if err != nil {
1163                                 return fmt.Errorf("gonpy.NewWriter: %w", err)
1164                         }
1165                         npw.Shape = []int{outrows, outcols}
1166                         err = npw.WriteFloat64(out)
1167                         if err != nil {
1168                                 return fmt.Errorf("WriteFloat64: %w", err)
1169                         }
1170                         err = output.Close()
1171                         if err != nil {
1172                                 return err
1173                         }
1174                         log.Print("done")
1175                 }
1176         }
1177         if !*mergeOutput && !*onehotChunked && !*onehotSingle && !*onlyPCA {
1178                 tagoffsetFilename := *outputDir + "/chunk-tag-offset.csv"
1179                 log.Infof("writing tag offsets to %s", tagoffsetFilename)
1180                 var f *os.File
1181                 f, err = os.Create(tagoffsetFilename)
1182                 if err != nil {
1183                         return err
1184                 }
1185                 defer f.Close()
1186                 for idx, offset := range chunkStartTag {
1187                         _, err = fmt.Fprintf(f, "%q,%d\n", fmt.Sprintf("matrix.%04d.npy", idx), offset)
1188                         if err != nil {
1189                                 err = fmt.Errorf("write %s: %w", tagoffsetFilename, err)
1190                                 return err
1191                         }
1192                 }
1193                 err = f.Close()
1194                 if err != nil {
1195                         err = fmt.Errorf("close %s: %w", tagoffsetFilename, err)
1196                         return err
1197                 }
1198         }
1199         return nil
1200 }
1201
1202 // Read case/control files, remove non-case/control entries from
1203 // cmd.cgnames, and build cmd.chi2Cases.
1204 func (cmd *sliceNumpy) useCaseControlFiles() error {
1205         if cmd.chi2CaseControlFile == "" {
1206                 return nil
1207         }
1208         infiles, err := allFiles(cmd.chi2CaseControlFile, nil)
1209         if err != nil {
1210                 return err
1211         }
1212         // index in cmd.cgnames => case(true) / control(false)
1213         cc := map[int]bool{}
1214         for _, infile := range infiles {
1215                 f, err := open(infile)
1216                 if err != nil {
1217                         return err
1218                 }
1219                 buf, err := io.ReadAll(f)
1220                 f.Close()
1221                 if err != nil {
1222                         return err
1223                 }
1224                 ccCol := -1
1225                 for _, tsv := range bytes.Split(buf, []byte{'\n'}) {
1226                         if len(tsv) == 0 {
1227                                 continue
1228                         }
1229                         split := strings.Split(string(tsv), "\t")
1230                         if ccCol < 0 {
1231                                 // header row
1232                                 for col, name := range split {
1233                                         if name == cmd.chi2CaseControlColumn {
1234                                                 ccCol = col
1235                                                 break
1236                                         }
1237                                 }
1238                                 if ccCol < 0 {
1239                                         return fmt.Errorf("%s: no column named %q in header row %q", infile, cmd.chi2CaseControlColumn, tsv)
1240                                 }
1241                                 continue
1242                         }
1243                         if len(split) <= ccCol {
1244                                 continue
1245                         }
1246                         pattern := split[0]
1247                         found := -1
1248                         for i, name := range cmd.cgnames {
1249                                 if strings.Contains(name, pattern) {
1250                                         if found >= 0 {
1251                                                 log.Warnf("pattern %q in %s matches multiple genome IDs (%qs, %q)", pattern, infile, cmd.cgnames[found], name)
1252                                         }
1253                                         found = i
1254                                 }
1255                         }
1256                         if found < 0 {
1257                                 log.Warnf("pattern %q in %s does not match any genome IDs", pattern, infile)
1258                                 continue
1259                         }
1260                         if split[ccCol] == "0" {
1261                                 cc[found] = false
1262                         }
1263                         if split[ccCol] == "1" {
1264                                 cc[found] = true
1265                         }
1266                 }
1267         }
1268         allnames := cmd.cgnames
1269         cmd.cgnames = nil
1270         cmd.chi2Cases = nil
1271         ncases := 0
1272         for i, name := range allnames {
1273                 if cc, ok := cc[i]; ok {
1274                         cmd.cgnames = append(cmd.cgnames, name)
1275                         cmd.chi2Cases = append(cmd.chi2Cases, cc)
1276                         if cc {
1277                                 ncases++
1278                         }
1279                 }
1280         }
1281         log.Printf("%d cases, %d controls, %d neither (dropped)", ncases, len(cmd.cgnames)-ncases, len(allnames)-len(cmd.cgnames))
1282         return nil
1283 }
1284
1285 func (cmd *sliceNumpy) filterHGVScolpair(colpair [2][]int8) bool {
1286         if cmd.chi2PValue >= 1 {
1287                 return true
1288         }
1289         col0 := make([]bool, 0, len(cmd.chi2Cases))
1290         col1 := make([]bool, 0, len(cmd.chi2Cases))
1291         cases := make([]bool, 0, len(cmd.chi2Cases))
1292         for i, c := range cmd.chi2Cases {
1293                 if colpair[0][i] < 0 {
1294                         continue
1295                 }
1296                 col0 = append(col0, colpair[0][i] != 0)
1297                 col1 = append(col1, colpair[1][i] != 0)
1298                 cases = append(cases, c)
1299         }
1300         return len(cases) >= cmd.minCoverage &&
1301                 (pvalue(col0, cases) <= cmd.chi2PValue || pvalue(col1, cases) <= cmd.chi2PValue)
1302 }
1303
1304 func writeNumpyUint32(fnm string, out []uint32, rows, cols int) error {
1305         output, err := os.Create(fnm)
1306         if err != nil {
1307                 return err
1308         }
1309         defer output.Close()
1310         bufw := bufio.NewWriterSize(output, 1<<26)
1311         npw, err := gonpy.NewWriter(nopCloser{bufw})
1312         if err != nil {
1313                 return err
1314         }
1315         log.WithFields(log.Fields{
1316                 "filename": fnm,
1317                 "rows":     rows,
1318                 "cols":     cols,
1319                 "bytes":    rows * cols * 4,
1320         }).Infof("writing numpy: %s", fnm)
1321         npw.Shape = []int{rows, cols}
1322         npw.WriteUint32(out)
1323         err = bufw.Flush()
1324         if err != nil {
1325                 return err
1326         }
1327         return output.Close()
1328 }
1329
1330 func writeNumpyInt32(fnm string, out []int32, rows, cols int) error {
1331         output, err := os.Create(fnm)
1332         if err != nil {
1333                 return err
1334         }
1335         defer output.Close()
1336         bufw := bufio.NewWriterSize(output, 1<<26)
1337         npw, err := gonpy.NewWriter(nopCloser{bufw})
1338         if err != nil {
1339                 return err
1340         }
1341         log.WithFields(log.Fields{
1342                 "filename": fnm,
1343                 "rows":     rows,
1344                 "cols":     cols,
1345                 "bytes":    rows * cols * 4,
1346         }).Infof("writing numpy: %s", fnm)
1347         npw.Shape = []int{rows, cols}
1348         npw.WriteInt32(out)
1349         err = bufw.Flush()
1350         if err != nil {
1351                 return err
1352         }
1353         return output.Close()
1354 }
1355
1356 func writeNumpyInt16(fnm string, out []int16, rows, cols int) error {
1357         output, err := os.Create(fnm)
1358         if err != nil {
1359                 return err
1360         }
1361         defer output.Close()
1362         bufw := bufio.NewWriterSize(output, 1<<26)
1363         npw, err := gonpy.NewWriter(nopCloser{bufw})
1364         if err != nil {
1365                 return err
1366         }
1367         log.WithFields(log.Fields{
1368                 "filename": fnm,
1369                 "rows":     rows,
1370                 "cols":     cols,
1371                 "bytes":    rows * cols * 2,
1372         }).Infof("writing numpy: %s", fnm)
1373         npw.Shape = []int{rows, cols}
1374         npw.WriteInt16(out)
1375         err = bufw.Flush()
1376         if err != nil {
1377                 return err
1378         }
1379         return output.Close()
1380 }
1381
1382 func writeNumpyInt8(fnm string, out []int8, rows, cols int) error {
1383         output, err := os.Create(fnm)
1384         if err != nil {
1385                 return err
1386         }
1387         defer output.Close()
1388         bufw := bufio.NewWriterSize(output, 1<<26)
1389         npw, err := gonpy.NewWriter(nopCloser{bufw})
1390         if err != nil {
1391                 return err
1392         }
1393         log.WithFields(log.Fields{
1394                 "filename": fnm,
1395                 "rows":     rows,
1396                 "cols":     cols,
1397                 "bytes":    rows * cols,
1398         }).Infof("writing numpy: %s", fnm)
1399         npw.Shape = []int{rows, cols}
1400         npw.WriteInt8(out)
1401         err = bufw.Flush()
1402         if err != nil {
1403                 return err
1404         }
1405         return output.Close()
1406 }
1407
1408 func allele2homhet(colpair [2][]int8) {
1409         a, b := colpair[0], colpair[1]
1410         for i, av := range a {
1411                 bv := b[i]
1412                 if av < 0 || bv < 0 {
1413                         // no-call
1414                         a[i], b[i] = -1, -1
1415                 } else if av > 0 && bv > 0 {
1416                         // hom
1417                         a[i], b[i] = 1, 0
1418                 } else if av > 0 || bv > 0 {
1419                         // het
1420                         a[i], b[i] = 0, 1
1421                 } else {
1422                         // ref (or a different variant in same position)
1423                         // (this is a no-op) a[i], b[i] = 0, 0
1424                 }
1425         }
1426 }
1427
1428 type onehotXref struct {
1429         tag     tagID
1430         variant tileVariantID
1431         hom     bool
1432         pvalue  float64
1433 }
1434
1435 const onehotXrefSize = unsafe.Sizeof(onehotXref{})
1436
1437 // Build onehot matrix (m[tileVariantIndex][genome] == 0 or 1) for all
1438 // variants of a single tile/tag#.
1439 //
1440 // Return nil if no tile variant passes Χ² filter.
1441 func (cmd *sliceNumpy) tv2homhet(cgs map[string]CompactGenome, maxv tileVariantID, remap []tileVariantID, tag, chunkstarttag tagID, seq map[tagID][]TileVariant) ([][]int8, []onehotXref) {
1442         if tag == cmd.debugTag {
1443                 tv := make([]tileVariantID, len(cmd.cgnames)*2)
1444                 for i, name := range cmd.cgnames {
1445                         copy(tv[i*2:(i+1)*2], cgs[name].Variants[(tag-chunkstarttag)*2:])
1446                 }
1447                 log.WithFields(logrus.Fields{
1448                         "cgs[i].Variants[tag*2+j]": tv,
1449                         "maxv":                     maxv,
1450                         "remap":                    remap,
1451                         "tag":                      tag,
1452                         "chunkstarttag":            chunkstarttag,
1453                 }).Info("tv2homhet()")
1454         }
1455         if maxv < 1 || (maxv < 2 && !cmd.includeVariant1) {
1456                 // everyone has the most common variant (of the variants we don't drop)
1457                 return nil, nil
1458         }
1459         tagoffset := tag - chunkstarttag
1460         coverage := 0
1461         for _, cg := range cgs {
1462                 alleles := 0
1463                 for _, v := range cg.Variants[tagoffset*2 : tagoffset*2+2] {
1464                         if v > 0 && int(v) < len(seq[tag]) && len(seq[tag][v].Sequence) > 0 {
1465                                 alleles++
1466                         }
1467                 }
1468                 if alleles == 2 {
1469                         coverage++
1470                 }
1471         }
1472         if coverage < cmd.minCoverage {
1473                 return nil, nil
1474         }
1475         obs := make([][]bool, (maxv+1)*2) // 2 slices (hom + het) for each variant#
1476         for i := range obs {
1477                 obs[i] = make([]bool, len(cmd.cgnames))
1478         }
1479         for cgid, name := range cmd.cgnames {
1480                 cgvars := cgs[name].Variants[tagoffset*2:]
1481                 tv0, tv1 := remap[cgvars[0]], remap[cgvars[1]]
1482                 for v := tileVariantID(1); v <= maxv; v++ {
1483                         if tv0 == v && tv1 == v {
1484                                 obs[v*2][cgid] = true
1485                         } else if tv0 == v || tv1 == v {
1486                                 obs[v*2+1][cgid] = true
1487                         }
1488                 }
1489         }
1490         var onehot [][]int8
1491         var xref []onehotXref
1492         for col := 2; col < len(obs); col++ {
1493                 // col 0,1 correspond to tile variant 0, i.e.,
1494                 // no-call; col 2,3 correspond to the most common
1495                 // variant; so we (normally) start at col 4.
1496                 if col < 4 && !cmd.includeVariant1 {
1497                         continue
1498                 }
1499                 p := pvalue(obs[col], cmd.chi2Cases)
1500                 if cmd.chi2PValue < 1 && !(p < cmd.chi2PValue) {
1501                         continue
1502                 }
1503                 onehot = append(onehot, bool2int8(obs[col]))
1504                 xref = append(xref, onehotXref{
1505                         tag:     tag,
1506                         variant: tileVariantID(col >> 1),
1507                         hom:     col&1 == 0,
1508                         pvalue:  p,
1509                 })
1510         }
1511         return onehot, xref
1512 }
1513
1514 func bool2int8(in []bool) []int8 {
1515         out := make([]int8, len(in))
1516         for i, v := range in {
1517                 if v {
1518                         out[i] = 1
1519                 }
1520         }
1521         return out
1522 }
1523
1524 // convert a []onehotXref with length N to a numpy-style []int32
1525 // matrix with N columns, one row per field of onehotXref struct.
1526 //
1527 // Hom/het row contains hom=0, het=1.
1528 //
1529 // P-value row contains 1000000x actual p-value.
1530 func onehotXref2int32(xrefs []onehotXref) []int32 {
1531         xcols := len(xrefs)
1532         xdata := make([]int32, 5*xcols)
1533         for i, xref := range xrefs {
1534                 xdata[i] = int32(xref.tag)
1535                 xdata[xcols+i] = int32(xref.variant)
1536                 if xref.hom {
1537                         xdata[xcols*2+i] = 1
1538                 }
1539                 xdata[xcols*3+i] = int32(xref.pvalue * 1000000)
1540                 xdata[xcols*4+i] = int32(-math.Log10(xref.pvalue) * 1000000)
1541         }
1542         return xdata
1543 }
1544
1545 // transpose onehot data from in[col][row] to numpy-style
1546 // out[row*cols+col].
1547 func onehotcols2int8(in [][]int8) []int8 {
1548         if len(in) == 0 {
1549                 return nil
1550         }
1551         cols := len(in)
1552         rows := len(in[0])
1553         out := make([]int8, rows*cols)
1554         for row := 0; row < rows; row++ {
1555                 outrow := out[row*cols:]
1556                 for col, incol := range in {
1557                         outrow[col] = incol[row]
1558                 }
1559         }
1560         return out
1561 }
1562
1563 // Return [2][]uint32{rowIndices, colIndices} indicating which
1564 // elements of matrixT[c][r] have non-zero values.
1565 func onehotChunk2Indirect(matrixT [][]int8) [2][]uint32 {
1566         var nz [2][]uint32
1567         for c, col := range matrixT {
1568                 for r, val := range col {
1569                         if val != 0 {
1570                                 nz[0] = append(nz[0], uint32(r))
1571                                 nz[1] = append(nz[1], uint32(c))
1572                         }
1573                 }
1574         }
1575         return nz
1576 }