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         pcaComponents   int
  47         minCoverage     int
  48         includeVariant1 bool
  49         debugTag        tagID
  50
  51         cgnames         []string
  52         samples         []sampleInfo
  53         trainingSet     []int // samples index => training set index, or -1 if not in training set
  54         trainingSetSize int
  55 }
  56
  57 func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  58         err := cmd.run(prog, args, stdin, stdout, stderr)
  59         if err != nil {
  60                 fmt.Fprintf(stderr, "%s\n", err)
  61                 return 1
  62         }
  63         return 0
  64 }
  65
  66 func (cmd *sliceNumpy) run(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) error {
  67         flags := flag.NewFlagSet("", flag.ContinueOnError)
  68         flags.SetOutput(stderr)
  69         pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
  70         runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
  71         arvadosRAM := flags.Int("arvados-ram", 750000000000, "amount of memory to request for arvados container (`bytes`)")
  72         arvadosVCPUs := flags.Int("arvados-vcpus", 96, "number of VCPUs to request for arvados container")
  73         projectUUID := flags.String("project", "", "project `UUID` for output data")
  74         priority := flags.Int("priority", 500, "container request priority")
  75         inputDir := flags.String("input-dir", "./in", "input `directory`")
  76         outputDir := flags.String("output-dir", "./out", "output `directory`")
  77         ref := flags.String("ref", "", "reference name (if blank, choose last one that appears in input)")
  78         regionsFilename := flags.String("regions", "", "only output columns/annotations that intersect regions in specified bed `file`")
  79         expandRegions := flags.Int("expand-regions", 0, "expand specified regions by `N` base pairs on each side`")
  80         mergeOutput := flags.Bool("merge-output", false, "merge output into one matrix.npy and one matrix.annotations.csv")
  81         hgvsSingle := flags.Bool("single-hgvs-matrix", false, "also generate hgvs-based matrix")
  82         hgvsChunked := flags.Bool("chunked-hgvs-matrix", false, "also generate hgvs-based matrix per chromosome")
  83         onehotSingle := flags.Bool("single-onehot", false, "generate one-hot tile-based matrix")
  84         onehotChunked := flags.Bool("chunked-onehot", false, "generate one-hot tile-based matrix per input chunk")
  85         samplesFilename := flags.String("samples", "", "`samples.csv` file with training/validation and case/control groups (see 'lightning choose-samples')")
  86         caseControlOnly := flags.Bool("case-control-only", false, "drop samples that are not in case/control groups")
  87         onlyPCA := flags.Bool("pca", false, "run principal component analysis, write components to pca.npy and samples.csv")
  88         flags.IntVar(&cmd.pcaComponents, "pca-components", 4, "number of PCA components to compute / use in logistic regression")
  89         maxPCATiles := flags.Int("max-pca-tiles", 0, "maximum tiles to use as PCA input (filter, then drop every 2nd colum pair until below max)")
  90         debugTag := flags.Int("debug-tag", -1, "log debugging details about specified tag")
  91         flags.IntVar(&cmd.threads, "threads", 16, "number of memory-hungry assembly threads, and number of VCPUs to request for arvados container")
  92         flags.Float64Var(&cmd.chi2PValue, "chi2-p-value", 1, "do Χ² test (or logistic regression if -samples file has PCA components) and omit columns with p-value above this threshold")
  93         flags.BoolVar(&cmd.includeVariant1, "include-variant-1", false, "include most common variant when building one-hot matrix")
  94         cmd.filter.Flags(flags)
  95         err := flags.Parse(args)
  96         if err == flag.ErrHelp {
  97                 return nil
  98         } else if err != nil {
  99                 return err
 100         } else if flags.NArg() > 0 {
 101                 return fmt.Errorf("errant command line arguments after parsed flags: %v", flags.Args())
 102         }
 103
 104         if *pprof != "" {
 105                 go func() {
 106                         log.Println(http.ListenAndServe(*pprof, nil))
 107                 }()
 108         }
 109
 110         if cmd.chi2PValue != 1 && *samplesFilename == "" {
 111                 return fmt.Errorf("cannot use provided -chi2-p-value=%f because -samples= value is empty", cmd.chi2PValue)
 112         }
 113
 114         cmd.debugTag = tagID(*debugTag)
 115
 116         if !*runlocal {
 117                 runner := arvadosContainerRunner{
 118                         Name:        "lightning slice-numpy",
 119                         Client:      arvados.NewClientFromEnv(),
 120                         ProjectUUID: *projectUUID,
 121                         RAM:         int64(*arvadosRAM),
 122                         VCPUs:       *arvadosVCPUs,
 123                         Priority:    *priority,
 124                         KeepCache:   2,
 125                         APIAccess:   true,
 126                 }
 127                 err = runner.TranslatePaths(inputDir, regionsFilename, samplesFilename)
 128                 if err != nil {
 129                         return err
 130                 }
 131                 runner.Args = []string{"slice-numpy", "-local=true",
 132                         "-pprof=:6060",
 133                         "-input-dir=" + *inputDir,
 134                         "-output-dir=/mnt/output",
 135                         "-threads=" + fmt.Sprintf("%d", cmd.threads),
 136                         "-regions=" + *regionsFilename,
 137                         "-expand-regions=" + fmt.Sprintf("%d", *expandRegions),
 138                         "-merge-output=" + fmt.Sprintf("%v", *mergeOutput),
 139                         "-single-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsSingle),
 140                         "-chunked-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsChunked),
 141                         "-single-onehot=" + fmt.Sprintf("%v", *onehotSingle),
 142                         "-chunked-onehot=" + fmt.Sprintf("%v", *onehotChunked),
 143                         "-samples=" + *samplesFilename,
 144                         "-case-control-only=" + fmt.Sprintf("%v", *caseControlOnly),
 145                         "-pca=" + fmt.Sprintf("%v", *onlyPCA),
 146                         "-pca-components=" + fmt.Sprintf("%d", cmd.pcaComponents),
 147                         "-max-pca-tiles=" + fmt.Sprintf("%d", *maxPCATiles),
 148                         "-chi2-p-value=" + fmt.Sprintf("%f", cmd.chi2PValue),
 149                         "-include-variant-1=" + fmt.Sprintf("%v", cmd.includeVariant1),
 150                         "-debug-tag=" + fmt.Sprintf("%d", cmd.debugTag),
 151                 }
 152                 runner.Args = append(runner.Args, cmd.filter.Args()...)
 153                 var output string
 154                 output, err = runner.Run()
 155                 if err != nil {
 156                         return err
 157                 }
 158                 fmt.Fprintln(stdout, output)
 159                 return nil
 160         }
 161
 162         infiles, err := allFiles(*inputDir, matchGobFile)
 163         if err != nil {
 164                 return err
 165         }
 166         if len(infiles) == 0 {
 167                 err = fmt.Errorf("no input files found in %s", *inputDir)
 168                 return err
 169         }
 170         sort.Strings(infiles)
 171
 172         var refseq map[string][]tileLibRef
 173         var reftiledata = make(map[tileLibRef][]byte, 11000000)
 174         in0, err := open(infiles[0])
 175         if err != nil {
 176                 return err
 177         }
 178
 179         matchGenome, err := regexp.Compile(cmd.filter.MatchGenome)
 180         if err != nil {
 181                 err = fmt.Errorf("-match-genome: invalid regexp: %q", cmd.filter.MatchGenome)
 182                 return err
 183         }
 184
 185         if *samplesFilename != "" {
 186                 cmd.samples, err = loadSampleInfo(*samplesFilename)
 187                 if err != nil {
 188                         return err
 189                 }
 190         } else if *caseControlOnly {
 191                 return fmt.Errorf("-case-control-only does not make sense without -samples")
 192         }
 193
 194         cmd.cgnames = nil
 195         var tagset [][]byte
 196         err = DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
 197                 if len(ent.TagSet) > 0 {
 198                         tagset = ent.TagSet
 199                 }
 200                 for _, cseq := range ent.CompactSequences {
 201                         if cseq.Name == *ref || *ref == "" {
 202                                 refseq = cseq.TileSequences
 203                         }
 204                 }
 205                 for _, cg := range ent.CompactGenomes {
 206                         if matchGenome.MatchString(cg.Name) {
 207                                 cmd.cgnames = append(cmd.cgnames, cg.Name)
 208                         }
 209                 }
 210                 for _, tv := range ent.TileVariants {
 211                         if tv.Ref {
 212                                 reftiledata[tileLibRef{tv.Tag, tv.Variant}] = tv.Sequence
 213                         }
 214                 }
 215                 return nil
 216         })
 217         if err != nil {
 218                 return err
 219         }
 220         in0.Close()
 221         if refseq == nil {
 222                 err = fmt.Errorf("%s: reference sequence not found", infiles[0])
 223                 return err
 224         }
 225         if len(tagset) == 0 {
 226                 err = fmt.Errorf("tagset not found")
 227                 return err
 228         }
 229
 230         taglib := &tagLibrary{}
 231         err = taglib.setTags(tagset)
 232         if err != nil {
 233                 return err
 234         }
 235         taglen := taglib.TagLen()
 236         sort.Strings(cmd.cgnames)
 237
 238         if len(cmd.cgnames) == 0 {
 239                 return fmt.Errorf("fatal: 0 matching samples in library, nothing to do")
 240         }
 241         cmd.trainingSet = make([]int, len(cmd.cgnames))
 242         if *samplesFilename == "" {
 243                 cmd.trainingSetSize = len(cmd.cgnames)
 244                 for i, name := range cmd.cgnames {
 245                         cmd.samples = append(cmd.samples, sampleInfo{
 246                                 id:         trimFilenameForLabel(name),
 247                                 isTraining: true,
 248                         })
 249                         cmd.trainingSet[i] = i
 250                 }
 251         } else if len(cmd.cgnames) != len(cmd.samples) {
 252                 return fmt.Errorf("mismatched sample list: %d samples in library, %d in %s", len(cmd.cgnames), len(cmd.samples), *samplesFilename)
 253         } else {
 254                 for i, name := range cmd.cgnames {
 255                         if s := trimFilenameForLabel(name); s != cmd.samples[i].id {
 256                                 return fmt.Errorf("mismatched sample list: sample %d is %q in library, %q in %s", i, s, cmd.samples[i].id, *samplesFilename)
 257                         }
 258                 }
 259                 if *caseControlOnly {
 260                         for i := 0; i < len(cmd.samples); i++ {
 261                                 if !cmd.samples[i].isTraining && !cmd.samples[i].isValidation {
 262                                         if i+1 < len(cmd.samples) {
 263                                                 copy(cmd.samples[i:], cmd.samples[i+1:])
 264                                                 copy(cmd.cgnames[i:], cmd.cgnames[i+1:])
 265                                         }
 266                                         cmd.samples = cmd.samples[:len(cmd.samples)-1]
 267                                         cmd.cgnames = cmd.cgnames[:len(cmd.cgnames)-1]
 268                                         i--
 269                                 }
 270                         }
 271                 }
 272                 cmd.chi2Cases = nil
 273                 cmd.trainingSetSize = 0
 274                 for i := range cmd.cgnames {
 275                         if cmd.samples[i].isTraining {
 276                                 cmd.trainingSet[i] = cmd.trainingSetSize
 277                                 cmd.trainingSetSize++
 278                                 cmd.chi2Cases = append(cmd.chi2Cases, cmd.samples[i].isCase)
 279                         } else {
 280                                 cmd.trainingSet[i] = -1
 281                         }
 282                 }
 283         }
 284         if cmd.filter.MinCoverage == 1 {
 285                 // In the generic formula below, floating point
 286                 // arithmetic can effectively push the coverage
 287                 // threshold above 1.0, which is impossible/useless.
 288                 // 1.0 needs to mean exactly 100% coverage.
 289                 cmd.minCoverage = len(cmd.cgnames)
 290         } else {
 291                 cmd.minCoverage = int(math.Ceil(cmd.filter.MinCoverage * float64(len(cmd.cgnames))))
 292         }
 293
 294         {
 295                 samplesOutFilename := *outputDir + "/samples.csv"
 296                 log.Infof("writing sample metadata to %s", samplesOutFilename)
 297                 var f *os.File
 298                 f, err = os.Create(samplesOutFilename)
 299                 if err != nil {
 300                         return err
 301                 }
 302                 defer f.Close()
 303                 for i, si := range cmd.samples {
 304                         var cc, tv string
 305                         if si.isCase {
 306                                 cc = "1"
 307                         } else if si.isControl {
 308                                 cc = "0"
 309                         }
 310                         if si.isTraining {
 311                                 tv = "1"
 312                         } else {
 313                                 tv = "0"
 314                         }
 315                         _, err = fmt.Fprintf(f, "%d,%s,%s,%s\n", i, si.id, cc, tv)
 316                         if err != nil {
 317                                 err = fmt.Errorf("write %s: %w", samplesOutFilename, err)
 318                                 return err
 319                         }
 320                 }
 321                 err = f.Close()
 322                 if err != nil {
 323                         err = fmt.Errorf("close %s: %w", samplesOutFilename, err)
 324                         return err
 325                 }
 326                 log.Print("done")
 327         }
 328
 329         log.Info("indexing reference tiles")
 330         type reftileinfo struct {
 331                 variant  tileVariantID
 332                 seqname  string // chr1
 333                 pos      int    // distance from start of chromosome to starttag
 334                 tiledata []byte // acgtggcaa...
 335                 excluded bool   // true if excluded by regions file
 336                 nexttag  tagID  // tagID of following tile (-1 for last tag of chromosome)
 337         }
 338         isdup := map[tagID]bool{}
 339         reftile := map[tagID]*reftileinfo{}
 340         for seqname, cseq := range refseq {
 341                 pos := 0
 342                 lastreftag := tagID(-1)
 343                 for _, libref := range cseq {
 344                         if cmd.filter.MaxTag >= 0 && libref.Tag > tagID(cmd.filter.MaxTag) {
 345                                 continue
 346                         }
 347                         tiledata := reftiledata[libref]
 348                         if len(tiledata) == 0 {
 349                                 err = fmt.Errorf("missing tiledata for tag %d variant %d in %s in ref", libref.Tag, libref.Variant, seqname)
 350                                 return err
 351                         }
 352                         foundthistag := false
 353                         taglib.FindAll(tiledata[:len(tiledata)-1], func(tagid tagID, offset, _ int) {
 354                                 if !foundthistag && tagid == libref.Tag {
 355                                         foundthistag = true
 356                                         return
 357                                 }
 358                                 if dupref, ok := reftile[tagid]; ok {
 359                                         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)
 360                                         delete(reftile, tagid)
 361                                 } else {
 362                                         log.Printf("found tag %d at offset %d inside tile variant %+v on %s @ %d", tagid, offset, libref, seqname, pos+offset+1)
 363                                 }
 364                                 isdup[tagid] = true
 365                         })
 366                         if isdup[libref.Tag] {
 367                                 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
 368                         } else if reftile[libref.Tag] != nil {
 369                                 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)
 370                                 delete(reftile, libref.Tag)
 371                                 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
 372                                 isdup[libref.Tag] = true
 373                         } else {
 374                                 reftile[libref.Tag] = &reftileinfo{
 375                                         seqname:  seqname,
 376                                         variant:  libref.Variant,
 377                                         tiledata: tiledata,
 378                                         pos:      pos,
 379                                         nexttag:  -1,
 380                                 }
 381                                 if lastreftag >= 0 {
 382                                         reftile[lastreftag].nexttag = libref.Tag
 383                                 }
 384                                 lastreftag = libref.Tag
 385                         }
 386                         pos += len(tiledata) - taglen
 387                 }
 388                 log.Printf("... %s done, len %d", seqname, pos+taglen)
 389         }
 390
 391         var mask *mask
 392         if *regionsFilename != "" {
 393                 log.Printf("loading regions from %s", *regionsFilename)
 394                 mask, err = makeMask(*regionsFilename, *expandRegions)
 395                 if err != nil {
 396                         return err
 397                 }
 398                 log.Printf("before applying mask, len(reftile) == %d", len(reftile))
 399                 log.Printf("deleting reftile entries for regions outside %d intervals", mask.Len())
 400                 for _, rt := range reftile {
 401                         if !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(rt.tiledata)) {
 402                                 rt.excluded = true
 403                         }
 404                 }
 405                 log.Printf("after applying mask, len(reftile) == %d", len(reftile))
 406         }
 407
 408         type hgvsColSet map[hgvs.Variant][2][]int8
 409         encodeHGVS := throttle{Max: len(refseq)}
 410         encodeHGVSTodo := map[string]chan hgvsColSet{}
 411         tmpHGVSCols := map[string]*os.File{}
 412         if *hgvsChunked {
 413                 for seqname := range refseq {
 414                         var f *os.File
 415                         f, err = os.Create(*outputDir + "/tmp." + seqname + ".gob")
 416                         if err != nil {
 417                                 return err
 418                         }
 419                         defer os.Remove(f.Name())
 420                         bufw := bufio.NewWriterSize(f, 1<<24)
 421                         enc := gob.NewEncoder(bufw)
 422                         tmpHGVSCols[seqname] = f
 423                         todo := make(chan hgvsColSet, 128)
 424                         encodeHGVSTodo[seqname] = todo
 425                         encodeHGVS.Go(func() error {
 426                                 for colset := range todo {
 427                                         err := enc.Encode(colset)
 428                                         if err != nil {
 429                                                 encodeHGVS.Report(err)
 430                                                 for range todo {
 431                                                 }
 432                                                 return err
 433                                         }
 434                                 }
 435                                 return bufw.Flush()
 436                         })
 437                 }
 438         }
 439
 440         var toMerge [][]int16
 441         if *mergeOutput || *hgvsSingle {
 442                 toMerge = make([][]int16, len(infiles))
 443         }
 444         var onehotIndirect [][2][]uint32 // [chunkIndex][axis][index]
 445         var onehotChunkSize []uint32
 446         var onehotXrefs [][]onehotXref
 447         if *onehotSingle || *onlyPCA {
 448                 onehotIndirect = make([][2][]uint32, len(infiles))
 449                 onehotChunkSize = make([]uint32, len(infiles))
 450                 onehotXrefs = make([][]onehotXref, len(infiles))
 451         }
 452         chunkStartTag := make([]tagID, len(infiles))
 453
 454         throttleMem := throttle{Max: cmd.threads} // TODO: estimate using mem and data size
 455         throttleNumpyMem := throttle{Max: cmd.threads/2 + 1}
 456         log.Info("generating annotations and numpy matrix for each slice")
 457         var errSkip = errors.New("skip infile")
 458         var done int64
 459         for infileIdx, infile := range infiles {
 460                 infileIdx, infile := infileIdx, infile
 461                 throttleMem.Go(func() error {
 462                         seq := make(map[tagID][]TileVariant, 50000)
 463                         cgs := make(map[string]CompactGenome, len(cmd.cgnames))
 464                         f, err := open(infile)
 465                         if err != nil {
 466                                 return err
 467                         }
 468                         defer f.Close()
 469                         log.Infof("%04d: reading %s", infileIdx, infile)
 470                         err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
 471                                 for _, tv := range ent.TileVariants {
 472                                         if tv.Ref {
 473                                                 continue
 474                                         }
 475                                         // Skip tile with no
 476                                         // corresponding ref tile, if
 477                                         // mask is in play (we can't
 478                                         // determine coordinates for
 479                                         // these)
 480                                         if mask != nil && reftile[tv.Tag] == nil {
 481                                                 continue
 482                                         }
 483                                         // Skip tile whose
 484                                         // corresponding ref tile is
 485                                         // outside target regions --
 486                                         // unless it's a potential
 487                                         // spanning tile.
 488                                         if mask != nil && reftile[tv.Tag].excluded &&
 489                                                 (int(tv.Tag+1) >= len(tagset) ||
 490                                                         (bytes.HasSuffix(tv.Sequence, tagset[tv.Tag+1]) && reftile[tv.Tag+1] != nil && !reftile[tv.Tag+1].excluded)) {
 491                                                 continue
 492                                         }
 493                                         if tv.Tag == cmd.debugTag {
 494                                                 log.Printf("infile %d %s tag %d variant %d hash %x", infileIdx, infile, tv.Tag, tv.Variant, tv.Blake2b[:3])
 495                                         }
 496                                         variants := seq[tv.Tag]
 497                                         if len(variants) == 0 {
 498                                                 variants = make([]TileVariant, 100)
 499                                         }
 500                                         for len(variants) <= int(tv.Variant) {
 501                                                 variants = append(variants, TileVariant{})
 502                                         }
 503                                         variants[int(tv.Variant)] = tv
 504                                         seq[tv.Tag] = variants
 505                                 }
 506                                 for _, cg := range ent.CompactGenomes {
 507                                         if cmd.filter.MaxTag >= 0 && cg.StartTag > tagID(cmd.filter.MaxTag) {
 508                                                 return errSkip
 509                                         }
 510                                         if !matchGenome.MatchString(cg.Name) {
 511                                                 continue
 512                                         }
 513                                         // pad to full slice size
 514                                         // to avoid out-of-bounds
 515                                         // checks later
 516                                         if sliceSize := 2 * int(cg.EndTag-cg.StartTag); len(cg.Variants) < sliceSize {
 517                                                 cg.Variants = append(cg.Variants, make([]tileVariantID, sliceSize-len(cg.Variants))...)
 518                                         }
 519                                         cgs[cg.Name] = cg
 520                                 }
 521                                 return nil
 522                         })
 523                         if err == errSkip {
 524                                 return nil
 525                         } else if err != nil {
 526                                 return fmt.Errorf("%04d: DecodeLibrary(%s): err", infileIdx, infile)
 527                         }
 528                         tagstart := cgs[cmd.cgnames[0]].StartTag
 529                         tagend := cgs[cmd.cgnames[0]].EndTag
 530                         chunkStartTag[infileIdx] = tagstart
 531
 532                         // TODO: filters
 533
 534                         log.Infof("%04d: renumber/dedup variants for tags %d-%d", infileIdx, tagstart, tagend)
 535                         variantRemap := make([][]tileVariantID, tagend-tagstart)
 536                         throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
 537                         for tag, variants := range seq {
 538                                 tag, variants := tag, variants
 539                                 throttleCPU.Go(func() error {
 540                                         alleleCoverage := 0
 541                                         count := make(map[[blake2b.Size256]byte]int, len(variants))
 542
 543                                         rt := reftile[tag]
 544                                         if rt != nil {
 545                                                 count[blake2b.Sum256(rt.tiledata)] = 0
 546                                         }
 547
 548                                         for cgname, cg := range cgs {
 549                                                 idx := int(tag-tagstart) * 2
 550                                                 for allele := 0; allele < 2; allele++ {
 551                                                         v := cg.Variants[idx+allele]
 552                                                         if v > 0 && len(variants[v].Sequence) > 0 {
 553                                                                 count[variants[v].Blake2b]++
 554                                                                 alleleCoverage++
 555                                                         }
 556                                                         if v > 0 && tag == cmd.debugTag {
 557                                                                 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])
 558                                                         }
 559                                                 }
 560                                         }
 561                                         if alleleCoverage < cmd.minCoverage*2 {
 562                                                 idx := int(tag-tagstart) * 2
 563                                                 for _, cg := range cgs {
 564                                                         cg.Variants[idx] = 0
 565                                                         cg.Variants[idx+1] = 0
 566                                                 }
 567                                                 if tag == cmd.debugTag {
 568                                                         log.Printf("tag %d alleleCoverage %d < min %d, sample data wiped", tag, alleleCoverage, cmd.minCoverage*2)
 569                                                 }
 570                                                 return nil
 571                                         }
 572
 573                                         // hash[i] will be the hash of
 574                                         // the variant(s) that should
 575                                         // be at rank i (0-based).
 576                                         hash := make([][blake2b.Size256]byte, 0, len(count))
 577                                         for b := range count {
 578                                                 hash = append(hash, b)
 579                                         }
 580                                         sort.Slice(hash, func(i, j int) bool {
 581                                                 bi, bj := &hash[i], &hash[j]
 582                                                 if ci, cj := count[*bi], count[*bj]; ci != cj {
 583                                                         return ci > cj
 584                                                 } else {
 585                                                         return bytes.Compare((*bi)[:], (*bj)[:]) < 0
 586                                                 }
 587                                         })
 588                                         // rank[b] will be the 1-based
 589                                         // new variant number for
 590                                         // variants whose hash is b.
 591                                         rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
 592                                         for i, h := range hash {
 593                                                 rank[h] = tileVariantID(i + 1)
 594                                         }
 595                                         if tag == cmd.debugTag {
 596                                                 for h, r := range rank {
 597                                                         log.Printf("tag %d rank(%x) = %v", tag, h[:3], r)
 598                                                 }
 599                                         }
 600                                         // remap[v] will be the new
 601                                         // variant number for original
 602                                         // variant number v.
 603                                         remap := make([]tileVariantID, len(variants))
 604                                         for i, tv := range variants {
 605                                                 remap[i] = rank[tv.Blake2b]
 606                                         }
 607                                         if tag == cmd.debugTag {
 608                                                 for in, out := range remap {
 609                                                         if out > 0 {
 610                                                                 log.Printf("tag %d remap %d => %d", tag, in, out)
 611                                                         }
 612                                                 }
 613                                         }
 614                                         variantRemap[tag-tagstart] = remap
 615                                         if rt != nil {
 616                                                 refrank := rank[blake2b.Sum256(rt.tiledata)]
 617                                                 if tag == cmd.debugTag {
 618                                                         log.Printf("tag %d reftile variant %d => %d", tag, rt.variant, refrank)
 619                                                 }
 620                                                 rt.variant = refrank
 621                                         }
 622                                         return nil
 623                                 })
 624                         }
 625                         throttleCPU.Wait()
 626
 627                         var onehotChunk [][]int8
 628                         var onehotXref []onehotXref
 629
 630                         var annotationsFilename string
 631                         if *onlyPCA {
 632                                 annotationsFilename = "/dev/null"
 633                         } else {
 634                                 annotationsFilename = fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
 635                                 log.Infof("%04d: writing %s", infileIdx, annotationsFilename)
 636                         }
 637                         annof, err := os.Create(annotationsFilename)
 638                         if err != nil {
 639                                 return err
 640                         }
 641                         annow := bufio.NewWriterSize(annof, 1<<20)
 642                         outcol := 0
 643                         for tag := tagstart; tag < tagend; tag++ {
 644                                 rt := reftile[tag]
 645                                 if rt == nil && mask != nil {
 646                                         // With no ref tile, we don't
 647                                         // have coordinates to say
 648                                         // this is in the desired
 649                                         // regions -- so it's not.
 650                                         // TODO: handle ref spanning
 651                                         // tile case.
 652                                         continue
 653                                 }
 654                                 if rt != nil && rt.excluded {
 655                                         // TODO: don't skip yet --
 656                                         // first check for spanning
 657                                         // tile variants that
 658                                         // intersect non-excluded ref
 659                                         // tiles.
 660                                         continue
 661                                 }
 662                                 if cmd.filter.MaxTag >= 0 && tag > tagID(cmd.filter.MaxTag) {
 663                                         break
 664                                 }
 665                                 remap := variantRemap[tag-tagstart]
 666                                 if remap == nil {
 667                                         // was not assigned above,
 668                                         // because minCoverage
 669                                         outcol++
 670                                         continue
 671                                 }
 672                                 maxv := tileVariantID(0)
 673                                 for _, v := range remap {
 674                                         if maxv < v {
 675                                                 maxv = v
 676                                         }
 677                                 }
 678                                 if *onehotChunked || *onehotSingle || *onlyPCA {
 679                                         onehot, xrefs := cmd.tv2homhet(cgs, maxv, remap, tag, tagstart, seq)
 680                                         if tag == cmd.debugTag {
 681                                                 log.WithFields(logrus.Fields{
 682                                                         "onehot": onehot,
 683                                                         "xrefs":  xrefs,
 684                                                 }).Info("tv2homhet()")
 685                                         }
 686                                         onehotChunk = append(onehotChunk, onehot...)
 687                                         onehotXref = append(onehotXref, xrefs...)
 688                                 }
 689                                 if *onlyPCA {
 690                                         outcol++
 691                                         continue
 692                                 }
 693                                 if rt == nil {
 694                                         // Reference does not use any
 695                                         // variant of this tile
 696                                         //
 697                                         // TODO: diff against the
 698                                         // relevant portion of the
 699                                         // ref's spanning tile
 700                                         outcol++
 701                                         continue
 702                                 }
 703                                 fmt.Fprintf(annow, "%d,%d,%d,=,%s,%d,,,\n", tag, outcol, rt.variant, rt.seqname, rt.pos)
 704                                 variants := seq[tag]
 705                                 reftilestr := strings.ToUpper(string(rt.tiledata))
 706
 707                                 done := make([]bool, maxv+1)
 708                                 variantDiffs := make([][]hgvs.Variant, maxv+1)
 709                                 for v, tv := range variants {
 710                                         v := remap[v]
 711                                         if v == 0 || v == rt.variant || done[v] {
 712                                                 continue
 713                                         } else {
 714                                                 done[v] = true
 715                                         }
 716                                         if len(tv.Sequence) < taglen {
 717                                                 continue
 718                                         }
 719                                         // if reftilestr doesn't end
 720                                         // in the same tag as tv,
 721                                         // extend reftilestr with
 722                                         // following ref tiles until
 723                                         // it does (up to an arbitrary
 724                                         // sanity-check limit)
 725                                         reftilestr := reftilestr
 726                                         endtagstr := strings.ToUpper(string(tv.Sequence[len(tv.Sequence)-taglen:]))
 727                                         for i, rt := 0, rt; i < annotationMaxTileSpan && !strings.HasSuffix(reftilestr, endtagstr) && rt.nexttag >= 0; i++ {
 728                                                 rt = reftile[rt.nexttag]
 729                                                 if rt == nil {
 730                                                         break
 731                                                 }
 732                                                 reftilestr += strings.ToUpper(string(rt.tiledata[taglen:]))
 733                                         }
 734                                         if mask != nil && !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(reftilestr)) {
 735                                                 continue
 736                                         }
 737                                         if !strings.HasSuffix(reftilestr, endtagstr) {
 738                                                 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
 739                                                 continue
 740                                         }
 741                                         if lendiff := len(reftilestr) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
 742                                                 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
 743                                                 continue
 744                                         }
 745                                         diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
 746                                         for i := range diffs {
 747                                                 diffs[i].Position += rt.pos
 748                                         }
 749                                         for _, diff := range diffs {
 750                                                 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)
 751                                         }
 752                                         if *hgvsChunked {
 753                                                 variantDiffs[v] = diffs
 754                                         }
 755                                 }
 756                                 if *hgvsChunked {
 757                                         // We can now determine, for each HGVS
 758                                         // variant (diff) in this reftile
 759                                         // region, whether a given genome
 760                                         // phase/allele (1) has the variant, (0) has
 761                                         // =ref or a different variant in that
 762                                         // position, or (-1) is lacking
 763                                         // coverage / couldn't be diffed.
 764                                         hgvsCol := hgvsColSet{}
 765                                         for _, diffs := range variantDiffs {
 766                                                 for _, diff := range diffs {
 767                                                         if _, ok := hgvsCol[diff]; ok {
 768                                                                 continue
 769                                                         }
 770                                                         hgvsCol[diff] = [2][]int8{
 771                                                                 make([]int8, len(cmd.cgnames)),
 772                                                                 make([]int8, len(cmd.cgnames)),
 773                                                         }
 774                                                 }
 775                                         }
 776                                         for row, name := range cmd.cgnames {
 777                                                 variants := cgs[name].Variants[(tag-tagstart)*2:]
 778                                                 for ph := 0; ph < 2; ph++ {
 779                                                         v := variants[ph]
 780                                                         if int(v) >= len(remap) {
 781                                                                 v = 0
 782                                                         } else {
 783                                                                 v = remap[v]
 784                                                         }
 785                                                         if v == rt.variant {
 786                                                                 // hgvsCol[*][ph][row] is already 0
 787                                                         } else if len(variantDiffs[v]) == 0 {
 788                                                                 // lacking coverage / couldn't be diffed
 789                                                                 for _, col := range hgvsCol {
 790                                                                         col[ph][row] = -1
 791                                                                 }
 792                                                         } else {
 793                                                                 for _, diff := range variantDiffs[v] {
 794                                                                         hgvsCol[diff][ph][row] = 1
 795                                                                 }
 796                                                         }
 797                                                 }
 798                                         }
 799                                         for diff, colpair := range hgvsCol {
 800                                                 allele2homhet(colpair)
 801                                                 if !cmd.filterHGVScolpair(colpair) {
 802                                                         delete(hgvsCol, diff)
 803                                                 }
 804                                         }
 805                                         if len(hgvsCol) > 0 {
 806                                                 encodeHGVSTodo[rt.seqname] <- hgvsCol
 807                                         }
 808                                 }
 809                                 outcol++
 810                         }
 811                         err = annow.Flush()
 812                         if err != nil {
 813                                 return err
 814                         }
 815                         err = annof.Close()
 816                         if err != nil {
 817                                 return err
 818                         }
 819
 820                         if *onehotChunked {
 821                                 // transpose onehotChunk[col][row] to numpy[row*ncols+col]
 822                                 rows := len(cmd.cgnames)
 823                                 cols := len(onehotChunk)
 824                                 log.Infof("%04d: preparing onehot numpy (rows=%d, cols=%d, mem=%d)", infileIdx, rows, cols, rows*cols)
 825                                 throttleNumpyMem.Acquire()
 826                                 out := onehotcols2int8(onehotChunk)
 827                                 fnm := fmt.Sprintf("%s/onehot.%04d.npy", *outputDir, infileIdx)
 828                                 err = writeNumpyInt8(fnm, out, rows, cols)
 829                                 if err != nil {
 830                                         return err
 831                                 }
 832                                 fnm = fmt.Sprintf("%s/onehot-columns.%04d.npy", *outputDir, infileIdx)
 833                                 err = writeNumpyInt32(fnm, onehotXref2int32(onehotXref), 4, len(onehotXref))
 834                                 if err != nil {
 835                                         return err
 836                                 }
 837                                 debug.FreeOSMemory()
 838                                 throttleNumpyMem.Release()
 839                         }
 840                         if *onehotSingle || *onlyPCA {
 841                                 onehotIndirect[infileIdx] = onehotChunk2Indirect(onehotChunk)
 842                                 onehotChunkSize[infileIdx] = uint32(len(onehotChunk))
 843                                 onehotXrefs[infileIdx] = onehotXref
 844                                 n := len(onehotIndirect[infileIdx][0])
 845                                 log.Infof("%04d: keeping onehot coordinates in memory (n=%d, mem=%d)", infileIdx, n, n*8*2)
 846                         }
 847                         if !(*onehotSingle || *onehotChunked || *onlyPCA) || *mergeOutput || *hgvsSingle {
 848                                 log.Infof("%04d: preparing numpy (rows=%d, cols=%d)", infileIdx, len(cmd.cgnames), 2*outcol)
 849                                 throttleNumpyMem.Acquire()
 850                                 rows := len(cmd.cgnames)
 851                                 cols := 2 * outcol
 852                                 out := make([]int16, rows*cols)
 853                                 for row, name := range cmd.cgnames {
 854                                         outidx := row * cols
 855                                         for col, v := range cgs[name].Variants {
 856                                                 tag := tagstart + tagID(col/2)
 857                                                 if cmd.filter.MaxTag >= 0 && tag > tagID(cmd.filter.MaxTag) {
 858                                                         break
 859                                                 }
 860                                                 if rt := reftile[tag]; rt == nil || rt.excluded {
 861                                                         continue
 862                                                 }
 863                                                 if v == 0 {
 864                                                         out[outidx] = 0 // tag not found / spanning tile
 865                                                 } else if variants, ok := seq[tag]; ok && int(v) < len(variants) && len(variants[v].Sequence) > 0 {
 866                                                         out[outidx] = int16(variantRemap[tag-tagstart][v])
 867                                                 } else {
 868                                                         out[outidx] = -1 // low quality tile variant
 869                                                 }
 870                                                 if tag == cmd.debugTag {
 871                                                         log.Printf("tag %d row %d col %d outidx %d v %d out %d", tag, row, col, outidx, v, out[outidx])
 872                                                 }
 873                                                 outidx++
 874                                         }
 875                                 }
 876                                 seq = nil
 877                                 cgs = nil
 878                                 debug.FreeOSMemory()
 879                                 throttleNumpyMem.Release()
 880                                 if *mergeOutput || *hgvsSingle {
 881                                         log.Infof("%04d: matrix fragment %d rows x %d cols", infileIdx, rows, cols)
 882                                         toMerge[infileIdx] = out
 883                                 }
 884                                 if !*mergeOutput && !*onehotChunked && !*onehotSingle {
 885                                         fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
 886                                         err = writeNumpyInt16(fnm, out, rows, cols)
 887                                         if err != nil {
 888                                                 return err
 889                                         }
 890                                 }
 891                         }
 892                         debug.FreeOSMemory()
 893                         log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
 894                         return nil
 895                 })
 896         }
 897         if err = throttleMem.Wait(); err != nil {
 898                 return err
 899         }
 900
 901         if *hgvsChunked {
 902                 log.Info("flushing hgvsCols temp files")
 903                 for seqname := range refseq {
 904                         close(encodeHGVSTodo[seqname])
 905                 }
 906                 err = encodeHGVS.Wait()
 907                 if err != nil {
 908                         return err
 909                 }
 910                 for seqname := range refseq {
 911                         log.Infof("%s: reading hgvsCols from temp file", seqname)
 912                         f := tmpHGVSCols[seqname]
 913                         _, err = f.Seek(0, io.SeekStart)
 914                         if err != nil {
 915                                 return err
 916                         }
 917                         var hgvsCols hgvsColSet
 918                         dec := gob.NewDecoder(bufio.NewReaderSize(f, 1<<24))
 919                         for err == nil {
 920                                 err = dec.Decode(&hgvsCols)
 921                         }
 922                         if err != io.EOF {
 923                                 return err
 924                         }
 925                         log.Infof("%s: sorting %d hgvs variants", seqname, len(hgvsCols))
 926                         variants := make([]hgvs.Variant, 0, len(hgvsCols))
 927                         for v := range hgvsCols {
 928                                 variants = append(variants, v)
 929                         }
 930                         sort.Slice(variants, func(i, j int) bool {
 931                                 vi, vj := &variants[i], &variants[j]
 932                                 if vi.Position != vj.Position {
 933                                         return vi.Position < vj.Position
 934                                 } else if vi.Ref != vj.Ref {
 935                                         return vi.Ref < vj.Ref
 936                                 } else {
 937                                         return vi.New < vj.New
 938                                 }
 939                         })
 940                         rows := len(cmd.cgnames)
 941                         cols := len(variants) * 2
 942                         log.Infof("%s: building hgvs matrix (rows=%d, cols=%d, mem=%d)", seqname, rows, cols, rows*cols)
 943                         out := make([]int8, rows*cols)
 944                         for varIdx, variant := range variants {
 945                                 hgvsCols := hgvsCols[variant]
 946                                 for row := range cmd.cgnames {
 947                                         for ph := 0; ph < 2; ph++ {
 948                                                 out[row*cols+varIdx+ph] = hgvsCols[ph][row]
 949                                         }
 950                                 }
 951                         }
 952                         err = writeNumpyInt8(fmt.Sprintf("%s/hgvs.%s.npy", *outputDir, seqname), out, rows, cols)
 953                         if err != nil {
 954                                 return err
 955                         }
 956                         out = nil
 957
 958                         fnm := fmt.Sprintf("%s/hgvs.%s.annotations.csv", *outputDir, seqname)
 959                         log.Infof("%s: writing hgvs column labels to %s", seqname, fnm)
 960                         var hgvsLabels bytes.Buffer
 961                         for varIdx, variant := range variants {
 962                                 fmt.Fprintf(&hgvsLabels, "%d,%s:g.%s\n", varIdx, seqname, variant.String())
 963                         }
 964                         err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0666)
 965                         if err != nil {
 966                                 return err
 967                         }
 968                 }
 969         }
 970
 971         if *mergeOutput || *hgvsSingle {
 972                 var annow *bufio.Writer
 973                 var annof *os.File
 974                 if *mergeOutput {
 975                         annoFilename := fmt.Sprintf("%s/matrix.annotations.csv", *outputDir)
 976                         annof, err = os.Create(annoFilename)
 977                         if err != nil {
 978                                 return err
 979                         }
 980                         annow = bufio.NewWriterSize(annof, 1<<20)
 981                 }
 982
 983                 rows := len(cmd.cgnames)
 984                 cols := 0
 985                 for _, chunk := range toMerge {
 986                         cols += len(chunk) / rows
 987                 }
 988                 log.Infof("merging output matrix (rows=%d, cols=%d, mem=%d) and annotations", rows, cols, rows*cols*2)
 989                 var out []int16
 990                 if *mergeOutput {
 991                         out = make([]int16, rows*cols)
 992                 }
 993                 hgvsCols := map[string][2][]int16{} // hgvs -> [[g0,g1,g2,...], [g0,g1,g2,...]] (slice of genomes for each phase)
 994                 startcol := 0
 995                 for outIdx, chunk := range toMerge {
 996                         chunkcols := len(chunk) / rows
 997                         if *mergeOutput {
 998                                 for row := 0; row < rows; row++ {
 999                                         copy(out[row*cols+startcol:], chunk[row*chunkcols:(row+1)*chunkcols])
1000                                 }
1001                         }
1002                         toMerge[outIdx] = nil
1003
1004                         annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, outIdx)
1005                         log.Infof("reading %s", annotationsFilename)
1006                         buf, err := os.ReadFile(annotationsFilename)
1007                         if err != nil {
1008                                 return err
1009                         }
1010                         if *mergeOutput {
1011                                 err = os.Remove(annotationsFilename)
1012                                 if err != nil {
1013                                         return err
1014                                 }
1015                         }
1016                         for _, line := range bytes.Split(buf, []byte{'\n'}) {
1017                                 if len(line) == 0 {
1018                                         continue
1019                                 }
1020                                 fields := bytes.SplitN(line, []byte{','}, 9)
1021                                 tag, _ := strconv.Atoi(string(fields[0]))
1022                                 incol, _ := strconv.Atoi(string(fields[1]))
1023                                 tileVariant, _ := strconv.Atoi(string(fields[2]))
1024                                 hgvsID := string(fields[3])
1025                                 seqname := string(fields[4])
1026                                 pos, _ := strconv.Atoi(string(fields[5]))
1027                                 refseq := fields[6]
1028                                 if hgvsID == "" {
1029                                         // Null entry for un-diffable
1030                                         // tile variant
1031                                         continue
1032                                 }
1033                                 if hgvsID == "=" {
1034                                         // Null entry for ref tile
1035                                         continue
1036                                 }
1037                                 if mask != nil && !mask.Check(strings.TrimPrefix(seqname, "chr"), pos, pos+len(refseq)) {
1038                                         // The tile intersects one of
1039                                         // the selected regions, but
1040                                         // this particular HGVS
1041                                         // variant does not.
1042                                         continue
1043                                 }
1044                                 hgvsColPair := hgvsCols[hgvsID]
1045                                 if hgvsColPair[0] == nil {
1046                                         // values in new columns start
1047                                         // out as -1 ("no data yet")
1048                                         // or 0 ("=ref") here, may
1049                                         // change to 1 ("hgvs variant
1050                                         // present") below, either on
1051                                         // this line or a future line.
1052                                         hgvsColPair = [2][]int16{make([]int16, len(cmd.cgnames)), make([]int16, len(cmd.cgnames))}
1053                                         rt, ok := reftile[tagID(tag)]
1054                                         if !ok {
1055                                                 err = fmt.Errorf("bug: seeing annotations for tag %d, but it has no reftile entry", tag)
1056                                                 return err
1057                                         }
1058                                         for ph := 0; ph < 2; ph++ {
1059                                                 for row := 0; row < rows; row++ {
1060                                                         v := chunk[row*chunkcols+incol*2+ph]
1061                                                         if tileVariantID(v) == rt.variant {
1062                                                                 hgvsColPair[ph][row] = 0
1063                                                         } else {
1064                                                                 hgvsColPair[ph][row] = -1
1065                                                         }
1066                                                 }
1067                                         }
1068                                         hgvsCols[hgvsID] = hgvsColPair
1069                                         if annow != nil {
1070                                                 hgvsref := hgvs.Variant{
1071                                                         Position: pos,
1072                                                         Ref:      string(refseq),
1073                                                         New:      string(refseq),
1074                                                 }
1075                                                 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])
1076                                         }
1077                                 }
1078                                 if annow != nil {
1079                                         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])
1080                                 }
1081                                 for ph := 0; ph < 2; ph++ {
1082                                         for row := 0; row < rows; row++ {
1083                                                 v := chunk[row*chunkcols+incol*2+ph]
1084                                                 if int(v) == tileVariant {
1085                                                         hgvsColPair[ph][row] = 1
1086                                                 }
1087                                         }
1088                                 }
1089                         }
1090
1091                         startcol += chunkcols
1092                 }
1093                 if *mergeOutput {
1094                         err = annow.Flush()
1095                         if err != nil {
1096                                 return err
1097                         }
1098                         err = annof.Close()
1099                         if err != nil {
1100                                 return err
1101                         }
1102                         err = writeNumpyInt16(fmt.Sprintf("%s/matrix.npy", *outputDir), out, rows, cols)
1103                         if err != nil {
1104                                 return err
1105                         }
1106                 }
1107                 out = nil
1108
1109                 if *hgvsSingle {
1110                         cols = len(hgvsCols) * 2
1111                         log.Printf("building hgvs-based matrix: %d rows x %d cols", rows, cols)
1112                         out = make([]int16, rows*cols)
1113                         hgvsIDs := make([]string, 0, cols/2)
1114                         for hgvsID := range hgvsCols {
1115                                 hgvsIDs = append(hgvsIDs, hgvsID)
1116                         }
1117                         sort.Strings(hgvsIDs)
1118                         var hgvsLabels bytes.Buffer
1119                         for idx, hgvsID := range hgvsIDs {
1120                                 fmt.Fprintf(&hgvsLabels, "%d,%s\n", idx, hgvsID)
1121                                 for ph := 0; ph < 2; ph++ {
1122                                         hgvscol := hgvsCols[hgvsID][ph]
1123                                         for row, val := range hgvscol {
1124                                                 out[row*cols+idx*2+ph] = val
1125                                         }
1126                                 }
1127                         }
1128                         err = writeNumpyInt16(fmt.Sprintf("%s/hgvs.npy", *outputDir), out, rows, cols)
1129                         if err != nil {
1130                                 return err
1131                         }
1132
1133                         fnm := fmt.Sprintf("%s/hgvs.annotations.csv", *outputDir)
1134                         log.Printf("writing hgvs labels: %s", fnm)
1135                         err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0777)
1136                         if err != nil {
1137                                 return err
1138                         }
1139                 }
1140         }
1141         if *onehotSingle || *onlyPCA {
1142                 nzCount := 0
1143                 for _, part := range onehotIndirect {
1144                         nzCount += len(part[0])
1145                 }
1146                 onehot := make([]uint32, nzCount*2) // [r,r,r,...,c,c,c,...]
1147                 var xrefs []onehotXref
1148                 chunkOffset := uint32(0)
1149                 outcol := 0
1150                 for i, part := range onehotIndirect {
1151                         for i := range part[1] {
1152                                 part[1][i] += chunkOffset
1153                         }
1154                         copy(onehot[outcol:], part[0])
1155                         copy(onehot[outcol+nzCount:], part[1])
1156                         xrefs = append(xrefs, onehotXrefs[i]...)
1157
1158                         outcol += len(part[0])
1159                         chunkOffset += onehotChunkSize[i]
1160
1161                         part[0] = nil
1162                         part[1] = nil
1163                         onehotXrefs[i] = nil
1164                         debug.FreeOSMemory()
1165                 }
1166                 if *onehotSingle {
1167                         fnm := fmt.Sprintf("%s/onehot.npy", *outputDir)
1168                         err = writeNumpyUint32(fnm, onehot, 2, nzCount)
1169                         if err != nil {
1170                                 return err
1171                         }
1172                         fnm = fmt.Sprintf("%s/onehot-columns.npy", *outputDir)
1173                         err = writeNumpyInt32(fnm, onehotXref2int32(xrefs), 5, len(xrefs))
1174                         if err != nil {
1175                                 return err
1176                         }
1177                 }
1178                 if *onlyPCA {
1179                         cols := 0
1180                         for _, c := range onehot[nzCount:] {
1181                                 if int(c) >= cols {
1182                                         cols = int(c) + 1
1183                                 }
1184                         }
1185                         if cols == 0 {
1186                                 return fmt.Errorf("cannot do PCA: one-hot matrix is empty")
1187                         }
1188                         log.Printf("have %d one-hot cols", cols)
1189                         stride := 1
1190                         for *maxPCATiles > 0 && cols > *maxPCATiles*2 {
1191                                 cols = (cols + 1) / 2
1192                                 stride = stride * 2
1193                         }
1194                         if cols%2 == 1 {
1195                                 // we work with pairs of columns
1196                                 cols++
1197                         }
1198                         log.Printf("creating full matrix (%d rows) and training matrix (%d rows) with %d cols, stride %d", len(cmd.cgnames), cmd.trainingSetSize, cols, stride)
1199                         mtxFull := mat.NewDense(len(cmd.cgnames), cols, nil)
1200                         mtxTrain := mat.NewDense(cmd.trainingSetSize, cols, nil)
1201                         for i, c := range onehot[nzCount:] {
1202                                 if int(c/2)%stride == 0 {
1203                                         outcol := int(c/2)/stride*2 + int(c)%2
1204                                         mtxFull.Set(int(onehot[i]), outcol, 1)
1205                                         if trainRow := cmd.trainingSet[int(onehot[i])]; trainRow >= 0 {
1206                                                 mtxTrain.Set(trainRow, outcol, 1)
1207                                         }
1208                                 }
1209                         }
1210                         log.Print("fitting")
1211                         transformer := nlp.NewPCA(cmd.pcaComponents)
1212                         transformer.Fit(mtxTrain.T())
1213                         log.Printf("transforming")
1214                         pca, err := transformer.Transform(mtxFull.T())
1215                         if err != nil {
1216                                 return err
1217                         }
1218                         pca = pca.T()
1219                         outrows, outcols := pca.Dims()
1220                         log.Printf("copying result to numpy output array: %d rows, %d cols", outrows, outcols)
1221                         out := make([]float64, outrows*outcols)
1222                         for i := 0; i < outrows; i++ {
1223                                 for j := 0; j < outcols; j++ {
1224                                         out[i*outcols+j] = pca.At(i, j)
1225                                 }
1226                         }
1227                         fnm := fmt.Sprintf("%s/pca.npy", *outputDir)
1228                         log.Printf("writing numpy: %s", fnm)
1229                         output, err := os.OpenFile(fnm, os.O_CREATE|os.O_TRUNC|os.O_WRONLY, 0777)
1230                         if err != nil {
1231                                 return err
1232                         }
1233                         npw, err := gonpy.NewWriter(nopCloser{output})
1234                         if err != nil {
1235                                 return fmt.Errorf("gonpy.NewWriter: %w", err)
1236                         }
1237                         npw.Shape = []int{outrows, outcols}
1238                         err = npw.WriteFloat64(out)
1239                         if err != nil {
1240                                 return fmt.Errorf("WriteFloat64: %w", err)
1241                         }
1242                         err = output.Close()
1243                         if err != nil {
1244                                 return err
1245                         }
1246                         log.Print("done")
1247
1248                         samplesOutFilename := *outputDir + "/samples.csv"
1249                         log.Infof("writing sample metadata to %s", samplesOutFilename)
1250                         var f *os.File
1251                         f, err = os.Create(samplesOutFilename)
1252                         if err != nil {
1253                                 return err
1254                         }
1255                         defer f.Close()
1256                         for i, si := range cmd.samples {
1257                                 var cc, tv string
1258                                 if si.isCase {
1259                                         cc = "1"
1260                                 } else if si.isControl {
1261                                         cc = "0"
1262                                 }
1263                                 if si.isTraining {
1264                                         tv = "1"
1265                                 } else {
1266                                         tv = "0"
1267                                 }
1268                                 var pcavals string
1269                                 for c := 0; c < outcols; c++ {
1270                                         pcavals += fmt.Sprintf(",%f", pca.At(i, c))
1271                                 }
1272                                 _, err = fmt.Fprintf(f, "%d,%s,%s,%s%s\n", i, si.id, cc, tv, pcavals)
1273                                 if err != nil {
1274                                         err = fmt.Errorf("write %s: %w", samplesOutFilename, err)
1275                                         return err
1276                                 }
1277                         }
1278                         err = f.Close()
1279                         if err != nil {
1280                                 err = fmt.Errorf("close %s: %w", samplesOutFilename, err)
1281                                 return err
1282                         }
1283                         log.Print("done")
1284                 }
1285         }
1286         if !*mergeOutput && !*onehotChunked && !*onehotSingle && !*onlyPCA {
1287                 tagoffsetFilename := *outputDir + "/chunk-tag-offset.csv"
1288                 log.Infof("writing tag offsets to %s", tagoffsetFilename)
1289                 var f *os.File
1290                 f, err = os.Create(tagoffsetFilename)
1291                 if err != nil {
1292                         return err
1293                 }
1294                 defer f.Close()
1295                 for idx, offset := range chunkStartTag {
1296                         _, err = fmt.Fprintf(f, "%q,%d\n", fmt.Sprintf("matrix.%04d.npy", idx), offset)
1297                         if err != nil {
1298                                 err = fmt.Errorf("write %s: %w", tagoffsetFilename, err)
1299                                 return err
1300                         }
1301                 }
1302                 err = f.Close()
1303                 if err != nil {
1304                         err = fmt.Errorf("close %s: %w", tagoffsetFilename, err)
1305                         return err
1306                 }
1307         }
1308
1309         return nil
1310 }
1311
1312 type sampleInfo struct {
1313         id            string
1314         isCase        bool
1315         isControl     bool
1316         isTraining    bool
1317         isValidation  bool
1318         pcaComponents []float64
1319 }
1320
1321 // Read samples.csv file with case/control and training/validation
1322 // flags.
1323 func loadSampleInfo(samplesFilename string) ([]sampleInfo, error) {
1324         var si []sampleInfo
1325         f, err := open(samplesFilename)
1326         if err != nil {
1327                 return nil, err
1328         }
1329         buf, err := io.ReadAll(f)
1330         f.Close()
1331         if err != nil {
1332                 return nil, err
1333         }
1334         lineNum := 0
1335         for _, csv := range bytes.Split(buf, []byte{'\n'}) {
1336                 lineNum++
1337                 if len(csv) == 0 {
1338                         continue
1339                 }
1340                 split := strings.Split(string(csv), ",")
1341                 if len(split) < 4 {
1342                         return nil, fmt.Errorf("%d fields < 4 in %s line %d: %q", len(split), samplesFilename, lineNum, csv)
1343                 }
1344                 if split[0] == "Index" && split[1] == "SampleID" && split[2] == "CaseControl" && split[3] == "TrainingValidation" {
1345                         continue
1346                 }
1347                 idx, err := strconv.Atoi(split[0])
1348                 if err != nil {
1349                         if lineNum == 1 {
1350                                 return nil, fmt.Errorf("header does not look right: %q", csv)
1351                         }
1352                         return nil, fmt.Errorf("%s line %d: index: %s", samplesFilename, lineNum, err)
1353                 }
1354                 if idx != len(si) {
1355                         return nil, fmt.Errorf("%s line %d: index %d out of order", samplesFilename, lineNum, idx)
1356                 }
1357                 var pcaComponents []float64
1358                 if len(split) > 4 {
1359                         for _, s := range split[4:] {
1360                                 f, err := strconv.ParseFloat(s, 64)
1361                                 if err != nil {
1362                                         return nil, fmt.Errorf("%s line %d: cannot parse float %q: %s", samplesFilename, lineNum, s, err)
1363                                 }
1364                                 pcaComponents = append(pcaComponents, f)
1365                         }
1366                 }
1367                 si = append(si, sampleInfo{
1368                         id:            split[1],
1369                         isCase:        split[2] == "1",
1370                         isControl:     split[2] == "0",
1371                         isTraining:    split[3] == "1",
1372                         isValidation:  split[3] == "0",
1373                         pcaComponents: pcaComponents,
1374                 })
1375         }
1376         return si, nil
1377 }
1378
1379 func (cmd *sliceNumpy) filterHGVScolpair(colpair [2][]int8) bool {
1380         if cmd.chi2PValue >= 1 {
1381                 return true
1382         }
1383         col0 := make([]bool, 0, len(cmd.chi2Cases))
1384         col1 := make([]bool, 0, len(cmd.chi2Cases))
1385         cases := make([]bool, 0, len(cmd.chi2Cases))
1386         for i, c := range cmd.chi2Cases {
1387                 if colpair[0][i] < 0 {
1388                         continue
1389                 }
1390                 col0 = append(col0, colpair[0][i] != 0)
1391                 col1 = append(col1, colpair[1][i] != 0)
1392                 cases = append(cases, c)
1393         }
1394         return len(cases) >= cmd.minCoverage &&
1395                 (pvalue(col0, cases) <= cmd.chi2PValue || pvalue(col1, cases) <= cmd.chi2PValue)
1396 }
1397
1398 func writeNumpyUint32(fnm string, out []uint32, rows, cols int) error {
1399         output, err := os.Create(fnm)
1400         if err != nil {
1401                 return err
1402         }
1403         defer output.Close()
1404         bufw := bufio.NewWriterSize(output, 1<<26)
1405         npw, err := gonpy.NewWriter(nopCloser{bufw})
1406         if err != nil {
1407                 return err
1408         }
1409         log.WithFields(log.Fields{
1410                 "filename": fnm,
1411                 "rows":     rows,
1412                 "cols":     cols,
1413                 "bytes":    rows * cols * 4,
1414         }).Infof("writing numpy: %s", fnm)
1415         npw.Shape = []int{rows, cols}
1416         npw.WriteUint32(out)
1417         err = bufw.Flush()
1418         if err != nil {
1419                 return err
1420         }
1421         return output.Close()
1422 }
1423
1424 func writeNumpyInt32(fnm string, out []int32, rows, cols int) error {
1425         output, err := os.Create(fnm)
1426         if err != nil {
1427                 return err
1428         }
1429         defer output.Close()
1430         bufw := bufio.NewWriterSize(output, 1<<26)
1431         npw, err := gonpy.NewWriter(nopCloser{bufw})
1432         if err != nil {
1433                 return err
1434         }
1435         log.WithFields(log.Fields{
1436                 "filename": fnm,
1437                 "rows":     rows,
1438                 "cols":     cols,
1439                 "bytes":    rows * cols * 4,
1440         }).Infof("writing numpy: %s", fnm)
1441         npw.Shape = []int{rows, cols}
1442         npw.WriteInt32(out)
1443         err = bufw.Flush()
1444         if err != nil {
1445                 return err
1446         }
1447         return output.Close()
1448 }
1449
1450 func writeNumpyInt16(fnm string, out []int16, rows, cols int) error {
1451         output, err := os.Create(fnm)
1452         if err != nil {
1453                 return err
1454         }
1455         defer output.Close()
1456         bufw := bufio.NewWriterSize(output, 1<<26)
1457         npw, err := gonpy.NewWriter(nopCloser{bufw})
1458         if err != nil {
1459                 return err
1460         }
1461         log.WithFields(log.Fields{
1462                 "filename": fnm,
1463                 "rows":     rows,
1464                 "cols":     cols,
1465                 "bytes":    rows * cols * 2,
1466         }).Infof("writing numpy: %s", fnm)
1467         npw.Shape = []int{rows, cols}
1468         npw.WriteInt16(out)
1469         err = bufw.Flush()
1470         if err != nil {
1471                 return err
1472         }
1473         return output.Close()
1474 }
1475
1476 func writeNumpyInt8(fnm string, out []int8, rows, cols int) error {
1477         output, err := os.Create(fnm)
1478         if err != nil {
1479                 return err
1480         }
1481         defer output.Close()
1482         bufw := bufio.NewWriterSize(output, 1<<26)
1483         npw, err := gonpy.NewWriter(nopCloser{bufw})
1484         if err != nil {
1485                 return err
1486         }
1487         log.WithFields(log.Fields{
1488                 "filename": fnm,
1489                 "rows":     rows,
1490                 "cols":     cols,
1491                 "bytes":    rows * cols,
1492         }).Infof("writing numpy: %s", fnm)
1493         npw.Shape = []int{rows, cols}
1494         npw.WriteInt8(out)
1495         err = bufw.Flush()
1496         if err != nil {
1497                 return err
1498         }
1499         return output.Close()
1500 }
1501
1502 func allele2homhet(colpair [2][]int8) {
1503         a, b := colpair[0], colpair[1]
1504         for i, av := range a {
1505                 bv := b[i]
1506                 if av < 0 || bv < 0 {
1507                         // no-call
1508                         a[i], b[i] = -1, -1
1509                 } else if av > 0 && bv > 0 {
1510                         // hom
1511                         a[i], b[i] = 1, 0
1512                 } else if av > 0 || bv > 0 {
1513                         // het
1514                         a[i], b[i] = 0, 1
1515                 } else {
1516                         // ref (or a different variant in same position)
1517                         // (this is a no-op) a[i], b[i] = 0, 0
1518                 }
1519         }
1520 }
1521
1522 type onehotXref struct {
1523         tag     tagID
1524         variant tileVariantID
1525         hom     bool
1526         pvalue  float64
1527 }
1528
1529 const onehotXrefSize = unsafe.Sizeof(onehotXref{})
1530
1531 // Build onehot matrix (m[tileVariantIndex][genome] == 0 or 1) for all
1532 // variants of a single tile/tag#.
1533 //
1534 // Return nil if no tile variant passes Χ² filter.
1535 func (cmd *sliceNumpy) tv2homhet(cgs map[string]CompactGenome, maxv tileVariantID, remap []tileVariantID, tag, chunkstarttag tagID, seq map[tagID][]TileVariant) ([][]int8, []onehotXref) {
1536         if tag == cmd.debugTag {
1537                 tv := make([]tileVariantID, len(cmd.cgnames)*2)
1538                 for i, name := range cmd.cgnames {
1539                         copy(tv[i*2:(i+1)*2], cgs[name].Variants[(tag-chunkstarttag)*2:])
1540                 }
1541                 log.WithFields(logrus.Fields{
1542                         "cgs[i].Variants[tag*2+j]": tv,
1543                         "maxv":                     maxv,
1544                         "remap":                    remap,
1545                         "tag":                      tag,
1546                         "chunkstarttag":            chunkstarttag,
1547                 }).Info("tv2homhet()")
1548         }
1549         if maxv < 1 || (maxv < 2 && !cmd.includeVariant1) {
1550                 // everyone has the most common variant (of the variants we don't drop)
1551                 return nil, nil
1552         }
1553         tagoffset := tag - chunkstarttag
1554         coverage := 0
1555         for _, cg := range cgs {
1556                 alleles := 0
1557                 for _, v := range cg.Variants[tagoffset*2 : tagoffset*2+2] {
1558                         if v > 0 && int(v) < len(seq[tag]) && len(seq[tag][v].Sequence) > 0 {
1559                                 alleles++
1560                         }
1561                 }
1562                 if alleles == 2 {
1563                         coverage++
1564                 }
1565         }
1566         if coverage < cmd.minCoverage {
1567                 return nil, nil
1568         }
1569         // "observed" array for p-value calculation (training set
1570         // only)
1571         obs := make([][]bool, (maxv+1)*2) // 2 slices (hom + het) for each variant#
1572         // one-hot output (all samples)
1573         outcols := make([][]int8, (maxv+1)*2)
1574         for i := range obs {
1575                 obs[i] = make([]bool, cmd.trainingSetSize)
1576                 outcols[i] = make([]int8, len(cmd.cgnames))
1577         }
1578         for cgid, name := range cmd.cgnames {
1579                 tsid := cmd.trainingSet[cgid]
1580                 cgvars := cgs[name].Variants[tagoffset*2:]
1581                 tv0, tv1 := remap[cgvars[0]], remap[cgvars[1]]
1582                 for v := tileVariantID(1); v <= maxv; v++ {
1583                         if tv0 == v && tv1 == v {
1584                                 if tsid >= 0 {
1585                                         obs[v*2][tsid] = true
1586                                 }
1587                                 outcols[v*2][cgid] = 1
1588                         } else if tv0 == v || tv1 == v {
1589                                 if tsid >= 0 {
1590                                         obs[v*2+1][tsid] = true
1591                                 }
1592                                 outcols[v*2+1][cgid] = 1
1593                         }
1594                 }
1595         }
1596         var onehot [][]int8
1597         var xref []onehotXref
1598         for col := 2; col < len(obs); col++ {
1599                 // col 0,1 correspond to tile variant 0, i.e.,
1600                 // no-call; col 2,3 correspond to the most common
1601                 // variant; so we (normally) start at col 4.
1602                 if col < 4 && !cmd.includeVariant1 {
1603                         continue
1604                 }
1605                 var p float64
1606                 if len(cmd.samples[0].pcaComponents) > 0 {
1607                         p = pvalueGLM(cmd.samples, obs[col], cmd.pcaComponents)
1608                 } else {
1609                         p = pvalue(obs[col], cmd.chi2Cases)
1610                 }
1611                 if cmd.chi2PValue < 1 && !(p < cmd.chi2PValue) {
1612                         continue
1613                 }
1614                 onehot = append(onehot, outcols[col])
1615                 xref = append(xref, onehotXref{
1616                         tag:     tag,
1617                         variant: tileVariantID(col >> 1),
1618                         hom:     col&1 == 0,
1619                         pvalue:  p,
1620                 })
1621         }
1622         return onehot, xref
1623 }
1624
1625 // convert a []onehotXref with length N to a numpy-style []int32
1626 // matrix with N columns, one row per field of onehotXref struct.
1627 //
1628 // Hom/het row contains hom=0, het=1.
1629 //
1630 // P-value row contains 1000000x actual p-value.
1631 func onehotXref2int32(xrefs []onehotXref) []int32 {
1632         xcols := len(xrefs)
1633         xdata := make([]int32, 5*xcols)
1634         for i, xref := range xrefs {
1635                 xdata[i] = int32(xref.tag)
1636                 xdata[xcols+i] = int32(xref.variant)
1637                 if xref.hom {
1638                         xdata[xcols*2+i] = 1
1639                 }
1640                 xdata[xcols*3+i] = int32(xref.pvalue * 1000000)
1641                 xdata[xcols*4+i] = int32(-math.Log10(xref.pvalue) * 1000000)
1642         }
1643         return xdata
1644 }
1645
1646 // transpose onehot data from in[col][row] to numpy-style
1647 // out[row*cols+col].
1648 func onehotcols2int8(in [][]int8) []int8 {
1649         if len(in) == 0 {
1650                 return nil
1651         }
1652         cols := len(in)
1653         rows := len(in[0])
1654         out := make([]int8, rows*cols)
1655         for row := 0; row < rows; row++ {
1656                 outrow := out[row*cols:]
1657                 for col, incol := range in {
1658                         outrow[col] = incol[row]
1659                 }
1660         }
1661         return out
1662 }
1663
1664 // Return [2][]uint32{rowIndices, colIndices} indicating which
1665 // elements of matrixT[c][r] have non-zero values.
1666 func onehotChunk2Indirect(matrixT [][]int8) [2][]uint32 {
1667         var nz [2][]uint32
1668         for c, col := range matrixT {
1669                 for r, val := range col {
1670                         if val != 0 {
1671                                 nz[0] = append(nz[0], uint32(r))
1672                                 nz[1] = append(nz[1], uint32(c))
1673                         }
1674                 }
1675         }
1676         return nz
1677 }