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