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         chi2Cases       []bool
  45         chi2PValue      float64
  46         minCoverage     int
  47         includeVariant1 bool
  48         debugTag        tagID
  49
  50         cgnames         []string
  51         samples         []sampleInfo
  52         trainingSet     []int // samples index => training set index, or -1 if not in training set
  53         trainingSetSize int
  54 }
  55
  56 func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  57         err := cmd.run(prog, args, stdin, stdout, stderr)
  58         if err != nil {
  59                 fmt.Fprintf(stderr, "%s\n", err)
  60                 return 1
  61         }
  62         return 0
  63 }
  64
  65 func (cmd *sliceNumpy) run(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) error {
  66         flags := flag.NewFlagSet("", flag.ContinueOnError)
  67         flags.SetOutput(stderr)
  68         pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
  69         runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
  70         arvadosRAM := flags.Int("arvados-ram", 750000000000, "amount of memory to request for arvados container (`bytes`)")
  71         arvadosVCPUs := flags.Int("arvados-vcpus", 96, "number of VCPUs to request for arvados container")
  72         projectUUID := flags.String("project", "", "project `UUID` for output data")
  73         priority := flags.Int("priority", 500, "container request priority")
  74         inputDir := flags.String("input-dir", "./in", "input `directory`")
  75         outputDir := flags.String("output-dir", "./out", "output `directory`")
  76         ref := flags.String("ref", "", "reference name (if blank, choose last one that appears in input)")
  77         regionsFilename := flags.String("regions", "", "only output columns/annotations that intersect regions in specified bed `file`")
  78         expandRegions := flags.Int("expand-regions", 0, "expand specified regions by `N` base pairs on each side`")
  79         mergeOutput := flags.Bool("merge-output", false, "merge output into one matrix.npy and one matrix.annotations.csv")
  80         hgvsSingle := flags.Bool("single-hgvs-matrix", false, "also generate hgvs-based matrix")
  81         hgvsChunked := flags.Bool("chunked-hgvs-matrix", false, "also generate hgvs-based matrix per chromosome")
  82         onehotSingle := flags.Bool("single-onehot", false, "generate one-hot tile-based matrix")
  83         onehotChunked := flags.Bool("chunked-onehot", false, "generate one-hot tile-based matrix per input chunk")
  84         samplesFilename := flags.String("samples", "", "`samples.csv` file with training/validation and case/control groups (see 'lightning choose-samples')")
  85         caseControlOnly := flags.Bool("case-control-only", false, "drop samples that are not in case/control groups")
  86         onlyPCA := flags.Bool("pca", false, "generate pca matrix")
  87         pcaComponents := flags.Int("pca-components", 4, "number of PCA components")
  88         maxPCATiles := flags.Int("max-pca-tiles", 0, "maximum tiles to use as PCA input (filter, then drop every 2nd colum pair until below max)")
  89         debugTag := flags.Int("debug-tag", -1, "log debugging details about specified tag")
  90         flags.IntVar(&cmd.threads, "threads", 16, "number of memory-hungry assembly threads, and number of VCPUs to request for arvados container")
  91         flags.Float64Var(&cmd.chi2PValue, "chi2-p-value", 1, "do Χ² test and omit columns with p-value above this threshold")
  92         flags.BoolVar(&cmd.includeVariant1, "include-variant-1", false, "include most common variant when building one-hot matrix")
  93         cmd.filter.Flags(flags)
  94         err := flags.Parse(args)
  95         if err == flag.ErrHelp {
  96                 return nil
  97         } else if err != nil {
  98                 return err
  99         }
 100
 101         if *pprof != "" {
 102                 go func() {
 103                         log.Println(http.ListenAndServe(*pprof, nil))
 104                 }()
 105         }
 106
 107         if cmd.chi2PValue != 1 && *samplesFilename == "" {
 108                 return fmt.Errorf("cannot use provided -chi2-p-value=%f because -samples= value is empty", cmd.chi2PValue)
 109         }
 110
 111         cmd.debugTag = tagID(*debugTag)
 112
 113         if !*runlocal {
 114                 runner := arvadosContainerRunner{
 115                         Name:        "lightning slice-numpy",
 116                         Client:      arvados.NewClientFromEnv(),
 117                         ProjectUUID: *projectUUID,
 118                         RAM:         int64(*arvadosRAM),
 119                         VCPUs:       *arvadosVCPUs,
 120                         Priority:    *priority,
 121                         KeepCache:   2,
 122                         APIAccess:   true,
 123                 }
 124                 err = runner.TranslatePaths(inputDir, regionsFilename, samplesFilename)
 125                 if err != nil {
 126                         return err
 127                 }
 128                 runner.Args = []string{"slice-numpy", "-local=true",
 129                         "-pprof=:6060",
 130                         "-input-dir=" + *inputDir,
 131                         "-output-dir=/mnt/output",
 132                         "-threads=" + fmt.Sprintf("%d", cmd.threads),
 133                         "-regions=" + *regionsFilename,
 134                         "-expand-regions=" + fmt.Sprintf("%d", *expandRegions),
 135                         "-merge-output=" + fmt.Sprintf("%v", *mergeOutput),
 136                         "-single-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsSingle),
 137                         "-chunked-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsChunked),
 138                         "-single-onehot=" + fmt.Sprintf("%v", *onehotSingle),
 139                         "-chunked-onehot=" + fmt.Sprintf("%v", *onehotChunked),
 140                         "-samples=" + *samplesFilename,
 141                         "-case-control-only=" + fmt.Sprintf("%v", *caseControlOnly),
 142                         "-pca=" + fmt.Sprintf("%v", *onlyPCA),
 143                         "-pca-components=" + fmt.Sprintf("%d", *pcaComponents),
 144                         "-max-pca-tiles=" + fmt.Sprintf("%d", *maxPCATiles),
 145                         "-chi2-p-value=" + fmt.Sprintf("%f", cmd.chi2PValue),
 146                         "-include-variant-1=" + fmt.Sprintf("%v", cmd.includeVariant1),
 147                         "-debug-tag=" + fmt.Sprintf("%d", cmd.debugTag),
 148                 }
 149                 runner.Args = append(runner.Args, cmd.filter.Args()...)
 150                 var output string
 151                 output, err = runner.Run()
 152                 if err != nil {
 153                         return err
 154                 }
 155                 fmt.Fprintln(stdout, output)
 156                 return nil
 157         }
 158
 159         infiles, err := allFiles(*inputDir, matchGobFile)
 160         if err != nil {
 161                 return err
 162         }
 163         if len(infiles) == 0 {
 164                 err = fmt.Errorf("no input files found in %s", *inputDir)
 165                 return err
 166         }
 167         sort.Strings(infiles)
 168
 169         var refseq map[string][]tileLibRef
 170         var reftiledata = make(map[tileLibRef][]byte, 11000000)
 171         in0, err := open(infiles[0])
 172         if err != nil {
 173                 return err
 174         }
 175
 176         matchGenome, err := regexp.Compile(cmd.filter.MatchGenome)
 177         if err != nil {
 178                 err = fmt.Errorf("-match-genome: invalid regexp: %q", cmd.filter.MatchGenome)
 179                 return err
 180         }
 181
 182         if *samplesFilename != "" {
 183                 cmd.samples, err = cmd.loadSampleInfo(*samplesFilename)
 184                 if err != nil {
 185                         return err
 186                 }
 187         } else if *caseControlOnly {
 188                 return fmt.Errorf("-case-control-only does not make sense without -samples")
 189         }
 190
 191         cmd.cgnames = nil
 192         var tagset [][]byte
 193         err = DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
 194                 if len(ent.TagSet) > 0 {
 195                         tagset = ent.TagSet
 196                 }
 197                 for _, cseq := range ent.CompactSequences {
 198                         if cseq.Name == *ref || *ref == "" {
 199                                 refseq = cseq.TileSequences
 200                         }
 201                 }
 202                 for _, cg := range ent.CompactGenomes {
 203                         if matchGenome.MatchString(cg.Name) {
 204                                 cmd.cgnames = append(cmd.cgnames, cg.Name)
 205                         }
 206                 }
 207                 for _, tv := range ent.TileVariants {
 208                         if tv.Ref {
 209                                 reftiledata[tileLibRef{tv.Tag, tv.Variant}] = tv.Sequence
 210                         }
 211                 }
 212                 return nil
 213         })
 214         if err != nil {
 215                 return err
 216         }
 217         in0.Close()
 218         if refseq == nil {
 219                 err = fmt.Errorf("%s: reference sequence not found", infiles[0])
 220                 return err
 221         }
 222         if len(tagset) == 0 {
 223                 err = fmt.Errorf("tagset not found")
 224                 return err
 225         }
 226
 227         taglib := &tagLibrary{}
 228         err = taglib.setTags(tagset)
 229         if err != nil {
 230                 return err
 231         }
 232         taglen := taglib.TagLen()
 233         sort.Strings(cmd.cgnames)
 234
 235         if len(cmd.cgnames) == 0 {
 236                 return fmt.Errorf("fatal: 0 matching samples in library, nothing to do")
 237         }
 238         cmd.trainingSet = make([]int, len(cmd.cgnames))
 239         if *samplesFilename == "" {
 240                 cmd.trainingSetSize = len(cmd.cgnames)
 241                 for i, name := range cmd.cgnames {
 242                         cmd.samples = append(cmd.samples, sampleInfo{
 243                                 id:         trimFilenameForLabel(name),
 244                                 isTraining: true,
 245                         })
 246                         cmd.trainingSet[i] = i
 247                 }
 248         } else if len(cmd.cgnames) != len(cmd.samples) {
 249                 return fmt.Errorf("mismatched sample list: %d samples in library, %d in %s", len(cmd.cgnames), len(cmd.samples), *samplesFilename)
 250         } else {
 251                 for i, name := range cmd.cgnames {
 252                         if s := trimFilenameForLabel(name); s != cmd.samples[i].id {
 253                                 return fmt.Errorf("mismatched sample list: sample %d is %q in library, %q in %s", i, s, cmd.samples[i].id, *samplesFilename)
 254                         }
 255                 }
 256                 if *caseControlOnly {
 257                         for i := 0; i < len(cmd.samples); i++ {
 258                                 if !cmd.samples[i].isTraining && !cmd.samples[i].isValidation {
 259                                         if i+1 < len(cmd.samples) {
 260                                                 copy(cmd.samples[i:], cmd.samples[i+1:])
 261                                                 copy(cmd.cgnames[i:], cmd.cgnames[i+1:])
 262                                         }
 263                                         cmd.samples = cmd.samples[:len(cmd.samples)-1]
 264                                         cmd.cgnames = cmd.cgnames[:len(cmd.cgnames)-1]
 265                                         i--
 266                                 }
 267                         }
 268                 }
 269                 cmd.trainingSetSize = 0
 270                 for i := range cmd.cgnames {
 271                         if cmd.samples[i].isTraining {
 272                                 cmd.trainingSet[i] = cmd.trainingSetSize
 273                                 cmd.trainingSetSize++
 274                         } else {
 275                                 cmd.trainingSet[i] = -1
 276                         }
 277                 }
 278         }
 279         if cmd.filter.MinCoverage == 1 {
 280                 // In the generic formula below, floating point
 281                 // arithmetic can effectively push the coverage
 282                 // threshold above 1.0, which is impossible/useless.
 283                 // 1.0 needs to mean exactly 100% coverage.
 284                 cmd.minCoverage = len(cmd.cgnames)
 285         } else {
 286                 cmd.minCoverage = int(math.Ceil(cmd.filter.MinCoverage * float64(len(cmd.cgnames))))
 287         }
 288
 289         {
 290                 samplesOutFilename := *outputDir + "/samples.csv"
 291                 log.Infof("writing sample metadata to %s", samplesOutFilename)
 292                 var f *os.File
 293                 f, err = os.Create(samplesOutFilename)
 294                 if err != nil {
 295                         return err
 296                 }
 297                 defer f.Close()
 298                 for i, si := range cmd.samples {
 299                         var cc, tv string
 300                         if si.isCase {
 301                                 cc = "1"
 302                         } else if si.isControl {
 303                                 cc = "0"
 304                         }
 305                         if si.isTraining {
 306                                 tv = "1"
 307                         } else {
 308                                 tv = "0"
 309                         }
 310                         _, err = fmt.Fprintf(f, "%d,%s,%s,%s\n", i, si.id, cc, tv)
 311                         if err != nil {
 312                                 err = fmt.Errorf("write %s: %w", samplesOutFilename, err)
 313                                 return err
 314                         }
 315                 }
 316                 err = f.Close()
 317                 if err != nil {
 318                         err = fmt.Errorf("close %s: %w", samplesOutFilename, err)
 319                         return err
 320                 }
 321                 log.Print("done")
 322         }
 323
 324         log.Info("indexing reference tiles")
 325         type reftileinfo struct {
 326                 variant  tileVariantID
 327                 seqname  string // chr1
 328                 pos      int    // distance from start of chromosome to starttag
 329                 tiledata []byte // acgtggcaa...
 330                 excluded bool   // true if excluded by regions file
 331                 nexttag  tagID  // tagID of following tile (-1 for last tag of chromosome)
 332         }
 333         isdup := map[tagID]bool{}
 334         reftile := map[tagID]*reftileinfo{}
 335         for seqname, cseq := range refseq {
 336                 pos := 0
 337                 lastreftag := tagID(-1)
 338                 for _, libref := range cseq {
 339                         if cmd.filter.MaxTag >= 0 && libref.Tag > tagID(cmd.filter.MaxTag) {
 340                                 continue
 341                         }
 342                         tiledata := reftiledata[libref]
 343                         if len(tiledata) == 0 {
 344                                 err = fmt.Errorf("missing tiledata for tag %d variant %d in %s in ref", libref.Tag, libref.Variant, seqname)
 345                                 return err
 346                         }
 347                         foundthistag := false
 348                         taglib.FindAll(tiledata[:len(tiledata)-1], func(tagid tagID, offset, _ int) {
 349                                 if !foundthistag && tagid == libref.Tag {
 350                                         foundthistag = true
 351                                         return
 352                                 }
 353                                 if dupref, ok := reftile[tagid]; ok {
 354                                         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)
 355                                         delete(reftile, tagid)
 356                                 } else {
 357                                         log.Printf("found tag %d at offset %d inside tile variant %+v on %s @ %d", tagid, offset, libref, seqname, pos+offset+1)
 358                                 }
 359                                 isdup[tagid] = true
 360                         })
 361                         if isdup[libref.Tag] {
 362                                 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
 363                         } else if reftile[libref.Tag] != nil {
 364                                 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)
 365                                 delete(reftile, libref.Tag)
 366                                 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
 367                                 isdup[libref.Tag] = true
 368                         } else {
 369                                 reftile[libref.Tag] = &reftileinfo{
 370                                         seqname:  seqname,
 371                                         variant:  libref.Variant,
 372                                         tiledata: tiledata,
 373                                         pos:      pos,
 374                                         nexttag:  -1,
 375                                 }
 376                                 if lastreftag >= 0 {
 377                                         reftile[lastreftag].nexttag = libref.Tag
 378                                 }
 379                                 lastreftag = libref.Tag
 380                         }
 381                         pos += len(tiledata) - taglen
 382                 }
 383                 log.Printf("... %s done, len %d", seqname, pos+taglen)
 384         }
 385
 386         var mask *mask
 387         if *regionsFilename != "" {
 388                 log.Printf("loading regions from %s", *regionsFilename)
 389                 mask, err = makeMask(*regionsFilename, *expandRegions)
 390                 if err != nil {
 391                         return err
 392                 }
 393                 log.Printf("before applying mask, len(reftile) == %d", len(reftile))
 394                 log.Printf("deleting reftile entries for regions outside %d intervals", mask.Len())
 395                 for _, rt := range reftile {
 396                         if !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(rt.tiledata)) {
 397                                 rt.excluded = true
 398                         }
 399                 }
 400                 log.Printf("after applying mask, len(reftile) == %d", len(reftile))
 401         }
 402
 403         type hgvsColSet map[hgvs.Variant][2][]int8
 404         encodeHGVS := throttle{Max: len(refseq)}
 405         encodeHGVSTodo := map[string]chan hgvsColSet{}
 406         tmpHGVSCols := map[string]*os.File{}
 407         if *hgvsChunked {
 408                 for seqname := range refseq {
 409                         var f *os.File
 410                         f, err = os.Create(*outputDir + "/tmp." + seqname + ".gob")
 411                         if err != nil {
 412                                 return err
 413                         }
 414                         defer os.Remove(f.Name())
 415                         bufw := bufio.NewWriterSize(f, 1<<24)
 416                         enc := gob.NewEncoder(bufw)
 417                         tmpHGVSCols[seqname] = f
 418                         todo := make(chan hgvsColSet, 128)
 419                         encodeHGVSTodo[seqname] = todo
 420                         encodeHGVS.Go(func() error {
 421                                 for colset := range todo {
 422                                         err := enc.Encode(colset)
 423                                         if err != nil {
 424                                                 encodeHGVS.Report(err)
 425                                                 for range todo {
 426                                                 }
 427                                                 return err
 428                                         }
 429                                 }
 430                                 return bufw.Flush()
 431                         })
 432                 }
 433         }
 434
 435         var toMerge [][]int16
 436         if *mergeOutput || *hgvsSingle {
 437                 toMerge = make([][]int16, len(infiles))
 438         }
 439         var onehotIndirect [][2][]uint32 // [chunkIndex][axis][index]
 440         var onehotChunkSize []uint32
 441         var onehotXrefs [][]onehotXref
 442         if *onehotSingle || *onlyPCA {
 443                 onehotIndirect = make([][2][]uint32, len(infiles))
 444                 onehotChunkSize = make([]uint32, len(infiles))
 445                 onehotXrefs = make([][]onehotXref, len(infiles))
 446         }
 447         chunkStartTag := make([]tagID, len(infiles))
 448
 449         throttleMem := throttle{Max: cmd.threads} // TODO: estimate using mem and data size
 450         throttleNumpyMem := throttle{Max: cmd.threads/2 + 1}
 451         log.Info("generating annotations and numpy matrix for each slice")
 452         var errSkip = errors.New("skip infile")
 453         var done int64
 454         for infileIdx, infile := range infiles {
 455                 infileIdx, infile := infileIdx, infile
 456                 throttleMem.Go(func() error {
 457                         seq := make(map[tagID][]TileVariant, 50000)
 458                         cgs := make(map[string]CompactGenome, len(cmd.cgnames))
 459                         f, err := open(infile)
 460                         if err != nil {
 461                                 return err
 462                         }
 463                         defer f.Close()
 464                         log.Infof("%04d: reading %s", infileIdx, infile)
 465                         err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
 466                                 for _, tv := range ent.TileVariants {
 467                                         if tv.Ref {
 468                                                 continue
 469                                         }
 470                                         // Skip tile with no
 471                                         // corresponding ref tile, if
 472                                         // mask is in play (we can't
 473                                         // determine coordinates for
 474                                         // these)
 475                                         if mask != nil && reftile[tv.Tag] == nil {
 476                                                 continue
 477                                         }
 478                                         // Skip tile whose
 479                                         // corresponding ref tile is
 480                                         // outside target regions --
 481                                         // unless it's a potential
 482                                         // spanning tile.
 483                                         if mask != nil && reftile[tv.Tag].excluded &&
 484                                                 (int(tv.Tag+1) >= len(tagset) ||
 485                                                         (bytes.HasSuffix(tv.Sequence, tagset[tv.Tag+1]) && reftile[tv.Tag+1] != nil && !reftile[tv.Tag+1].excluded)) {
 486                                                 continue
 487                                         }
 488                                         if tv.Tag == cmd.debugTag {
 489                                                 log.Printf("infile %d %s tag %d variant %d hash %x", infileIdx, infile, tv.Tag, tv.Variant, tv.Blake2b[:3])
 490                                         }
 491                                         variants := seq[tv.Tag]
 492                                         if len(variants) == 0 {
 493                                                 variants = make([]TileVariant, 100)
 494                                         }
 495                                         for len(variants) <= int(tv.Variant) {
 496                                                 variants = append(variants, TileVariant{})
 497                                         }
 498                                         variants[int(tv.Variant)] = tv
 499                                         seq[tv.Tag] = variants
 500                                 }
 501                                 for _, cg := range ent.CompactGenomes {
 502                                         if cmd.filter.MaxTag >= 0 && cg.StartTag > tagID(cmd.filter.MaxTag) {
 503                                                 return errSkip
 504                                         }
 505                                         if !matchGenome.MatchString(cg.Name) {
 506                                                 continue
 507                                         }
 508                                         // pad to full slice size
 509                                         // to avoid out-of-bounds
 510                                         // checks later
 511                                         if sliceSize := 2 * int(cg.EndTag-cg.StartTag); len(cg.Variants) < sliceSize {
 512                                                 cg.Variants = append(cg.Variants, make([]tileVariantID, sliceSize-len(cg.Variants))...)
 513                                         }
 514                                         cgs[cg.Name] = cg
 515                                 }
 516                                 return nil
 517                         })
 518                         if err == errSkip {
 519                                 return nil
 520                         } else if err != nil {
 521                                 return fmt.Errorf("%04d: DecodeLibrary(%s): err", infileIdx, infile)
 522                         }
 523                         tagstart := cgs[cmd.cgnames[0]].StartTag
 524                         tagend := cgs[cmd.cgnames[0]].EndTag
 525                         chunkStartTag[infileIdx] = tagstart
 526
 527                         // TODO: filters
 528
 529                         log.Infof("%04d: renumber/dedup variants for tags %d-%d", infileIdx, tagstart, tagend)
 530                         variantRemap := make([][]tileVariantID, tagend-tagstart)
 531                         throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
 532                         for tag, variants := range seq {
 533                                 tag, variants := tag, variants
 534                                 throttleCPU.Go(func() error {
 535                                         alleleCoverage := 0
 536                                         count := make(map[[blake2b.Size256]byte]int, len(variants))
 537
 538                                         rt := reftile[tag]
 539                                         if rt != nil {
 540                                                 count[blake2b.Sum256(rt.tiledata)] = 0
 541                                         }
 542
 543                                         for cgname, cg := range cgs {
 544                                                 idx := int(tag-tagstart) * 2
 545                                                 for allele := 0; allele < 2; allele++ {
 546                                                         v := cg.Variants[idx+allele]
 547                                                         if v > 0 && len(variants[v].Sequence) > 0 {
 548                                                                 count[variants[v].Blake2b]++
 549                                                                 alleleCoverage++
 550                                                         }
 551                                                         if v > 0 && tag == cmd.debugTag {
 552                                                                 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])
 553                                                         }
 554                                                 }
 555                                         }
 556                                         if alleleCoverage < cmd.minCoverage*2 {
 557                                                 idx := int(tag-tagstart) * 2
 558                                                 for _, cg := range cgs {
 559                                                         cg.Variants[idx] = 0
 560                                                         cg.Variants[idx+1] = 0
 561                                                 }
 562                                                 if tag == cmd.debugTag {
 563                                                         log.Printf("tag %d alleleCoverage %d < min %d, sample data wiped", tag, alleleCoverage, cmd.minCoverage*2)
 564                                                 }
 565                                                 return nil
 566                                         }
 567
 568                                         // hash[i] will be the hash of
 569                                         // the variant(s) that should
 570                                         // be at rank i (0-based).
 571                                         hash := make([][blake2b.Size256]byte, 0, len(count))
 572                                         for b := range count {
 573                                                 hash = append(hash, b)
 574                                         }
 575                                         sort.Slice(hash, func(i, j int) bool {
 576                                                 bi, bj := &hash[i], &hash[j]
 577                                                 if ci, cj := count[*bi], count[*bj]; ci != cj {
 578                                                         return ci > cj
 579                                                 } else {
 580                                                         return bytes.Compare((*bi)[:], (*bj)[:]) < 0
 581                                                 }
 582                                         })
 583                                         // rank[b] will be the 1-based
 584                                         // new variant number for
 585                                         // variants whose hash is b.
 586                                         rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
 587                                         for i, h := range hash {
 588                                                 rank[h] = tileVariantID(i + 1)
 589                                         }
 590                                         if tag == cmd.debugTag {
 591                                                 for h, r := range rank {
 592                                                         log.Printf("tag %d rank(%x) = %v", tag, h[:3], r)
 593                                                 }
 594                                         }
 595                                         // remap[v] will be the new
 596                                         // variant number for original
 597                                         // variant number v.
 598                                         remap := make([]tileVariantID, len(variants))
 599                                         for i, tv := range variants {
 600                                                 remap[i] = rank[tv.Blake2b]
 601                                         }
 602                                         if tag == cmd.debugTag {
 603                                                 for in, out := range remap {
 604                                                         if out > 0 {
 605                                                                 log.Printf("tag %d remap %d => %d", tag, in, out)
 606                                                         }
 607                                                 }
 608                                         }
 609                                         variantRemap[tag-tagstart] = remap
 610                                         if rt != nil {
 611                                                 refrank := rank[blake2b.Sum256(rt.tiledata)]
 612                                                 if tag == cmd.debugTag {
 613                                                         log.Printf("tag %d reftile variant %d => %d", tag, rt.variant, refrank)
 614                                                 }
 615                                                 rt.variant = refrank
 616                                         }
 617                                         return nil
 618                                 })
 619                         }
 620                         throttleCPU.Wait()
 621
 622                         var onehotChunk [][]int8
 623                         var onehotXref []onehotXref
 624
 625                         var annotationsFilename string
 626                         if *onlyPCA {
 627                                 annotationsFilename = "/dev/null"
 628                         } else {
 629                                 annotationsFilename = fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
 630                                 log.Infof("%04d: writing %s", infileIdx, annotationsFilename)
 631                         }
 632                         annof, err := os.Create(annotationsFilename)
 633                         if err != nil {
 634                                 return err
 635                         }
 636                         annow := bufio.NewWriterSize(annof, 1<<20)
 637                         outcol := 0
 638                         for tag := tagstart; tag < tagend; tag++ {
 639                                 rt := reftile[tag]
 640                                 if rt == nil && mask != nil {
 641                                         // With no ref tile, we don't
 642                                         // have coordinates to say
 643                                         // this is in the desired
 644                                         // regions -- so it's not.
 645                                         // TODO: handle ref spanning
 646                                         // tile case.
 647                                         continue
 648                                 }
 649                                 if rt != nil && rt.excluded {
 650                                         // TODO: don't skip yet --
 651                                         // first check for spanning
 652                                         // tile variants that
 653                                         // intersect non-excluded ref
 654                                         // tiles.
 655                                         continue
 656                                 }
 657                                 if cmd.filter.MaxTag >= 0 && tag > tagID(cmd.filter.MaxTag) {
 658                                         break
 659                                 }
 660                                 remap := variantRemap[tag-tagstart]
 661                                 if remap == nil {
 662                                         // was not assigned above,
 663                                         // because minCoverage
 664                                         continue
 665                                 }
 666                                 maxv := tileVariantID(0)
 667                                 for _, v := range remap {
 668                                         if maxv < v {
 669                                                 maxv = v
 670                                         }
 671                                 }
 672                                 if *onehotChunked || *onehotSingle || *onlyPCA {
 673                                         onehot, xrefs := cmd.tv2homhet(cgs, maxv, remap, tag, tagstart, seq)
 674                                         if tag == cmd.debugTag {
 675                                                 log.WithFields(logrus.Fields{
 676                                                         "onehot": onehot,
 677                                                         "xrefs":  xrefs,
 678                                                 }).Info("tv2homhet()")
 679                                         }
 680                                         onehotChunk = append(onehotChunk, onehot...)
 681                                         onehotXref = append(onehotXref, xrefs...)
 682                                 }
 683                                 if *onlyPCA {
 684                                         outcol++
 685                                         continue
 686                                 }
 687                                 if rt == nil {
 688                                         // Reference does not use any
 689                                         // variant of this tile
 690                                         //
 691                                         // TODO: diff against the
 692                                         // relevant portion of the
 693                                         // ref's spanning tile
 694                                         outcol++
 695                                         continue
 696                                 }
 697                                 fmt.Fprintf(annow, "%d,%d,%d,=,%s,%d,,,\n", tag, outcol, rt.variant, rt.seqname, rt.pos)
 698                                 variants := seq[tag]
 699                                 reftilestr := strings.ToUpper(string(rt.tiledata))
 700
 701                                 done := make([]bool, maxv+1)
 702                                 variantDiffs := make([][]hgvs.Variant, maxv+1)
 703                                 for v, tv := range variants {
 704                                         v := remap[v]
 705                                         if v == 0 || v == rt.variant || done[v] {
 706                                                 continue
 707                                         } else {
 708                                                 done[v] = true
 709                                         }
 710                                         if len(tv.Sequence) < taglen {
 711                                                 continue
 712                                         }
 713                                         // if reftilestr doesn't end
 714                                         // in the same tag as tv,
 715                                         // extend reftilestr with
 716                                         // following ref tiles until
 717                                         // it does (up to an arbitrary
 718                                         // sanity-check limit)
 719                                         reftilestr := reftilestr
 720                                         endtagstr := strings.ToUpper(string(tv.Sequence[len(tv.Sequence)-taglen:]))
 721                                         for i, rt := 0, rt; i < annotationMaxTileSpan && !strings.HasSuffix(reftilestr, endtagstr) && rt.nexttag >= 0; i++ {
 722                                                 rt = reftile[rt.nexttag]
 723                                                 if rt == nil {
 724                                                         break
 725                                                 }
 726                                                 reftilestr += strings.ToUpper(string(rt.tiledata[taglen:]))
 727                                         }
 728                                         if mask != nil && !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(reftilestr)) {
 729                                                 continue
 730                                         }
 731                                         if !strings.HasSuffix(reftilestr, endtagstr) {
 732                                                 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
 733                                                 continue
 734                                         }
 735                                         if lendiff := len(reftilestr) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
 736                                                 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
 737                                                 continue
 738                                         }
 739                                         diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
 740                                         for i := range diffs {
 741                                                 diffs[i].Position += rt.pos
 742                                         }
 743                                         for _, diff := range diffs {
 744                                                 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)
 745                                         }
 746                                         if *hgvsChunked {
 747                                                 variantDiffs[v] = diffs
 748                                         }
 749                                 }
 750                                 if *hgvsChunked {
 751                                         // We can now determine, for each HGVS
 752                                         // variant (diff) in this reftile
 753                                         // region, whether a given genome
 754                                         // phase/allele (1) has the variant, (0) has
 755                                         // =ref or a different variant in that
 756                                         // position, or (-1) is lacking
 757                                         // coverage / couldn't be diffed.
 758                                         hgvsCol := hgvsColSet{}
 759                                         for _, diffs := range variantDiffs {
 760                                                 for _, diff := range diffs {
 761                                                         if _, ok := hgvsCol[diff]; ok {
 762                                                                 continue
 763                                                         }
 764                                                         hgvsCol[diff] = [2][]int8{
 765                                                                 make([]int8, len(cmd.cgnames)),
 766                                                                 make([]int8, len(cmd.cgnames)),
 767                                                         }
 768                                                 }
 769                                         }
 770                                         for row, name := range cmd.cgnames {
 771                                                 variants := cgs[name].Variants[(tag-tagstart)*2:]
 772                                                 for ph := 0; ph < 2; ph++ {
 773                                                         v := variants[ph]
 774                                                         if int(v) >= len(remap) {
 775                                                                 v = 0
 776                                                         } else {
 777                                                                 v = remap[v]
 778                                                         }
 779                                                         if v == rt.variant {
 780                                                                 // hgvsCol[*][ph][row] is already 0
 781                                                         } else if len(variantDiffs[v]) == 0 {
 782                                                                 // lacking coverage / couldn't be diffed
 783                                                                 for _, col := range hgvsCol {
 784                                                                         col[ph][row] = -1
 785                                                                 }
 786                                                         } else {
 787                                                                 for _, diff := range variantDiffs[v] {
 788                                                                         hgvsCol[diff][ph][row] = 1
 789                                                                 }
 790                                                         }
 791                                                 }
 792                                         }
 793                                         for diff, colpair := range hgvsCol {
 794                                                 allele2homhet(colpair)
 795                                                 if !cmd.filterHGVScolpair(colpair) {
 796                                                         delete(hgvsCol, diff)
 797                                                 }
 798                                         }
 799                                         if len(hgvsCol) > 0 {
 800                                                 encodeHGVSTodo[rt.seqname] <- hgvsCol
 801                                         }
 802                                 }
 803                                 outcol++
 804                         }
 805                         err = annow.Flush()
 806                         if err != nil {
 807                                 return err
 808                         }
 809                         err = annof.Close()
 810                         if err != nil {
 811                                 return err
 812                         }
 813
 814                         if *onehotChunked {
 815                                 // transpose onehotChunk[col][row] to numpy[row*ncols+col]
 816                                 rows := len(cmd.cgnames)
 817                                 cols := len(onehotChunk)
 818                                 log.Infof("%04d: preparing onehot numpy (rows=%d, cols=%d, mem=%d)", infileIdx, rows, cols, rows*cols)
 819                                 throttleNumpyMem.Acquire()
 820                                 out := onehotcols2int8(onehotChunk)
 821                                 fnm := fmt.Sprintf("%s/onehot.%04d.npy", *outputDir, infileIdx)
 822                                 err = writeNumpyInt8(fnm, out, rows, cols)
 823                                 if err != nil {
 824                                         return err
 825                                 }
 826                                 fnm = fmt.Sprintf("%s/onehot-columns.%04d.npy", *outputDir, infileIdx)
 827                                 err = writeNumpyInt32(fnm, onehotXref2int32(onehotXref), 4, len(onehotXref))
 828                                 if err != nil {
 829                                         return err
 830                                 }
 831                                 debug.FreeOSMemory()
 832                                 throttleNumpyMem.Release()
 833                         }
 834                         if *onehotSingle || *onlyPCA {
 835                                 onehotIndirect[infileIdx] = onehotChunk2Indirect(onehotChunk)
 836                                 onehotChunkSize[infileIdx] = uint32(len(onehotChunk))
 837                                 onehotXrefs[infileIdx] = onehotXref
 838                                 n := len(onehotIndirect[infileIdx][0])
 839                                 log.Infof("%04d: keeping onehot coordinates in memory (n=%d, mem=%d)", infileIdx, n, n*8*2)
 840                         }
 841                         if !(*onehotSingle || *onehotChunked || *onlyPCA) || *mergeOutput || *hgvsSingle {
 842                                 log.Infof("%04d: preparing numpy (rows=%d, cols=%d)", infileIdx, len(cmd.cgnames), 2*outcol)
 843                                 throttleNumpyMem.Acquire()
 844                                 rows := len(cmd.cgnames)
 845                                 cols := 2 * outcol
 846                                 out := make([]int16, rows*cols)
 847                                 for row, name := range cmd.cgnames {
 848                                         outidx := row * cols
 849                                         for col, v := range cgs[name].Variants {
 850                                                 tag := tagstart + tagID(col/2)
 851                                                 if cmd.filter.MaxTag >= 0 && tag > tagID(cmd.filter.MaxTag) {
 852                                                         break
 853                                                 }
 854                                                 if rt := reftile[tag]; rt == nil || rt.excluded {
 855                                                         continue
 856                                                 }
 857                                                 if v == 0 {
 858                                                         out[outidx] = 0 // tag not found / spanning tile
 859                                                 } else if variants, ok := seq[tag]; ok && int(v) < len(variants) && len(variants[v].Sequence) > 0 {
 860                                                         out[outidx] = int16(variantRemap[tag-tagstart][v])
 861                                                 } else {
 862                                                         out[outidx] = -1 // low quality tile variant
 863                                                 }
 864                                                 if tag == cmd.debugTag {
 865                                                         log.Printf("tag %d row %d col %d outidx %d v %d out %d", tag, row, col, outidx, v, out[outidx])
 866                                                 }
 867                                                 outidx++
 868                                         }
 869                                 }
 870                                 seq = nil
 871                                 cgs = nil
 872                                 debug.FreeOSMemory()
 873                                 throttleNumpyMem.Release()
 874                                 if *mergeOutput || *hgvsSingle {
 875                                         log.Infof("%04d: matrix fragment %d rows x %d cols", infileIdx, rows, cols)
 876                                         toMerge[infileIdx] = out
 877                                 }
 878                                 if !*mergeOutput && !*onehotChunked && !*onehotSingle {
 879                                         fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
 880                                         err = writeNumpyInt16(fnm, out, rows, cols)
 881                                         if err != nil {
 882                                                 return err
 883                                         }
 884                                 }
 885                         }
 886                         debug.FreeOSMemory()
 887                         log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
 888                         return nil
 889                 })
 890         }
 891         if err = throttleMem.Wait(); err != nil {
 892                 return err
 893         }
 894
 895         if *hgvsChunked {
 896                 log.Info("flushing hgvsCols temp files")
 897                 for seqname := range refseq {
 898                         close(encodeHGVSTodo[seqname])
 899                 }
 900                 err = encodeHGVS.Wait()
 901                 if err != nil {
 902                         return err
 903                 }
 904                 for seqname := range refseq {
 905                         log.Infof("%s: reading hgvsCols from temp file", seqname)
 906                         f := tmpHGVSCols[seqname]
 907                         _, err = f.Seek(0, io.SeekStart)
 908                         if err != nil {
 909                                 return err
 910                         }
 911                         var hgvsCols hgvsColSet
 912                         dec := gob.NewDecoder(bufio.NewReaderSize(f, 1<<24))
 913                         for err == nil {
 914                                 err = dec.Decode(&hgvsCols)
 915                         }
 916                         if err != io.EOF {
 917                                 return err
 918                         }
 919                         log.Infof("%s: sorting %d hgvs variants", seqname, len(hgvsCols))
 920                         variants := make([]hgvs.Variant, 0, len(hgvsCols))
 921                         for v := range hgvsCols {
 922                                 variants = append(variants, v)
 923                         }
 924                         sort.Slice(variants, func(i, j int) bool {
 925                                 vi, vj := &variants[i], &variants[j]
 926                                 if vi.Position != vj.Position {
 927                                         return vi.Position < vj.Position
 928                                 } else if vi.Ref != vj.Ref {
 929                                         return vi.Ref < vj.Ref
 930                                 } else {
 931                                         return vi.New < vj.New
 932                                 }
 933                         })
 934                         rows := len(cmd.cgnames)
 935                         cols := len(variants) * 2
 936                         log.Infof("%s: building hgvs matrix (rows=%d, cols=%d, mem=%d)", seqname, rows, cols, rows*cols)
 937                         out := make([]int8, rows*cols)
 938                         for varIdx, variant := range variants {
 939                                 hgvsCols := hgvsCols[variant]
 940                                 for row := range cmd.cgnames {
 941                                         for ph := 0; ph < 2; ph++ {
 942                                                 out[row*cols+varIdx+ph] = hgvsCols[ph][row]
 943                                         }
 944                                 }
 945                         }
 946                         err = writeNumpyInt8(fmt.Sprintf("%s/hgvs.%s.npy", *outputDir, seqname), out, rows, cols)
 947                         if err != nil {
 948                                 return err
 949                         }
 950                         out = nil
 951
 952                         fnm := fmt.Sprintf("%s/hgvs.%s.annotations.csv", *outputDir, seqname)
 953                         log.Infof("%s: writing hgvs column labels to %s", seqname, fnm)
 954                         var hgvsLabels bytes.Buffer
 955                         for varIdx, variant := range variants {
 956                                 fmt.Fprintf(&hgvsLabels, "%d,%s:g.%s\n", varIdx, seqname, variant.String())
 957                         }
 958                         err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0666)
 959                         if err != nil {
 960                                 return err
 961                         }
 962                 }
 963         }
 964
 965         if *mergeOutput || *hgvsSingle {
 966                 var annow *bufio.Writer
 967                 var annof *os.File
 968                 if *mergeOutput {
 969                         annoFilename := fmt.Sprintf("%s/matrix.annotations.csv", *outputDir)
 970                         annof, err = os.Create(annoFilename)
 971                         if err != nil {
 972                                 return err
 973                         }
 974                         annow = bufio.NewWriterSize(annof, 1<<20)
 975                 }
 976
 977                 rows := len(cmd.cgnames)
 978                 cols := 0
 979                 for _, chunk := range toMerge {
 980                         cols += len(chunk) / rows
 981                 }
 982                 log.Infof("merging output matrix (rows=%d, cols=%d, mem=%d) and annotations", rows, cols, rows*cols*2)
 983                 var out []int16
 984                 if *mergeOutput {
 985                         out = make([]int16, rows*cols)
 986                 }
 987                 hgvsCols := map[string][2][]int16{} // hgvs -> [[g0,g1,g2,...], [g0,g1,g2,...]] (slice of genomes for each phase)
 988                 startcol := 0
 989                 for outIdx, chunk := range toMerge {
 990                         chunkcols := len(chunk) / rows
 991                         if *mergeOutput {
 992                                 for row := 0; row < rows; row++ {
 993                                         copy(out[row*cols+startcol:], chunk[row*chunkcols:(row+1)*chunkcols])
 994                                 }
 995                         }
 996                         toMerge[outIdx] = nil
 997
 998                         annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, outIdx)
 999                         log.Infof("reading %s", annotationsFilename)
1000                         buf, err := os.ReadFile(annotationsFilename)
1001                         if err != nil {
1002                                 return err
1003                         }
1004                         if *mergeOutput {
1005                                 err = os.Remove(annotationsFilename)
1006                                 if err != nil {
1007                                         return err
1008                                 }
1009                         }
1010                         for _, line := range bytes.Split(buf, []byte{'\n'}) {
1011                                 if len(line) == 0 {
1012                                         continue
1013                                 }
1014                                 fields := bytes.SplitN(line, []byte{','}, 9)
1015                                 tag, _ := strconv.Atoi(string(fields[0]))
1016                                 incol, _ := strconv.Atoi(string(fields[1]))
1017                                 tileVariant, _ := strconv.Atoi(string(fields[2]))
1018                                 hgvsID := string(fields[3])
1019                                 seqname := string(fields[4])
1020                                 pos, _ := strconv.Atoi(string(fields[5]))
1021                                 refseq := fields[6]
1022                                 if hgvsID == "" {
1023                                         // Null entry for un-diffable
1024                                         // tile variant
1025                                         continue
1026                                 }
1027                                 if hgvsID == "=" {
1028                                         // Null entry for ref tile
1029                                         continue
1030                                 }
1031                                 if mask != nil && !mask.Check(strings.TrimPrefix(seqname, "chr"), pos, pos+len(refseq)) {
1032                                         // The tile intersects one of
1033                                         // the selected regions, but
1034                                         // this particular HGVS
1035                                         // variant does not.
1036                                         continue
1037                                 }
1038                                 hgvsColPair := hgvsCols[hgvsID]
1039                                 if hgvsColPair[0] == nil {
1040                                         // values in new columns start
1041                                         // out as -1 ("no data yet")
1042                                         // or 0 ("=ref") here, may
1043                                         // change to 1 ("hgvs variant
1044                                         // present") below, either on
1045                                         // this line or a future line.
1046                                         hgvsColPair = [2][]int16{make([]int16, len(cmd.cgnames)), make([]int16, len(cmd.cgnames))}
1047                                         rt, ok := reftile[tagID(tag)]
1048                                         if !ok {
1049                                                 err = fmt.Errorf("bug: seeing annotations for tag %d, but it has no reftile entry", tag)
1050                                                 return err
1051                                         }
1052                                         for ph := 0; ph < 2; ph++ {
1053                                                 for row := 0; row < rows; row++ {
1054                                                         v := chunk[row*chunkcols+incol*2+ph]
1055                                                         if tileVariantID(v) == rt.variant {
1056                                                                 hgvsColPair[ph][row] = 0
1057                                                         } else {
1058                                                                 hgvsColPair[ph][row] = -1
1059                                                         }
1060                                                 }
1061                                         }
1062                                         hgvsCols[hgvsID] = hgvsColPair
1063                                         if annow != nil {
1064                                                 hgvsref := hgvs.Variant{
1065                                                         Position: pos,
1066                                                         Ref:      string(refseq),
1067                                                         New:      string(refseq),
1068                                                 }
1069                                                 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])
1070                                         }
1071                                 }
1072                                 if annow != nil {
1073                                         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])
1074                                 }
1075                                 for ph := 0; ph < 2; ph++ {
1076                                         for row := 0; row < rows; row++ {
1077                                                 v := chunk[row*chunkcols+incol*2+ph]
1078                                                 if int(v) == tileVariant {
1079                                                         hgvsColPair[ph][row] = 1
1080                                                 }
1081                                         }
1082                                 }
1083                         }
1084
1085                         startcol += chunkcols
1086                 }
1087                 if *mergeOutput {
1088                         err = annow.Flush()
1089                         if err != nil {
1090                                 return err
1091                         }
1092                         err = annof.Close()
1093                         if err != nil {
1094                                 return err
1095                         }
1096                         err = writeNumpyInt16(fmt.Sprintf("%s/matrix.npy", *outputDir), out, rows, cols)
1097                         if err != nil {
1098                                 return err
1099                         }
1100                 }
1101                 out = nil
1102
1103                 if *hgvsSingle {
1104                         cols = len(hgvsCols) * 2
1105                         log.Printf("building hgvs-based matrix: %d rows x %d cols", rows, cols)
1106                         out = make([]int16, rows*cols)
1107                         hgvsIDs := make([]string, 0, cols/2)
1108                         for hgvsID := range hgvsCols {
1109                                 hgvsIDs = append(hgvsIDs, hgvsID)
1110                         }
1111                         sort.Strings(hgvsIDs)
1112                         var hgvsLabels bytes.Buffer
1113                         for idx, hgvsID := range hgvsIDs {
1114                                 fmt.Fprintf(&hgvsLabels, "%d,%s\n", idx, hgvsID)
1115                                 for ph := 0; ph < 2; ph++ {
1116                                         hgvscol := hgvsCols[hgvsID][ph]
1117                                         for row, val := range hgvscol {
1118                                                 out[row*cols+idx*2+ph] = val
1119                                         }
1120                                 }
1121                         }
1122                         err = writeNumpyInt16(fmt.Sprintf("%s/hgvs.npy", *outputDir), out, rows, cols)
1123                         if err != nil {
1124                                 return err
1125                         }
1126
1127                         fnm := fmt.Sprintf("%s/hgvs.annotations.csv", *outputDir)
1128                         log.Printf("writing hgvs labels: %s", fnm)
1129                         err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0777)
1130                         if err != nil {
1131                                 return err
1132                         }
1133                 }
1134         }
1135         if *onehotSingle || *onlyPCA {
1136                 nzCount := 0
1137                 for _, part := range onehotIndirect {
1138                         nzCount += len(part[0])
1139                 }
1140                 onehot := make([]uint32, nzCount*2) // [r,r,r,...,c,c,c,...]
1141                 var xrefs []onehotXref
1142                 chunkOffset := uint32(0)
1143                 outcol := 0
1144                 for i, part := range onehotIndirect {
1145                         for i := range part[1] {
1146                                 part[1][i] += chunkOffset
1147                         }
1148                         copy(onehot[outcol:], part[0])
1149                         copy(onehot[outcol+nzCount:], part[1])
1150                         xrefs = append(xrefs, onehotXrefs[i]...)
1151
1152                         outcol += len(part[0])
1153                         chunkOffset += onehotChunkSize[i]
1154
1155                         part[0] = nil
1156                         part[1] = nil
1157                         onehotXrefs[i] = nil
1158                         debug.FreeOSMemory()
1159                 }
1160                 if *onehotSingle {
1161                         fnm := fmt.Sprintf("%s/onehot.npy", *outputDir)
1162                         err = writeNumpyUint32(fnm, onehot, 2, nzCount)
1163                         if err != nil {
1164                                 return err
1165                         }
1166                         fnm = fmt.Sprintf("%s/onehot-columns.npy", *outputDir)
1167                         err = writeNumpyInt32(fnm, onehotXref2int32(xrefs), 5, len(xrefs))
1168                         if err != nil {
1169                                 return err
1170                         }
1171                 }
1172                 if *onlyPCA {
1173                         cols := 0
1174                         for _, c := range onehot[nzCount:] {
1175                                 if int(c) >= cols {
1176                                         cols = int(c) + 1
1177                                 }
1178                         }
1179                         if cols == 0 {
1180                                 return fmt.Errorf("cannot do PCA: one-hot matrix is empty")
1181                         }
1182                         log.Printf("have %d one-hot cols", cols)
1183                         stride := 1
1184                         for *maxPCATiles > 0 && cols > *maxPCATiles*2 {
1185                                 cols = (cols + 1) / 2
1186                                 stride = stride * 2
1187                         }
1188                         log.Printf("creating full matrix (%d rows) and training matrix (%d rows) with %d cols, stride %d", len(cmd.cgnames), cmd.trainingSetSize, cols, stride)
1189                         mtxFull := mat.NewDense(len(cmd.cgnames), cols, nil)
1190                         mtxTrain := mat.NewDense(cmd.trainingSetSize, cols, nil)
1191                         for i, c := range onehot[nzCount:] {
1192                                 if int(c/2)%stride == 0 {
1193                                         outcol := int(c/2)/stride*2 + int(c)%2
1194                                         mtxFull.Set(int(onehot[i]), outcol, 1)
1195                                         if trainRow := cmd.trainingSet[int(onehot[i])]; trainRow >= 0 {
1196                                                 mtxTrain.Set(trainRow, outcol, 1)
1197                                         }
1198                                 }
1199                         }
1200                         log.Print("fitting")
1201                         transformer := nlp.NewPCA(*pcaComponents)
1202                         transformer.Fit(mtxTrain.T())
1203                         log.Printf("transforming")
1204                         pca, err := transformer.Transform(mtxFull.T())
1205                         if err != nil {
1206                                 return err
1207                         }
1208                         pca = pca.T()
1209                         outrows, outcols := pca.Dims()
1210                         log.Printf("copying result to numpy output array: %d rows, %d cols", outrows, outcols)
1211                         out := make([]float64, outrows*outcols)
1212                         for i := 0; i < outrows; i++ {
1213                                 for j := 0; j < outcols; j++ {
1214                                         out[i*outcols+j] = pca.At(i, j)
1215                                 }
1216                         }
1217                         fnm := fmt.Sprintf("%s/pca.npy", *outputDir)
1218                         log.Printf("writing numpy: %s", fnm)
1219                         output, err := os.OpenFile(fnm, os.O_CREATE|os.O_TRUNC|os.O_WRONLY, 0777)
1220                         if err != nil {
1221                                 return err
1222                         }
1223                         npw, err := gonpy.NewWriter(nopCloser{output})
1224                         if err != nil {
1225                                 return fmt.Errorf("gonpy.NewWriter: %w", err)
1226                         }
1227                         npw.Shape = []int{outrows, outcols}
1228                         err = npw.WriteFloat64(out)
1229                         if err != nil {
1230                                 return fmt.Errorf("WriteFloat64: %w", err)
1231                         }
1232                         err = output.Close()
1233                         if err != nil {
1234                                 return err
1235                         }
1236                         log.Print("done")
1237
1238                         samplesOutFilename := *outputDir + "/samples.csv"
1239                         log.Infof("writing sample metadata to %s", samplesOutFilename)
1240                         var f *os.File
1241                         f, err = os.Create(samplesOutFilename)
1242                         if err != nil {
1243                                 return err
1244                         }
1245                         defer f.Close()
1246                         for i, si := range cmd.samples {
1247                                 var cc, tv string
1248                                 if si.isCase {
1249                                         cc = "1"
1250                                 } else if si.isControl {
1251                                         cc = "0"
1252                                 }
1253                                 if si.isTraining {
1254                                         tv = "1"
1255                                 } else {
1256                                         tv = "0"
1257                                 }
1258                                 var pcavals string
1259                                 for c := 0; c < outcols; c++ {
1260                                         pcavals += fmt.Sprintf(",%f", pca.At(i, c))
1261                                 }
1262                                 _, err = fmt.Fprintf(f, "%d,%s,%s,%s%s\n", i, si.id, cc, tv, pcavals)
1263                                 if err != nil {
1264                                         err = fmt.Errorf("write %s: %w", samplesOutFilename, err)
1265                                         return err
1266                                 }
1267                         }
1268                         err = f.Close()
1269                         if err != nil {
1270                                 err = fmt.Errorf("close %s: %w", samplesOutFilename, err)
1271                                 return err
1272                         }
1273                         log.Print("done")
1274                 }
1275         }
1276         if !*mergeOutput && !*onehotChunked && !*onehotSingle && !*onlyPCA {
1277                 tagoffsetFilename := *outputDir + "/chunk-tag-offset.csv"
1278                 log.Infof("writing tag offsets to %s", tagoffsetFilename)
1279                 var f *os.File
1280                 f, err = os.Create(tagoffsetFilename)
1281                 if err != nil {
1282                         return err
1283                 }
1284                 defer f.Close()
1285                 for idx, offset := range chunkStartTag {
1286                         _, err = fmt.Fprintf(f, "%q,%d\n", fmt.Sprintf("matrix.%04d.npy", idx), offset)
1287                         if err != nil {
1288                                 err = fmt.Errorf("write %s: %w", tagoffsetFilename, err)
1289                                 return err
1290                         }
1291                 }
1292                 err = f.Close()
1293                 if err != nil {
1294                         err = fmt.Errorf("close %s: %w", tagoffsetFilename, err)
1295                         return err
1296                 }
1297         }
1298
1299         return nil
1300 }
1301
1302 type sampleInfo struct {
1303         id            string
1304         isCase        bool
1305         isControl     bool
1306         isTraining    bool
1307         isValidation  bool
1308         pcaComponents []float64
1309 }
1310
1311 // Read samples.csv file with case/control and training/validation
1312 // flags.
1313 func (cmd *sliceNumpy) loadSampleInfo(samplesFilename string) ([]sampleInfo, error) {
1314         var si []sampleInfo
1315         f, err := open(samplesFilename)
1316         if err != nil {
1317                 return nil, err
1318         }
1319         buf, err := io.ReadAll(f)
1320         f.Close()
1321         if err != nil {
1322                 return nil, err
1323         }
1324         lineNum := 0
1325         for _, csv := range bytes.Split(buf, []byte{'\n'}) {
1326                 lineNum++
1327                 if len(csv) == 0 {
1328                         continue
1329                 }
1330                 split := strings.Split(string(csv), ",")
1331                 if len(split) != 4 {
1332                         return nil, fmt.Errorf("%d fields != 4 in %s line %d: %q", len(split), samplesFilename, lineNum, csv)
1333                 }
1334                 if split[0] == "Index" && split[1] == "SampleID" && split[2] == "CaseControl" && split[3] == "TrainingValidation" {
1335                         continue
1336                 }
1337                 idx, err := strconv.Atoi(split[0])
1338                 if err != nil {
1339                         if lineNum == 1 {
1340                                 return nil, fmt.Errorf("header does not look right: %q", csv)
1341                         }
1342                         return nil, fmt.Errorf("%s line %d: index: %s", samplesFilename, lineNum, err)
1343                 }
1344                 if idx != len(si) {
1345                         return nil, fmt.Errorf("%s line %d: index %d out of order", samplesFilename, lineNum, idx)
1346                 }
1347                 si = append(si, sampleInfo{
1348                         id:           split[1],
1349                         isCase:       split[2] == "1",
1350                         isControl:    split[2] == "0",
1351                         isTraining:   split[3] == "1",
1352                         isValidation: split[3] == "0",
1353                 })
1354         }
1355         return si, nil
1356 }
1357
1358 func (cmd *sliceNumpy) filterHGVScolpair(colpair [2][]int8) bool {
1359         if cmd.chi2PValue >= 1 {
1360                 return true
1361         }
1362         col0 := make([]bool, 0, len(cmd.chi2Cases))
1363         col1 := make([]bool, 0, len(cmd.chi2Cases))
1364         cases := make([]bool, 0, len(cmd.chi2Cases))
1365         for i, c := range cmd.chi2Cases {
1366                 if colpair[0][i] < 0 {
1367                         continue
1368                 }
1369                 col0 = append(col0, colpair[0][i] != 0)
1370                 col1 = append(col1, colpair[1][i] != 0)
1371                 cases = append(cases, c)
1372         }
1373         return len(cases) >= cmd.minCoverage &&
1374                 (pvalue(col0, cases) <= cmd.chi2PValue || pvalue(col1, cases) <= cmd.chi2PValue)
1375 }
1376
1377 func writeNumpyUint32(fnm string, out []uint32, rows, cols int) error {
1378         output, err := os.Create(fnm)
1379         if err != nil {
1380                 return err
1381         }
1382         defer output.Close()
1383         bufw := bufio.NewWriterSize(output, 1<<26)
1384         npw, err := gonpy.NewWriter(nopCloser{bufw})
1385         if err != nil {
1386                 return err
1387         }
1388         log.WithFields(log.Fields{
1389                 "filename": fnm,
1390                 "rows":     rows,
1391                 "cols":     cols,
1392                 "bytes":    rows * cols * 4,
1393         }).Infof("writing numpy: %s", fnm)
1394         npw.Shape = []int{rows, cols}
1395         npw.WriteUint32(out)
1396         err = bufw.Flush()
1397         if err != nil {
1398                 return err
1399         }
1400         return output.Close()
1401 }
1402
1403 func writeNumpyInt32(fnm string, out []int32, rows, cols int) error {
1404         output, err := os.Create(fnm)
1405         if err != nil {
1406                 return err
1407         }
1408         defer output.Close()
1409         bufw := bufio.NewWriterSize(output, 1<<26)
1410         npw, err := gonpy.NewWriter(nopCloser{bufw})
1411         if err != nil {
1412                 return err
1413         }
1414         log.WithFields(log.Fields{
1415                 "filename": fnm,
1416                 "rows":     rows,
1417                 "cols":     cols,
1418                 "bytes":    rows * cols * 4,
1419         }).Infof("writing numpy: %s", fnm)
1420         npw.Shape = []int{rows, cols}
1421         npw.WriteInt32(out)
1422         err = bufw.Flush()
1423         if err != nil {
1424                 return err
1425         }
1426         return output.Close()
1427 }
1428
1429 func writeNumpyInt16(fnm string, out []int16, rows, cols int) error {
1430         output, err := os.Create(fnm)
1431         if err != nil {
1432                 return err
1433         }
1434         defer output.Close()
1435         bufw := bufio.NewWriterSize(output, 1<<26)
1436         npw, err := gonpy.NewWriter(nopCloser{bufw})
1437         if err != nil {
1438                 return err
1439         }
1440         log.WithFields(log.Fields{
1441                 "filename": fnm,
1442                 "rows":     rows,
1443                 "cols":     cols,
1444                 "bytes":    rows * cols * 2,
1445         }).Infof("writing numpy: %s", fnm)
1446         npw.Shape = []int{rows, cols}
1447         npw.WriteInt16(out)
1448         err = bufw.Flush()
1449         if err != nil {
1450                 return err
1451         }
1452         return output.Close()
1453 }
1454
1455 func writeNumpyInt8(fnm string, out []int8, rows, cols int) error {
1456         output, err := os.Create(fnm)
1457         if err != nil {
1458                 return err
1459         }
1460         defer output.Close()
1461         bufw := bufio.NewWriterSize(output, 1<<26)
1462         npw, err := gonpy.NewWriter(nopCloser{bufw})
1463         if err != nil {
1464                 return err
1465         }
1466         log.WithFields(log.Fields{
1467                 "filename": fnm,
1468                 "rows":     rows,
1469                 "cols":     cols,
1470                 "bytes":    rows * cols,
1471         }).Infof("writing numpy: %s", fnm)
1472         npw.Shape = []int{rows, cols}
1473         npw.WriteInt8(out)
1474         err = bufw.Flush()
1475         if err != nil {
1476                 return err
1477         }
1478         return output.Close()
1479 }
1480
1481 func allele2homhet(colpair [2][]int8) {
1482         a, b := colpair[0], colpair[1]
1483         for i, av := range a {
1484                 bv := b[i]
1485                 if av < 0 || bv < 0 {
1486                         // no-call
1487                         a[i], b[i] = -1, -1
1488                 } else if av > 0 && bv > 0 {
1489                         // hom
1490                         a[i], b[i] = 1, 0
1491                 } else if av > 0 || bv > 0 {
1492                         // het
1493                         a[i], b[i] = 0, 1
1494                 } else {
1495                         // ref (or a different variant in same position)
1496                         // (this is a no-op) a[i], b[i] = 0, 0
1497                 }
1498         }
1499 }
1500
1501 type onehotXref struct {
1502         tag     tagID
1503         variant tileVariantID
1504         hom     bool
1505         pvalue  float64
1506 }
1507
1508 const onehotXrefSize = unsafe.Sizeof(onehotXref{})
1509
1510 // Build onehot matrix (m[tileVariantIndex][genome] == 0 or 1) for all
1511 // variants of a single tile/tag#.
1512 //
1513 // Return nil if no tile variant passes Χ² filter.
1514 func (cmd *sliceNumpy) tv2homhet(cgs map[string]CompactGenome, maxv tileVariantID, remap []tileVariantID, tag, chunkstarttag tagID, seq map[tagID][]TileVariant) ([][]int8, []onehotXref) {
1515         if tag == cmd.debugTag {
1516                 tv := make([]tileVariantID, len(cmd.cgnames)*2)
1517                 for i, name := range cmd.cgnames {
1518                         copy(tv[i*2:(i+1)*2], cgs[name].Variants[(tag-chunkstarttag)*2:])
1519                 }
1520                 log.WithFields(logrus.Fields{
1521                         "cgs[i].Variants[tag*2+j]": tv,
1522                         "maxv":                     maxv,
1523                         "remap":                    remap,
1524                         "tag":                      tag,
1525                         "chunkstarttag":            chunkstarttag,
1526                 }).Info("tv2homhet()")
1527         }
1528         if maxv < 1 || (maxv < 2 && !cmd.includeVariant1) {
1529                 // everyone has the most common variant (of the variants we don't drop)
1530                 return nil, nil
1531         }
1532         tagoffset := tag - chunkstarttag
1533         coverage := 0
1534         for _, cg := range cgs {
1535                 alleles := 0
1536                 for _, v := range cg.Variants[tagoffset*2 : tagoffset*2+2] {
1537                         if v > 0 && int(v) < len(seq[tag]) && len(seq[tag][v].Sequence) > 0 {
1538                                 alleles++
1539                         }
1540                 }
1541                 if alleles == 2 {
1542                         coverage++
1543                 }
1544         }
1545         if coverage < cmd.minCoverage {
1546                 return nil, nil
1547         }
1548         obs := make([][]bool, (maxv+1)*2) // 2 slices (hom + het) for each variant#
1549         for i := range obs {
1550                 obs[i] = make([]bool, cmd.trainingSetSize)
1551         }
1552         for cgid, name := range cmd.cgnames {
1553                 tsid := cmd.trainingSet[cgid]
1554                 if tsid < 0 {
1555                         continue
1556                 }
1557                 cgvars := cgs[name].Variants[tagoffset*2:]
1558                 tv0, tv1 := remap[cgvars[0]], remap[cgvars[1]]
1559                 for v := tileVariantID(1); v <= maxv; v++ {
1560                         if tv0 == v && tv1 == v {
1561                                 obs[v*2][tsid] = true
1562                         } else if tv0 == v || tv1 == v {
1563                                 obs[v*2+1][tsid] = true
1564                         }
1565                 }
1566         }
1567         var onehot [][]int8
1568         var xref []onehotXref
1569         for col := 2; col < len(obs); col++ {
1570                 // col 0,1 correspond to tile variant 0, i.e.,
1571                 // no-call; col 2,3 correspond to the most common
1572                 // variant; so we (normally) start at col 4.
1573                 if col < 4 && !cmd.includeVariant1 {
1574                         continue
1575                 }
1576                 p := pvalue(obs[col], cmd.chi2Cases)
1577                 if cmd.chi2PValue < 1 && !(p < cmd.chi2PValue) {
1578                         continue
1579                 }
1580                 onehot = append(onehot, bool2int8(obs[col]))
1581                 xref = append(xref, onehotXref{
1582                         tag:     tag,
1583                         variant: tileVariantID(col >> 1),
1584                         hom:     col&1 == 0,
1585                         pvalue:  p,
1586                 })
1587         }
1588         return onehot, xref
1589 }
1590
1591 func bool2int8(in []bool) []int8 {
1592         out := make([]int8, len(in))
1593         for i, v := range in {
1594                 if v {
1595                         out[i] = 1
1596                 }
1597         }
1598         return out
1599 }
1600
1601 // convert a []onehotXref with length N to a numpy-style []int32
1602 // matrix with N columns, one row per field of onehotXref struct.
1603 //
1604 // Hom/het row contains hom=0, het=1.
1605 //
1606 // P-value row contains 1000000x actual p-value.
1607 func onehotXref2int32(xrefs []onehotXref) []int32 {
1608         xcols := len(xrefs)
1609         xdata := make([]int32, 5*xcols)
1610         for i, xref := range xrefs {
1611                 xdata[i] = int32(xref.tag)
1612                 xdata[xcols+i] = int32(xref.variant)
1613                 if xref.hom {
1614                         xdata[xcols*2+i] = 1
1615                 }
1616                 xdata[xcols*3+i] = int32(xref.pvalue * 1000000)
1617                 xdata[xcols*4+i] = int32(-math.Log10(xref.pvalue) * 1000000)
1618         }
1619         return xdata
1620 }
1621
1622 // transpose onehot data from in[col][row] to numpy-style
1623 // out[row*cols+col].
1624 func onehotcols2int8(in [][]int8) []int8 {
1625         if len(in) == 0 {
1626                 return nil
1627         }
1628         cols := len(in)
1629         rows := len(in[0])
1630         out := make([]int8, rows*cols)
1631         for row := 0; row < rows; row++ {
1632                 outrow := out[row*cols:]
1633                 for col, incol := range in {
1634                         outrow[col] = incol[row]
1635                 }
1636         }
1637         return out
1638 }
1639
1640 // Return [2][]uint32{rowIndices, colIndices} indicating which
1641 // elements of matrixT[c][r] have non-zero values.
1642 func onehotChunk2Indirect(matrixT [][]int8) [2][]uint32 {
1643         var nz [2][]uint32
1644         for c, col := range matrixT {
1645                 for r, val := range col {
1646                         if val != 0 {
1647                                 nz[0] = append(nz[0], uint32(r))
1648                                 nz[1] = append(nz[1], uint32(c))
1649                         }
1650                 }
1651         }
1652         return nz
1653 }