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