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         pvalue          func(onehot []bool) float64
  56 }
  57
  58 func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  59         err := cmd.run(prog, args, stdin, stdout, stderr)
  60         if err != nil {
  61                 fmt.Fprintf(stderr, "%s\n", err)
  62                 return 1
  63         }
  64         return 0
  65 }
  66
  67 func (cmd *sliceNumpy) run(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) error {
  68         flags := flag.NewFlagSet("", flag.ContinueOnError)
  69         flags.SetOutput(stderr)
  70         pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
  71         runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
  72         arvadosRAM := flags.Int("arvados-ram", 750000000000, "amount of memory to request for arvados container (`bytes`)")
  73         arvadosVCPUs := flags.Int("arvados-vcpus", 96, "number of VCPUs to request for arvados container")
  74         projectUUID := flags.String("project", "", "project `UUID` for output data")
  75         priority := flags.Int("priority", 500, "container request priority")
  76         inputDir := flags.String("input-dir", "./in", "input `directory`")
  77         outputDir := flags.String("output-dir", "./out", "output `directory`")
  78         ref := flags.String("ref", "", "reference name (if blank, choose last one that appears in input)")
  79         regionsFilename := flags.String("regions", "", "only output columns/annotations that intersect regions in specified bed `file`")
  80         expandRegions := flags.Int("expand-regions", 0, "expand specified regions by `N` base pairs on each side`")
  81         mergeOutput := flags.Bool("merge-output", false, "merge output into one matrix.npy and one matrix.annotations.csv")
  82         hgvsSingle := flags.Bool("single-hgvs-matrix", false, "also generate hgvs-based matrix")
  83         hgvsChunked := flags.Bool("chunked-hgvs-matrix", false, "also generate hgvs-based matrix per chromosome")
  84         onehotSingle := flags.Bool("single-onehot", false, "generate one-hot tile-based matrix")
  85         onehotChunked := flags.Bool("chunked-onehot", false, "generate one-hot tile-based matrix per input chunk")
  86         samplesFilename := flags.String("samples", "", "`samples.csv` file with training/validation and case/control groups (see 'lightning choose-samples')")
  87         caseControlOnly := flags.Bool("case-control-only", false, "drop samples that are not in case/control groups")
  88         onlyPCA := flags.Bool("pca", false, "run principal component analysis, write components to pca.npy and samples.csv")
  89         flags.IntVar(&cmd.pcaComponents, "pca-components", 4, "number of PCA components to compute / use in logistic regression")
  90         maxPCATiles := flags.Int("max-pca-tiles", 0, "maximum tiles to use as PCA input (filter, then drop every 2nd colum pair until below max)")
  91         debugTag := flags.Int("debug-tag", -1, "log debugging details about specified tag")
  92         flags.IntVar(&cmd.threads, "threads", 16, "number of memory-hungry assembly threads, and number of VCPUs to request for arvados container")
  93         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")
  94         flags.BoolVar(&cmd.includeVariant1, "include-variant-1", false, "include most common variant when building one-hot matrix")
  95         cmd.filter.Flags(flags)
  96         err := flags.Parse(args)
  97         if err == flag.ErrHelp {
  98                 return nil
  99         } else if err != nil {
 100                 return err
 101         } else if flags.NArg() > 0 {
 102                 return fmt.Errorf("errant command line arguments after parsed flags: %v", flags.Args())
 103         }
 104
 105         if *pprof != "" {
 106                 go func() {
 107                         log.Println(http.ListenAndServe(*pprof, nil))
 108                 }()
 109         }
 110
 111         if cmd.chi2PValue != 1 && *samplesFilename == "" {
 112                 return fmt.Errorf("cannot use provided -chi2-p-value=%f because -samples= value is empty", cmd.chi2PValue)
 113         }
 114
 115         cmd.debugTag = tagID(*debugTag)
 116
 117         if !*runlocal {
 118                 runner := arvadosContainerRunner{
 119                         Name:        "lightning slice-numpy",
 120                         Client:      arvados.NewClientFromEnv(),
 121                         ProjectUUID: *projectUUID,
 122                         RAM:         int64(*arvadosRAM),
 123                         VCPUs:       *arvadosVCPUs,
 124                         Priority:    *priority,
 125                         KeepCache:   2,
 126                         APIAccess:   true,
 127                 }
 128                 err = runner.TranslatePaths(inputDir, regionsFilename, samplesFilename)
 129                 if err != nil {
 130                         return err
 131                 }
 132                 runner.Args = []string{"slice-numpy", "-local=true",
 133                         "-pprof=:6060",
 134                         "-input-dir=" + *inputDir,
 135                         "-output-dir=/mnt/output",
 136                         "-threads=" + fmt.Sprintf("%d", cmd.threads),
 137                         "-regions=" + *regionsFilename,
 138                         "-expand-regions=" + fmt.Sprintf("%d", *expandRegions),
 139                         "-merge-output=" + fmt.Sprintf("%v", *mergeOutput),
 140                         "-single-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsSingle),
 141                         "-chunked-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsChunked),
 142                         "-single-onehot=" + fmt.Sprintf("%v", *onehotSingle),
 143                         "-chunked-onehot=" + fmt.Sprintf("%v", *onehotChunked),
 144                         "-samples=" + *samplesFilename,
 145                         "-case-control-only=" + fmt.Sprintf("%v", *caseControlOnly),
 146                         "-pca=" + fmt.Sprintf("%v", *onlyPCA),
 147                         "-pca-components=" + fmt.Sprintf("%d", cmd.pcaComponents),
 148                         "-max-pca-tiles=" + fmt.Sprintf("%d", *maxPCATiles),
 149                         "-chi2-p-value=" + fmt.Sprintf("%f", cmd.chi2PValue),
 150                         "-include-variant-1=" + fmt.Sprintf("%v", cmd.includeVariant1),
 151                         "-debug-tag=" + fmt.Sprintf("%d", cmd.debugTag),
 152                 }
 153                 runner.Args = append(runner.Args, cmd.filter.Args()...)
 154                 var output string
 155                 output, err = runner.Run()
 156                 if err != nil {
 157                         return err
 158                 }
 159                 fmt.Fprintln(stdout, output)
 160                 return nil
 161         }
 162
 163         infiles, err := allFiles(*inputDir, matchGobFile)
 164         if err != nil {
 165                 return err
 166         }
 167         if len(infiles) == 0 {
 168                 err = fmt.Errorf("no input files found in %s", *inputDir)
 169                 return err
 170         }
 171         sort.Strings(infiles)
 172
 173         var refseq map[string][]tileLibRef
 174         var reftiledata = make(map[tileLibRef][]byte, 11000000)
 175         in0, err := open(infiles[0])
 176         if err != nil {
 177                 return err
 178         }
 179
 180         matchGenome, err := regexp.Compile(cmd.filter.MatchGenome)
 181         if err != nil {
 182                 err = fmt.Errorf("-match-genome: invalid regexp: %q", cmd.filter.MatchGenome)
 183                 return err
 184         }
 185
 186         if *samplesFilename != "" {
 187                 cmd.samples, err = loadSampleInfo(*samplesFilename)
 188                 if err != nil {
 189                         return err
 190                 }
 191                 if len(cmd.samples[0].pcaComponents) > 0 {
 192                         cmd.pvalue = glmPvalueFunc(cmd.samples, cmd.pcaComponents)
 193                         // Unfortunately, statsmodel/glm lib logs
 194                         // stuff to os.Stdout when it panics on an
 195                         // unsolvable problem. We recover() from the
 196                         // panic in glm.go, but we also need to
 197                         // commandeer os.Stdout to avoid producing
 198                         // large quantities of logs.
 199                         stdoutWas := os.Stdout
 200                         defer func() { os.Stdout = stdoutWas }()
 201                         os.Stdout, err = os.Open(os.DevNull)
 202                         if err != nil {
 203                                 return err
 204                         }
 205                 }
 206         } else if *caseControlOnly {
 207                 return fmt.Errorf("-case-control-only does not make sense without -samples")
 208         }
 209
 210         cmd.cgnames = nil
 211         var tagset [][]byte
 212         err = DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
 213                 if len(ent.TagSet) > 0 {
 214                         tagset = ent.TagSet
 215                 }
 216                 for _, cseq := range ent.CompactSequences {
 217                         if cseq.Name == *ref || *ref == "" {
 218                                 refseq = cseq.TileSequences
 219                         }
 220                 }
 221                 for _, cg := range ent.CompactGenomes {
 222                         if matchGenome.MatchString(cg.Name) {
 223                                 cmd.cgnames = append(cmd.cgnames, cg.Name)
 224                         }
 225                 }
 226                 for _, tv := range ent.TileVariants {
 227                         if tv.Ref {
 228                                 reftiledata[tileLibRef{tv.Tag, tv.Variant}] = tv.Sequence
 229                         }
 230                 }
 231                 return nil
 232         })
 233         if err != nil {
 234                 return err
 235         }
 236         in0.Close()
 237         if refseq == nil {
 238                 err = fmt.Errorf("%s: reference sequence not found", infiles[0])
 239                 return err
 240         }
 241         if len(tagset) == 0 {
 242                 err = fmt.Errorf("tagset not found")
 243                 return err
 244         }
 245
 246         taglib := &tagLibrary{}
 247         err = taglib.setTags(tagset)
 248         if err != nil {
 249                 return err
 250         }
 251         taglen := taglib.TagLen()
 252         sort.Strings(cmd.cgnames)
 253
 254         if len(cmd.cgnames) == 0 {
 255                 return fmt.Errorf("fatal: 0 matching samples in library, nothing to do")
 256         }
 257         cmd.trainingSet = make([]int, len(cmd.cgnames))
 258         if *samplesFilename == "" {
 259                 cmd.trainingSetSize = len(cmd.cgnames)
 260                 for i, name := range cmd.cgnames {
 261                         cmd.samples = append(cmd.samples, sampleInfo{
 262                                 id:         trimFilenameForLabel(name),
 263                                 isTraining: true,
 264                         })
 265                         cmd.trainingSet[i] = i
 266                 }
 267         } else if len(cmd.cgnames) != len(cmd.samples) {
 268                 return fmt.Errorf("mismatched sample list: %d samples in library, %d in %s", len(cmd.cgnames), len(cmd.samples), *samplesFilename)
 269         } else {
 270                 for i, name := range cmd.cgnames {
 271                         if s := trimFilenameForLabel(name); s != cmd.samples[i].id {
 272                                 return fmt.Errorf("mismatched sample list: sample %d is %q in library, %q in %s", i, s, cmd.samples[i].id, *samplesFilename)
 273                         }
 274                 }
 275                 if *caseControlOnly {
 276                         for i := 0; i < len(cmd.samples); i++ {
 277                                 if !cmd.samples[i].isTraining && !cmd.samples[i].isValidation {
 278                                         if i+1 < len(cmd.samples) {
 279                                                 copy(cmd.samples[i:], cmd.samples[i+1:])
 280                                                 copy(cmd.cgnames[i:], cmd.cgnames[i+1:])
 281                                         }
 282                                         cmd.samples = cmd.samples[:len(cmd.samples)-1]
 283                                         cmd.cgnames = cmd.cgnames[:len(cmd.cgnames)-1]
 284                                         i--
 285                                 }
 286                         }
 287                 }
 288                 cmd.chi2Cases = nil
 289                 cmd.trainingSetSize = 0
 290                 for i := range cmd.cgnames {
 291                         if cmd.samples[i].isTraining {
 292                                 cmd.trainingSet[i] = cmd.trainingSetSize
 293                                 cmd.trainingSetSize++
 294                                 cmd.chi2Cases = append(cmd.chi2Cases, cmd.samples[i].isCase)
 295                         } else {
 296                                 cmd.trainingSet[i] = -1
 297                         }
 298                 }
 299                 if cmd.pvalue == nil {
 300                         cmd.pvalue = func(onehot []bool) float64 {
 301                                 return pvalue(onehot, cmd.chi2Cases)
 302                         }
 303                 }
 304         }
 305         if cmd.filter.MinCoverage == 1 {
 306                 // In the generic formula below, floating point
 307                 // arithmetic can effectively push the coverage
 308                 // threshold above 1.0, which is impossible/useless.
 309                 // 1.0 needs to mean exactly 100% coverage.
 310                 cmd.minCoverage = len(cmd.cgnames)
 311         } else {
 312                 cmd.minCoverage = int(math.Ceil(cmd.filter.MinCoverage * float64(len(cmd.cgnames))))
 313         }
 314
 315         {
 316                 samplesOutFilename := *outputDir + "/samples.csv"
 317                 log.Infof("writing sample metadata to %s", samplesOutFilename)
 318                 var f *os.File
 319                 f, err = os.Create(samplesOutFilename)
 320                 if err != nil {
 321                         return err
 322                 }
 323                 defer f.Close()
 324                 for i, si := range cmd.samples {
 325                         var cc, tv string
 326                         if si.isCase {
 327                                 cc = "1"
 328                         } else if si.isControl {
 329                                 cc = "0"
 330                         }
 331                         if si.isTraining {
 332                                 tv = "1"
 333                         } else {
 334                                 tv = "0"
 335                         }
 336                         _, err = fmt.Fprintf(f, "%d,%s,%s,%s\n", i, si.id, cc, tv)
 337                         if err != nil {
 338                                 err = fmt.Errorf("write %s: %w", samplesOutFilename, err)
 339                                 return err
 340                         }
 341                 }
 342                 err = f.Close()
 343                 if err != nil {
 344                         err = fmt.Errorf("close %s: %w", samplesOutFilename, err)
 345                         return err
 346                 }
 347                 log.Print("done")
 348         }
 349
 350         log.Info("indexing reference tiles")
 351         type reftileinfo struct {
 352                 variant  tileVariantID
 353                 seqname  string // chr1
 354                 pos      int    // distance from start of chromosome to starttag
 355                 tiledata []byte // acgtggcaa...
 356                 excluded bool   // true if excluded by regions file
 357                 nexttag  tagID  // tagID of following tile (-1 for last tag of chromosome)
 358         }
 359         isdup := map[tagID]bool{}
 360         reftile := map[tagID]*reftileinfo{}
 361         for seqname, cseq := range refseq {
 362                 pos := 0
 363                 lastreftag := tagID(-1)
 364                 for _, libref := range cseq {
 365                         if cmd.filter.MaxTag >= 0 && libref.Tag > tagID(cmd.filter.MaxTag) {
 366                                 continue
 367                         }
 368                         tiledata := reftiledata[libref]
 369                         if len(tiledata) == 0 {
 370                                 err = fmt.Errorf("missing tiledata for tag %d variant %d in %s in ref", libref.Tag, libref.Variant, seqname)
 371                                 return err
 372                         }
 373                         foundthistag := false
 374                         taglib.FindAll(tiledata[:len(tiledata)-1], func(tagid tagID, offset, _ int) {
 375                                 if !foundthistag && tagid == libref.Tag {
 376                                         foundthistag = true
 377                                         return
 378                                 }
 379                                 if dupref, ok := reftile[tagid]; ok {
 380                                         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)
 381                                         delete(reftile, tagid)
 382                                 } else {
 383                                         log.Printf("found tag %d at offset %d inside tile variant %+v on %s @ %d", tagid, offset, libref, seqname, pos+offset+1)
 384                                 }
 385                                 isdup[tagid] = true
 386                         })
 387                         if isdup[libref.Tag] {
 388                                 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
 389                         } else if reftile[libref.Tag] != nil {
 390                                 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)
 391                                 delete(reftile, libref.Tag)
 392                                 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
 393                                 isdup[libref.Tag] = true
 394                         } else {
 395                                 reftile[libref.Tag] = &reftileinfo{
 396                                         seqname:  seqname,
 397                                         variant:  libref.Variant,
 398                                         tiledata: tiledata,
 399                                         pos:      pos,
 400                                         nexttag:  -1,
 401                                 }
 402                                 if lastreftag >= 0 {
 403                                         reftile[lastreftag].nexttag = libref.Tag
 404                                 }
 405                                 lastreftag = libref.Tag
 406                         }
 407                         pos += len(tiledata) - taglen
 408                 }
 409                 log.Printf("... %s done, len %d", seqname, pos+taglen)
 410         }
 411
 412         var mask *mask
 413         if *regionsFilename != "" {
 414                 log.Printf("loading regions from %s", *regionsFilename)
 415                 mask, err = makeMask(*regionsFilename, *expandRegions)
 416                 if err != nil {
 417                         return err
 418                 }
 419                 log.Printf("before applying mask, len(reftile) == %d", len(reftile))
 420                 log.Printf("deleting reftile entries for regions outside %d intervals", mask.Len())
 421                 for _, rt := range reftile {
 422                         if !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(rt.tiledata)) {
 423                                 rt.excluded = true
 424                         }
 425                 }
 426                 log.Printf("after applying mask, len(reftile) == %d", len(reftile))
 427         }
 428
 429         type hgvsColSet map[hgvs.Variant][2][]int8
 430         encodeHGVS := throttle{Max: len(refseq)}
 431         encodeHGVSTodo := map[string]chan hgvsColSet{}
 432         tmpHGVSCols := map[string]*os.File{}
 433         if *hgvsChunked {
 434                 for seqname := range refseq {
 435                         var f *os.File
 436                         f, err = os.Create(*outputDir + "/tmp." + seqname + ".gob")
 437                         if err != nil {
 438                                 return err
 439                         }
 440                         defer os.Remove(f.Name())
 441                         bufw := bufio.NewWriterSize(f, 1<<24)
 442                         enc := gob.NewEncoder(bufw)
 443                         tmpHGVSCols[seqname] = f
 444                         todo := make(chan hgvsColSet, 128)
 445                         encodeHGVSTodo[seqname] = todo
 446                         encodeHGVS.Go(func() error {
 447                                 for colset := range todo {
 448                                         err := enc.Encode(colset)
 449                                         if err != nil {
 450                                                 encodeHGVS.Report(err)
 451                                                 for range todo {
 452                                                 }
 453                                                 return err
 454                                         }
 455                                 }
 456                                 return bufw.Flush()
 457                         })
 458                 }
 459         }
 460
 461         var toMerge [][]int16
 462         if *mergeOutput || *hgvsSingle {
 463                 toMerge = make([][]int16, len(infiles))
 464         }
 465         var onehotIndirect [][2][]uint32 // [chunkIndex][axis][index]
 466         var onehotChunkSize []uint32
 467         var onehotXrefs [][]onehotXref
 468         if *onehotSingle || *onlyPCA {
 469                 onehotIndirect = make([][2][]uint32, len(infiles))
 470                 onehotChunkSize = make([]uint32, len(infiles))
 471                 onehotXrefs = make([][]onehotXref, len(infiles))
 472         }
 473         chunkStartTag := make([]tagID, len(infiles))
 474
 475         throttleMem := throttle{Max: cmd.threads} // TODO: estimate using mem and data size
 476         throttleNumpyMem := throttle{Max: cmd.threads/2 + 1}
 477         log.Info("generating annotations and numpy matrix for each slice")
 478         var errSkip = errors.New("skip infile")
 479         var done int64
 480         for infileIdx, infile := range infiles {
 481                 infileIdx, infile := infileIdx, infile
 482                 throttleMem.Go(func() error {
 483                         seq := make(map[tagID][]TileVariant, 50000)
 484                         cgs := make(map[string]CompactGenome, len(cmd.cgnames))
 485                         f, err := open(infile)
 486                         if err != nil {
 487                                 return err
 488                         }
 489                         defer f.Close()
 490                         log.Infof("%04d: reading %s", infileIdx, infile)
 491                         err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
 492                                 for _, tv := range ent.TileVariants {
 493                                         if tv.Ref {
 494                                                 continue
 495                                         }
 496                                         // Skip tile with no
 497                                         // corresponding ref tile, if
 498                                         // mask is in play (we can't
 499                                         // determine coordinates for
 500                                         // these)
 501                                         if mask != nil && reftile[tv.Tag] == nil {
 502                                                 continue
 503                                         }
 504                                         // Skip tile whose
 505                                         // corresponding ref tile is
 506                                         // outside target regions --
 507                                         // unless it's a potential
 508                                         // spanning tile.
 509                                         if mask != nil && reftile[tv.Tag].excluded &&
 510                                                 (int(tv.Tag+1) >= len(tagset) ||
 511                                                         (bytes.HasSuffix(tv.Sequence, tagset[tv.Tag+1]) && reftile[tv.Tag+1] != nil && !reftile[tv.Tag+1].excluded)) {
 512                                                 continue
 513                                         }
 514                                         if tv.Tag == cmd.debugTag {
 515                                                 log.Printf("infile %d %s tag %d variant %d hash %x", infileIdx, infile, tv.Tag, tv.Variant, tv.Blake2b[:3])
 516                                         }
 517                                         variants := seq[tv.Tag]
 518                                         if len(variants) == 0 {
 519                                                 variants = make([]TileVariant, 100)
 520                                         }
 521                                         for len(variants) <= int(tv.Variant) {
 522                                                 variants = append(variants, TileVariant{})
 523                                         }
 524                                         variants[int(tv.Variant)] = tv
 525                                         seq[tv.Tag] = variants
 526                                 }
 527                                 for _, cg := range ent.CompactGenomes {
 528                                         if cmd.filter.MaxTag >= 0 && cg.StartTag > tagID(cmd.filter.MaxTag) {
 529                                                 return errSkip
 530                                         }
 531                                         if !matchGenome.MatchString(cg.Name) {
 532                                                 continue
 533                                         }
 534                                         // pad to full slice size
 535                                         // to avoid out-of-bounds
 536                                         // checks later
 537                                         if sliceSize := 2 * int(cg.EndTag-cg.StartTag); len(cg.Variants) < sliceSize {
 538                                                 cg.Variants = append(cg.Variants, make([]tileVariantID, sliceSize-len(cg.Variants))...)
 539                                         }
 540                                         cgs[cg.Name] = cg
 541                                 }
 542                                 return nil
 543                         })
 544                         if err == errSkip {
 545                                 return nil
 546                         } else if err != nil {
 547                                 return fmt.Errorf("%04d: DecodeLibrary(%s): err", infileIdx, infile)
 548                         }
 549                         tagstart := cgs[cmd.cgnames[0]].StartTag
 550                         tagend := cgs[cmd.cgnames[0]].EndTag
 551                         chunkStartTag[infileIdx] = tagstart
 552
 553                         // TODO: filters
 554
 555                         log.Infof("%04d: renumber/dedup variants for tags %d-%d", infileIdx, tagstart, tagend)
 556                         variantRemap := make([][]tileVariantID, tagend-tagstart)
 557                         throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
 558                         for tag, variants := range seq {
 559                                 tag, variants := tag, variants
 560                                 throttleCPU.Go(func() error {
 561                                         alleleCoverage := 0
 562                                         count := make(map[[blake2b.Size256]byte]int, len(variants))
 563
 564                                         rt := reftile[tag]
 565                                         if rt != nil {
 566                                                 count[blake2b.Sum256(rt.tiledata)] = 0
 567                                         }
 568
 569                                         for cgname, cg := range cgs {
 570                                                 idx := int(tag-tagstart) * 2
 571                                                 for allele := 0; allele < 2; allele++ {
 572                                                         v := cg.Variants[idx+allele]
 573                                                         if v > 0 && len(variants[v].Sequence) > 0 {
 574                                                                 count[variants[v].Blake2b]++
 575                                                                 alleleCoverage++
 576                                                         }
 577                                                         if v > 0 && tag == cmd.debugTag {
 578                                                                 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])
 579                                                         }
 580                                                 }
 581                                         }
 582                                         if alleleCoverage < cmd.minCoverage*2 {
 583                                                 idx := int(tag-tagstart) * 2
 584                                                 for _, cg := range cgs {
 585                                                         cg.Variants[idx] = 0
 586                                                         cg.Variants[idx+1] = 0
 587                                                 }
 588                                                 if tag == cmd.debugTag {
 589                                                         log.Printf("tag %d alleleCoverage %d < min %d, sample data wiped", tag, alleleCoverage, cmd.minCoverage*2)
 590                                                 }
 591                                                 return nil
 592                                         }
 593
 594                                         // hash[i] will be the hash of
 595                                         // the variant(s) that should
 596                                         // be at rank i (0-based).
 597                                         hash := make([][blake2b.Size256]byte, 0, len(count))
 598                                         for b := range count {
 599                                                 hash = append(hash, b)
 600                                         }
 601                                         sort.Slice(hash, func(i, j int) bool {
 602                                                 bi, bj := &hash[i], &hash[j]
 603                                                 if ci, cj := count[*bi], count[*bj]; ci != cj {
 604                                                         return ci > cj
 605                                                 } else {
 606                                                         return bytes.Compare((*bi)[:], (*bj)[:]) < 0
 607                                                 }
 608                                         })
 609                                         // rank[b] will be the 1-based
 610                                         // new variant number for
 611                                         // variants whose hash is b.
 612                                         rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
 613                                         for i, h := range hash {
 614                                                 rank[h] = tileVariantID(i + 1)
 615                                         }
 616                                         if tag == cmd.debugTag {
 617                                                 for h, r := range rank {
 618                                                         log.Printf("tag %d rank(%x) = %v", tag, h[:3], r)
 619                                                 }
 620                                         }
 621                                         // remap[v] will be the new
 622                                         // variant number for original
 623                                         // variant number v.
 624                                         remap := make([]tileVariantID, len(variants))
 625                                         for i, tv := range variants {
 626                                                 remap[i] = rank[tv.Blake2b]
 627                                         }
 628                                         if tag == cmd.debugTag {
 629                                                 for in, out := range remap {
 630                                                         if out > 0 {
 631                                                                 log.Printf("tag %d remap %d => %d", tag, in, out)
 632                                                         }
 633                                                 }
 634                                         }
 635                                         variantRemap[tag-tagstart] = remap
 636                                         if rt != nil {
 637                                                 refrank := rank[blake2b.Sum256(rt.tiledata)]
 638                                                 if tag == cmd.debugTag {
 639                                                         log.Printf("tag %d reftile variant %d => %d", tag, rt.variant, refrank)
 640                                                 }
 641                                                 rt.variant = refrank
 642                                         }
 643                                         return nil
 644                                 })
 645                         }
 646                         throttleCPU.Wait()
 647
 648                         var onehotChunk [][]int8
 649                         var onehotXref []onehotXref
 650
 651                         var annotationsFilename string
 652                         if *onlyPCA {
 653                                 annotationsFilename = "/dev/null"
 654                         } else {
 655                                 annotationsFilename = fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
 656                                 log.Infof("%04d: writing %s", infileIdx, annotationsFilename)
 657                         }
 658                         annof, err := os.Create(annotationsFilename)
 659                         if err != nil {
 660                                 return err
 661                         }
 662                         annow := bufio.NewWriterSize(annof, 1<<20)
 663                         outcol := 0
 664                         for tag := tagstart; tag < tagend; tag++ {
 665                                 rt := reftile[tag]
 666                                 if rt == nil && mask != nil {
 667                                         // With no ref tile, we don't
 668                                         // have coordinates to say
 669                                         // this is in the desired
 670                                         // regions -- so it's not.
 671                                         // TODO: handle ref spanning
 672                                         // tile case.
 673                                         continue
 674                                 }
 675                                 if rt != nil && rt.excluded {
 676                                         // TODO: don't skip yet --
 677                                         // first check for spanning
 678                                         // tile variants that
 679                                         // intersect non-excluded ref
 680                                         // tiles.
 681                                         continue
 682                                 }
 683                                 if cmd.filter.MaxTag >= 0 && tag > tagID(cmd.filter.MaxTag) {
 684                                         break
 685                                 }
 686                                 remap := variantRemap[tag-tagstart]
 687                                 if remap == nil {
 688                                         // was not assigned above,
 689                                         // because minCoverage
 690                                         outcol++
 691                                         continue
 692                                 }
 693                                 maxv := tileVariantID(0)
 694                                 for _, v := range remap {
 695                                         if maxv < v {
 696                                                 maxv = v
 697                                         }
 698                                 }
 699                                 if *onehotChunked || *onehotSingle || *onlyPCA {
 700                                         onehot, xrefs := cmd.tv2homhet(cgs, maxv, remap, tag, tagstart, seq)
 701                                         if tag == cmd.debugTag {
 702                                                 log.WithFields(logrus.Fields{
 703                                                         "onehot": onehot,
 704                                                         "xrefs":  xrefs,
 705                                                 }).Info("tv2homhet()")
 706                                         }
 707                                         onehotChunk = append(onehotChunk, onehot...)
 708                                         onehotXref = append(onehotXref, xrefs...)
 709                                 }
 710                                 if *onlyPCA {
 711                                         outcol++
 712                                         continue
 713                                 }
 714                                 if rt == nil {
 715                                         // Reference does not use any
 716                                         // variant of this tile
 717                                         //
 718                                         // TODO: diff against the
 719                                         // relevant portion of the
 720                                         // ref's spanning tile
 721                                         outcol++
 722                                         continue
 723                                 }
 724                                 fmt.Fprintf(annow, "%d,%d,%d,=,%s,%d,,,\n", tag, outcol, rt.variant, rt.seqname, rt.pos)
 725                                 variants := seq[tag]
 726                                 reftilestr := strings.ToUpper(string(rt.tiledata))
 727
 728                                 done := make([]bool, maxv+1)
 729                                 variantDiffs := make([][]hgvs.Variant, maxv+1)
 730                                 for v, tv := range variants {
 731                                         v := remap[v]
 732                                         if v == 0 || v == rt.variant || done[v] {
 733                                                 continue
 734                                         } else {
 735                                                 done[v] = true
 736                                         }
 737                                         if len(tv.Sequence) < taglen {
 738                                                 continue
 739                                         }
 740                                         // if reftilestr doesn't end
 741                                         // in the same tag as tv,
 742                                         // extend reftilestr with
 743                                         // following ref tiles until
 744                                         // it does (up to an arbitrary
 745                                         // sanity-check limit)
 746                                         reftilestr := reftilestr
 747                                         endtagstr := strings.ToUpper(string(tv.Sequence[len(tv.Sequence)-taglen:]))
 748                                         for i, rt := 0, rt; i < annotationMaxTileSpan && !strings.HasSuffix(reftilestr, endtagstr) && rt.nexttag >= 0; i++ {
 749                                                 rt = reftile[rt.nexttag]
 750                                                 if rt == nil {
 751                                                         break
 752                                                 }
 753                                                 reftilestr += strings.ToUpper(string(rt.tiledata[taglen:]))
 754                                         }
 755                                         if mask != nil && !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(reftilestr)) {
 756                                                 continue
 757                                         }
 758                                         if !strings.HasSuffix(reftilestr, endtagstr) {
 759                                                 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
 760                                                 continue
 761                                         }
 762                                         if lendiff := len(reftilestr) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
 763                                                 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
 764                                                 continue
 765                                         }
 766                                         diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
 767                                         for i := range diffs {
 768                                                 diffs[i].Position += rt.pos
 769                                         }
 770                                         for _, diff := range diffs {
 771                                                 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)
 772                                         }
 773                                         if *hgvsChunked {
 774                                                 variantDiffs[v] = diffs
 775                                         }
 776                                 }
 777                                 if *hgvsChunked {
 778                                         // We can now determine, for each HGVS
 779                                         // variant (diff) in this reftile
 780                                         // region, whether a given genome
 781                                         // phase/allele (1) has the variant, (0) has
 782                                         // =ref or a different variant in that
 783                                         // position, or (-1) is lacking
 784                                         // coverage / couldn't be diffed.
 785                                         hgvsCol := hgvsColSet{}
 786                                         for _, diffs := range variantDiffs {
 787                                                 for _, diff := range diffs {
 788                                                         if _, ok := hgvsCol[diff]; ok {
 789                                                                 continue
 790                                                         }
 791                                                         hgvsCol[diff] = [2][]int8{
 792                                                                 make([]int8, len(cmd.cgnames)),
 793                                                                 make([]int8, len(cmd.cgnames)),
 794                                                         }
 795                                                 }
 796                                         }
 797                                         for row, name := range cmd.cgnames {
 798                                                 variants := cgs[name].Variants[(tag-tagstart)*2:]
 799                                                 for ph := 0; ph < 2; ph++ {
 800                                                         v := variants[ph]
 801                                                         if int(v) >= len(remap) {
 802                                                                 v = 0
 803                                                         } else {
 804                                                                 v = remap[v]
 805                                                         }
 806                                                         if v == rt.variant {
 807                                                                 // hgvsCol[*][ph][row] is already 0
 808                                                         } else if len(variantDiffs[v]) == 0 {
 809                                                                 // lacking coverage / couldn't be diffed
 810                                                                 for _, col := range hgvsCol {
 811                                                                         col[ph][row] = -1
 812                                                                 }
 813                                                         } else {
 814                                                                 for _, diff := range variantDiffs[v] {
 815                                                                         hgvsCol[diff][ph][row] = 1
 816                                                                 }
 817                                                         }
 818                                                 }
 819                                         }
 820                                         for diff, colpair := range hgvsCol {
 821                                                 allele2homhet(colpair)
 822                                                 if !cmd.filterHGVScolpair(colpair) {
 823                                                         delete(hgvsCol, diff)
 824                                                 }
 825                                         }
 826                                         if len(hgvsCol) > 0 {
 827                                                 encodeHGVSTodo[rt.seqname] <- hgvsCol
 828                                         }
 829                                 }
 830                                 outcol++
 831                         }
 832                         err = annow.Flush()
 833                         if err != nil {
 834                                 return err
 835                         }
 836                         err = annof.Close()
 837                         if err != nil {
 838                                 return err
 839                         }
 840
 841                         if *onehotChunked {
 842                                 // transpose onehotChunk[col][row] to numpy[row*ncols+col]
 843                                 rows := len(cmd.cgnames)
 844                                 cols := len(onehotChunk)
 845                                 log.Infof("%04d: preparing onehot numpy (rows=%d, cols=%d, mem=%d)", infileIdx, rows, cols, rows*cols)
 846                                 throttleNumpyMem.Acquire()
 847                                 out := onehotcols2int8(onehotChunk)
 848                                 fnm := fmt.Sprintf("%s/onehot.%04d.npy", *outputDir, infileIdx)
 849                                 err = writeNumpyInt8(fnm, out, rows, cols)
 850                                 if err != nil {
 851                                         return err
 852                                 }
 853                                 fnm = fmt.Sprintf("%s/onehot-columns.%04d.npy", *outputDir, infileIdx)
 854                                 err = writeNumpyInt32(fnm, onehotXref2int32(onehotXref), 4, len(onehotXref))
 855                                 if err != nil {
 856                                         return err
 857                                 }
 858                                 debug.FreeOSMemory()
 859                                 throttleNumpyMem.Release()
 860                         }
 861                         if *onehotSingle || *onlyPCA {
 862                                 onehotIndirect[infileIdx] = onehotChunk2Indirect(onehotChunk)
 863                                 onehotChunkSize[infileIdx] = uint32(len(onehotChunk))
 864                                 onehotXrefs[infileIdx] = onehotXref
 865                                 n := len(onehotIndirect[infileIdx][0])
 866                                 log.Infof("%04d: keeping onehot coordinates in memory (n=%d, mem=%d)", infileIdx, n, n*8*2)
 867                         }
 868                         if !(*onehotSingle || *onehotChunked || *onlyPCA) || *mergeOutput || *hgvsSingle {
 869                                 log.Infof("%04d: preparing numpy (rows=%d, cols=%d)", infileIdx, len(cmd.cgnames), 2*outcol)
 870                                 throttleNumpyMem.Acquire()
 871                                 rows := len(cmd.cgnames)
 872                                 cols := 2 * outcol
 873                                 out := make([]int16, rows*cols)
 874                                 for row, name := range cmd.cgnames {
 875                                         outidx := row * cols
 876                                         for col, v := range cgs[name].Variants {
 877                                                 tag := tagstart + tagID(col/2)
 878                                                 if cmd.filter.MaxTag >= 0 && tag > tagID(cmd.filter.MaxTag) {
 879                                                         break
 880                                                 }
 881                                                 if rt := reftile[tag]; rt == nil || rt.excluded {
 882                                                         continue
 883                                                 }
 884                                                 if v == 0 {
 885                                                         out[outidx] = 0 // tag not found / spanning tile
 886                                                 } else if variants, ok := seq[tag]; ok && int(v) < len(variants) && len(variants[v].Sequence) > 0 {
 887                                                         out[outidx] = int16(variantRemap[tag-tagstart][v])
 888                                                 } else {
 889                                                         out[outidx] = -1 // low quality tile variant
 890                                                 }
 891                                                 if tag == cmd.debugTag {
 892                                                         log.Printf("tag %d row %d col %d outidx %d v %d out %d", tag, row, col, outidx, v, out[outidx])
 893                                                 }
 894                                                 outidx++
 895                                         }
 896                                 }
 897                                 seq = nil
 898                                 cgs = nil
 899                                 debug.FreeOSMemory()
 900                                 throttleNumpyMem.Release()
 901                                 if *mergeOutput || *hgvsSingle {
 902                                         log.Infof("%04d: matrix fragment %d rows x %d cols", infileIdx, rows, cols)
 903                                         toMerge[infileIdx] = out
 904                                 }
 905                                 if !*mergeOutput && !*onehotChunked && !*onehotSingle {
 906                                         fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
 907                                         err = writeNumpyInt16(fnm, out, rows, cols)
 908                                         if err != nil {
 909                                                 return err
 910                                         }
 911                                 }
 912                         }
 913                         debug.FreeOSMemory()
 914                         log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
 915                         return nil
 916                 })
 917         }
 918         if err = throttleMem.Wait(); err != nil {
 919                 return err
 920         }
 921
 922         if *hgvsChunked {
 923                 log.Info("flushing hgvsCols temp files")
 924                 for seqname := range refseq {
 925                         close(encodeHGVSTodo[seqname])
 926                 }
 927                 err = encodeHGVS.Wait()
 928                 if err != nil {
 929                         return err
 930                 }
 931                 for seqname := range refseq {
 932                         log.Infof("%s: reading hgvsCols from temp file", seqname)
 933                         f := tmpHGVSCols[seqname]
 934                         _, err = f.Seek(0, io.SeekStart)
 935                         if err != nil {
 936                                 return err
 937                         }
 938                         var hgvsCols hgvsColSet
 939                         dec := gob.NewDecoder(bufio.NewReaderSize(f, 1<<24))
 940                         for err == nil {
 941                                 err = dec.Decode(&hgvsCols)
 942                         }
 943                         if err != io.EOF {
 944                                 return err
 945                         }
 946                         log.Infof("%s: sorting %d hgvs variants", seqname, len(hgvsCols))
 947                         variants := make([]hgvs.Variant, 0, len(hgvsCols))
 948                         for v := range hgvsCols {
 949                                 variants = append(variants, v)
 950                         }
 951                         sort.Slice(variants, func(i, j int) bool {
 952                                 vi, vj := &variants[i], &variants[j]
 953                                 if vi.Position != vj.Position {
 954                                         return vi.Position < vj.Position
 955                                 } else if vi.Ref != vj.Ref {
 956                                         return vi.Ref < vj.Ref
 957                                 } else {
 958                                         return vi.New < vj.New
 959                                 }
 960                         })
 961                         rows := len(cmd.cgnames)
 962                         cols := len(variants) * 2
 963                         log.Infof("%s: building hgvs matrix (rows=%d, cols=%d, mem=%d)", seqname, rows, cols, rows*cols)
 964                         out := make([]int8, rows*cols)
 965                         for varIdx, variant := range variants {
 966                                 hgvsCols := hgvsCols[variant]
 967                                 for row := range cmd.cgnames {
 968                                         for ph := 0; ph < 2; ph++ {
 969                                                 out[row*cols+varIdx+ph] = hgvsCols[ph][row]
 970                                         }
 971                                 }
 972                         }
 973                         err = writeNumpyInt8(fmt.Sprintf("%s/hgvs.%s.npy", *outputDir, seqname), out, rows, cols)
 974                         if err != nil {
 975                                 return err
 976                         }
 977                         out = nil
 978
 979                         fnm := fmt.Sprintf("%s/hgvs.%s.annotations.csv", *outputDir, seqname)
 980                         log.Infof("%s: writing hgvs column labels to %s", seqname, fnm)
 981                         var hgvsLabels bytes.Buffer
 982                         for varIdx, variant := range variants {
 983                                 fmt.Fprintf(&hgvsLabels, "%d,%s:g.%s\n", varIdx, seqname, variant.String())
 984                         }
 985                         err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0666)
 986                         if err != nil {
 987                                 return err
 988                         }
 989                 }
 990         }
 991
 992         if *mergeOutput || *hgvsSingle {
 993                 var annow *bufio.Writer
 994                 var annof *os.File
 995                 if *mergeOutput {
 996                         annoFilename := fmt.Sprintf("%s/matrix.annotations.csv", *outputDir)
 997                         annof, err = os.Create(annoFilename)
 998                         if err != nil {
 999                                 return err
1000                         }
1001                         annow = bufio.NewWriterSize(annof, 1<<20)
1002                 }
1003
1004                 rows := len(cmd.cgnames)
1005                 cols := 0
1006                 for _, chunk := range toMerge {
1007                         cols += len(chunk) / rows
1008                 }
1009                 log.Infof("merging output matrix (rows=%d, cols=%d, mem=%d) and annotations", rows, cols, rows*cols*2)
1010                 var out []int16
1011                 if *mergeOutput {
1012                         out = make([]int16, rows*cols)
1013                 }
1014                 hgvsCols := map[string][2][]int16{} // hgvs -> [[g0,g1,g2,...], [g0,g1,g2,...]] (slice of genomes for each phase)
1015                 startcol := 0
1016                 for outIdx, chunk := range toMerge {
1017                         chunkcols := len(chunk) / rows
1018                         if *mergeOutput {
1019                                 for row := 0; row < rows; row++ {
1020                                         copy(out[row*cols+startcol:], chunk[row*chunkcols:(row+1)*chunkcols])
1021                                 }
1022                         }
1023                         toMerge[outIdx] = nil
1024
1025                         annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, outIdx)
1026                         log.Infof("reading %s", annotationsFilename)
1027                         buf, err := os.ReadFile(annotationsFilename)
1028                         if err != nil {
1029                                 return err
1030                         }
1031                         if *mergeOutput {
1032                                 err = os.Remove(annotationsFilename)
1033                                 if err != nil {
1034                                         return err
1035                                 }
1036                         }
1037                         for _, line := range bytes.Split(buf, []byte{'\n'}) {
1038                                 if len(line) == 0 {
1039                                         continue
1040                                 }
1041                                 fields := bytes.SplitN(line, []byte{','}, 9)
1042                                 tag, _ := strconv.Atoi(string(fields[0]))
1043                                 incol, _ := strconv.Atoi(string(fields[1]))
1044                                 tileVariant, _ := strconv.Atoi(string(fields[2]))
1045                                 hgvsID := string(fields[3])
1046                                 seqname := string(fields[4])
1047                                 pos, _ := strconv.Atoi(string(fields[5]))
1048                                 refseq := fields[6]
1049                                 if hgvsID == "" {
1050                                         // Null entry for un-diffable
1051                                         // tile variant
1052                                         continue
1053                                 }
1054                                 if hgvsID == "=" {
1055                                         // Null entry for ref tile
1056                                         continue
1057                                 }
1058                                 if mask != nil && !mask.Check(strings.TrimPrefix(seqname, "chr"), pos, pos+len(refseq)) {
1059                                         // The tile intersects one of
1060                                         // the selected regions, but
1061                                         // this particular HGVS
1062                                         // variant does not.
1063                                         continue
1064                                 }
1065                                 hgvsColPair := hgvsCols[hgvsID]
1066                                 if hgvsColPair[0] == nil {
1067                                         // values in new columns start
1068                                         // out as -1 ("no data yet")
1069                                         // or 0 ("=ref") here, may
1070                                         // change to 1 ("hgvs variant
1071                                         // present") below, either on
1072                                         // this line or a future line.
1073                                         hgvsColPair = [2][]int16{make([]int16, len(cmd.cgnames)), make([]int16, len(cmd.cgnames))}
1074                                         rt, ok := reftile[tagID(tag)]
1075                                         if !ok {
1076                                                 err = fmt.Errorf("bug: seeing annotations for tag %d, but it has no reftile entry", tag)
1077                                                 return err
1078                                         }
1079                                         for ph := 0; ph < 2; ph++ {
1080                                                 for row := 0; row < rows; row++ {
1081                                                         v := chunk[row*chunkcols+incol*2+ph]
1082                                                         if tileVariantID(v) == rt.variant {
1083                                                                 hgvsColPair[ph][row] = 0
1084                                                         } else {
1085                                                                 hgvsColPair[ph][row] = -1
1086                                                         }
1087                                                 }
1088                                         }
1089                                         hgvsCols[hgvsID] = hgvsColPair
1090                                         if annow != nil {
1091                                                 hgvsref := hgvs.Variant{
1092                                                         Position: pos,
1093                                                         Ref:      string(refseq),
1094                                                         New:      string(refseq),
1095                                                 }
1096                                                 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])
1097                                         }
1098                                 }
1099                                 if annow != nil {
1100                                         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])
1101                                 }
1102                                 for ph := 0; ph < 2; ph++ {
1103                                         for row := 0; row < rows; row++ {
1104                                                 v := chunk[row*chunkcols+incol*2+ph]
1105                                                 if int(v) == tileVariant {
1106                                                         hgvsColPair[ph][row] = 1
1107                                                 }
1108                                         }
1109                                 }
1110                         }
1111
1112                         startcol += chunkcols
1113                 }
1114                 if *mergeOutput {
1115                         err = annow.Flush()
1116                         if err != nil {
1117                                 return err
1118                         }
1119                         err = annof.Close()
1120                         if err != nil {
1121                                 return err
1122                         }
1123                         err = writeNumpyInt16(fmt.Sprintf("%s/matrix.npy", *outputDir), out, rows, cols)
1124                         if err != nil {
1125                                 return err
1126                         }
1127                 }
1128                 out = nil
1129
1130                 if *hgvsSingle {
1131                         cols = len(hgvsCols) * 2
1132                         log.Printf("building hgvs-based matrix: %d rows x %d cols", rows, cols)
1133                         out = make([]int16, rows*cols)
1134                         hgvsIDs := make([]string, 0, cols/2)
1135                         for hgvsID := range hgvsCols {
1136                                 hgvsIDs = append(hgvsIDs, hgvsID)
1137                         }
1138                         sort.Strings(hgvsIDs)
1139                         var hgvsLabels bytes.Buffer
1140                         for idx, hgvsID := range hgvsIDs {
1141                                 fmt.Fprintf(&hgvsLabels, "%d,%s\n", idx, hgvsID)
1142                                 for ph := 0; ph < 2; ph++ {
1143                                         hgvscol := hgvsCols[hgvsID][ph]
1144                                         for row, val := range hgvscol {
1145                                                 out[row*cols+idx*2+ph] = val
1146                                         }
1147                                 }
1148                         }
1149                         err = writeNumpyInt16(fmt.Sprintf("%s/hgvs.npy", *outputDir), out, rows, cols)
1150                         if err != nil {
1151                                 return err
1152                         }
1153
1154                         fnm := fmt.Sprintf("%s/hgvs.annotations.csv", *outputDir)
1155                         log.Printf("writing hgvs labels: %s", fnm)
1156                         err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0777)
1157                         if err != nil {
1158                                 return err
1159                         }
1160                 }
1161         }
1162         if *onehotSingle || *onlyPCA {
1163                 nzCount := 0
1164                 for _, part := range onehotIndirect {
1165                         nzCount += len(part[0])
1166                 }
1167                 onehot := make([]uint32, nzCount*2) // [r,r,r,...,c,c,c,...]
1168                 var xrefs []onehotXref
1169                 chunkOffset := uint32(0)
1170                 outcol := 0
1171                 for i, part := range onehotIndirect {
1172                         for i := range part[1] {
1173                                 part[1][i] += chunkOffset
1174                         }
1175                         copy(onehot[outcol:], part[0])
1176                         copy(onehot[outcol+nzCount:], part[1])
1177                         xrefs = append(xrefs, onehotXrefs[i]...)
1178
1179                         outcol += len(part[0])
1180                         chunkOffset += onehotChunkSize[i]
1181
1182                         part[0] = nil
1183                         part[1] = nil
1184                         onehotXrefs[i] = nil
1185                         debug.FreeOSMemory()
1186                 }
1187                 if *onehotSingle {
1188                         fnm := fmt.Sprintf("%s/onehot.npy", *outputDir)
1189                         err = writeNumpyUint32(fnm, onehot, 2, nzCount)
1190                         if err != nil {
1191                                 return err
1192                         }
1193                         fnm = fmt.Sprintf("%s/onehot-columns.npy", *outputDir)
1194                         err = writeNumpyInt32(fnm, onehotXref2int32(xrefs), 5, len(xrefs))
1195                         if err != nil {
1196                                 return err
1197                         }
1198                 }
1199                 if *onlyPCA {
1200                         cols := 0
1201                         for _, c := range onehot[nzCount:] {
1202                                 if int(c) >= cols {
1203                                         cols = int(c) + 1
1204                                 }
1205                         }
1206                         if cols == 0 {
1207                                 return fmt.Errorf("cannot do PCA: one-hot matrix is empty")
1208                         }
1209                         log.Printf("have %d one-hot cols", cols)
1210                         stride := 1
1211                         for *maxPCATiles > 0 && cols > *maxPCATiles*2 {
1212                                 cols = (cols + 1) / 2
1213                                 stride = stride * 2
1214                         }
1215                         if cols%2 == 1 {
1216                                 // we work with pairs of columns
1217                                 cols++
1218                         }
1219                         log.Printf("creating full matrix (%d rows) and training matrix (%d rows) with %d cols, stride %d", len(cmd.cgnames), cmd.trainingSetSize, cols, stride)
1220                         mtxFull := mat.NewDense(len(cmd.cgnames), cols, nil)
1221                         mtxTrain := mat.NewDense(cmd.trainingSetSize, cols, nil)
1222                         for i, c := range onehot[nzCount:] {
1223                                 if int(c/2)%stride == 0 {
1224                                         outcol := int(c/2)/stride*2 + int(c)%2
1225                                         mtxFull.Set(int(onehot[i]), outcol, 1)
1226                                         if trainRow := cmd.trainingSet[int(onehot[i])]; trainRow >= 0 {
1227                                                 mtxTrain.Set(trainRow, outcol, 1)
1228                                         }
1229                                 }
1230                         }
1231                         log.Print("fitting")
1232                         transformer := nlp.NewPCA(cmd.pcaComponents)
1233                         transformer.Fit(mtxTrain.T())
1234                         log.Printf("transforming")
1235                         pca, err := transformer.Transform(mtxFull.T())
1236                         if err != nil {
1237                                 return err
1238                         }
1239                         pca = pca.T()
1240                         outrows, outcols := pca.Dims()
1241                         log.Printf("copying result to numpy output array: %d rows, %d cols", outrows, outcols)
1242                         out := make([]float64, outrows*outcols)
1243                         for i := 0; i < outrows; i++ {
1244                                 for j := 0; j < outcols; j++ {
1245                                         out[i*outcols+j] = pca.At(i, j)
1246                                 }
1247                         }
1248                         fnm := fmt.Sprintf("%s/pca.npy", *outputDir)
1249                         log.Printf("writing numpy: %s", fnm)
1250                         output, err := os.OpenFile(fnm, os.O_CREATE|os.O_TRUNC|os.O_WRONLY, 0777)
1251                         if err != nil {
1252                                 return err
1253                         }
1254                         npw, err := gonpy.NewWriter(nopCloser{output})
1255                         if err != nil {
1256                                 return fmt.Errorf("gonpy.NewWriter: %w", err)
1257                         }
1258                         npw.Shape = []int{outrows, outcols}
1259                         err = npw.WriteFloat64(out)
1260                         if err != nil {
1261                                 return fmt.Errorf("WriteFloat64: %w", err)
1262                         }
1263                         err = output.Close()
1264                         if err != nil {
1265                                 return err
1266                         }
1267                         log.Print("done")
1268
1269                         samplesOutFilename := *outputDir + "/samples.csv"
1270                         log.Infof("writing sample metadata to %s", samplesOutFilename)
1271                         var f *os.File
1272                         f, err = os.Create(samplesOutFilename)
1273                         if err != nil {
1274                                 return err
1275                         }
1276                         defer f.Close()
1277                         for i, si := range cmd.samples {
1278                                 var cc, tv string
1279                                 if si.isCase {
1280                                         cc = "1"
1281                                 } else if si.isControl {
1282                                         cc = "0"
1283                                 }
1284                                 if si.isTraining {
1285                                         tv = "1"
1286                                 } else {
1287                                         tv = "0"
1288                                 }
1289                                 var pcavals string
1290                                 for c := 0; c < outcols; c++ {
1291                                         pcavals += fmt.Sprintf(",%f", pca.At(i, c))
1292                                 }
1293                                 _, err = fmt.Fprintf(f, "%d,%s,%s,%s%s\n", i, si.id, cc, tv, pcavals)
1294                                 if err != nil {
1295                                         err = fmt.Errorf("write %s: %w", samplesOutFilename, err)
1296                                         return err
1297                                 }
1298                         }
1299                         err = f.Close()
1300                         if err != nil {
1301                                 err = fmt.Errorf("close %s: %w", samplesOutFilename, err)
1302                                 return err
1303                         }
1304                         log.Print("done")
1305                 }
1306         }
1307         if !*mergeOutput && !*onehotChunked && !*onehotSingle && !*onlyPCA {
1308                 tagoffsetFilename := *outputDir + "/chunk-tag-offset.csv"
1309                 log.Infof("writing tag offsets to %s", tagoffsetFilename)
1310                 var f *os.File
1311                 f, err = os.Create(tagoffsetFilename)
1312                 if err != nil {
1313                         return err
1314                 }
1315                 defer f.Close()
1316                 for idx, offset := range chunkStartTag {
1317                         _, err = fmt.Fprintf(f, "%q,%d\n", fmt.Sprintf("matrix.%04d.npy", idx), offset)
1318                         if err != nil {
1319                                 err = fmt.Errorf("write %s: %w", tagoffsetFilename, err)
1320                                 return err
1321                         }
1322                 }
1323                 err = f.Close()
1324                 if err != nil {
1325                         err = fmt.Errorf("close %s: %w", tagoffsetFilename, err)
1326                         return err
1327                 }
1328         }
1329
1330         return nil
1331 }
1332
1333 type sampleInfo struct {
1334         id            string
1335         isCase        bool
1336         isControl     bool
1337         isTraining    bool
1338         isValidation  bool
1339         pcaComponents []float64
1340 }
1341
1342 // Read samples.csv file with case/control and training/validation
1343 // flags.
1344 func loadSampleInfo(samplesFilename string) ([]sampleInfo, error) {
1345         var si []sampleInfo
1346         f, err := open(samplesFilename)
1347         if err != nil {
1348                 return nil, err
1349         }
1350         buf, err := io.ReadAll(f)
1351         f.Close()
1352         if err != nil {
1353                 return nil, err
1354         }
1355         lineNum := 0
1356         for _, csv := range bytes.Split(buf, []byte{'\n'}) {
1357                 lineNum++
1358                 if len(csv) == 0 {
1359                         continue
1360                 }
1361                 split := strings.Split(string(csv), ",")
1362                 if len(split) < 4 {
1363                         return nil, fmt.Errorf("%d fields < 4 in %s line %d: %q", len(split), samplesFilename, lineNum, csv)
1364                 }
1365                 if split[0] == "Index" && split[1] == "SampleID" && split[2] == "CaseControl" && split[3] == "TrainingValidation" {
1366                         continue
1367                 }
1368                 idx, err := strconv.Atoi(split[0])
1369                 if err != nil {
1370                         if lineNum == 1 {
1371                                 return nil, fmt.Errorf("header does not look right: %q", csv)
1372                         }
1373                         return nil, fmt.Errorf("%s line %d: index: %s", samplesFilename, lineNum, err)
1374                 }
1375                 if idx != len(si) {
1376                         return nil, fmt.Errorf("%s line %d: index %d out of order", samplesFilename, lineNum, idx)
1377                 }
1378                 var pcaComponents []float64
1379                 if len(split) > 4 {
1380                         for _, s := range split[4:] {
1381                                 f, err := strconv.ParseFloat(s, 64)
1382                                 if err != nil {
1383                                         return nil, fmt.Errorf("%s line %d: cannot parse float %q: %s", samplesFilename, lineNum, s, err)
1384                                 }
1385                                 pcaComponents = append(pcaComponents, f)
1386                         }
1387                 }
1388                 si = append(si, sampleInfo{
1389                         id:            split[1],
1390                         isCase:        split[2] == "1",
1391                         isControl:     split[2] == "0",
1392                         isTraining:    split[3] == "1",
1393                         isValidation:  split[3] == "0",
1394                         pcaComponents: pcaComponents,
1395                 })
1396         }
1397         return si, nil
1398 }
1399
1400 func (cmd *sliceNumpy) filterHGVScolpair(colpair [2][]int8) bool {
1401         if cmd.chi2PValue >= 1 {
1402                 return true
1403         }
1404         col0 := make([]bool, 0, len(cmd.chi2Cases))
1405         col1 := make([]bool, 0, len(cmd.chi2Cases))
1406         cases := make([]bool, 0, len(cmd.chi2Cases))
1407         for i, c := range cmd.chi2Cases {
1408                 if colpair[0][i] < 0 {
1409                         continue
1410                 }
1411                 col0 = append(col0, colpair[0][i] != 0)
1412                 col1 = append(col1, colpair[1][i] != 0)
1413                 cases = append(cases, c)
1414         }
1415         return len(cases) >= cmd.minCoverage &&
1416                 (pvalue(col0, cases) <= cmd.chi2PValue || pvalue(col1, cases) <= cmd.chi2PValue)
1417 }
1418
1419 func writeNumpyUint32(fnm string, out []uint32, rows, cols int) error {
1420         output, err := os.Create(fnm)
1421         if err != nil {
1422                 return err
1423         }
1424         defer output.Close()
1425         bufw := bufio.NewWriterSize(output, 1<<26)
1426         npw, err := gonpy.NewWriter(nopCloser{bufw})
1427         if err != nil {
1428                 return err
1429         }
1430         log.WithFields(log.Fields{
1431                 "filename": fnm,
1432                 "rows":     rows,
1433                 "cols":     cols,
1434                 "bytes":    rows * cols * 4,
1435         }).Infof("writing numpy: %s", fnm)
1436         npw.Shape = []int{rows, cols}
1437         npw.WriteUint32(out)
1438         err = bufw.Flush()
1439         if err != nil {
1440                 return err
1441         }
1442         return output.Close()
1443 }
1444
1445 func writeNumpyInt32(fnm string, out []int32, rows, cols int) error {
1446         output, err := os.Create(fnm)
1447         if err != nil {
1448                 return err
1449         }
1450         defer output.Close()
1451         bufw := bufio.NewWriterSize(output, 1<<26)
1452         npw, err := gonpy.NewWriter(nopCloser{bufw})
1453         if err != nil {
1454                 return err
1455         }
1456         log.WithFields(log.Fields{
1457                 "filename": fnm,
1458                 "rows":     rows,
1459                 "cols":     cols,
1460                 "bytes":    rows * cols * 4,
1461         }).Infof("writing numpy: %s", fnm)
1462         npw.Shape = []int{rows, cols}
1463         npw.WriteInt32(out)
1464         err = bufw.Flush()
1465         if err != nil {
1466                 return err
1467         }
1468         return output.Close()
1469 }
1470
1471 func writeNumpyInt16(fnm string, out []int16, rows, cols int) error {
1472         output, err := os.Create(fnm)
1473         if err != nil {
1474                 return err
1475         }
1476         defer output.Close()
1477         bufw := bufio.NewWriterSize(output, 1<<26)
1478         npw, err := gonpy.NewWriter(nopCloser{bufw})
1479         if err != nil {
1480                 return err
1481         }
1482         log.WithFields(log.Fields{
1483                 "filename": fnm,
1484                 "rows":     rows,
1485                 "cols":     cols,
1486                 "bytes":    rows * cols * 2,
1487         }).Infof("writing numpy: %s", fnm)
1488         npw.Shape = []int{rows, cols}
1489         npw.WriteInt16(out)
1490         err = bufw.Flush()
1491         if err != nil {
1492                 return err
1493         }
1494         return output.Close()
1495 }
1496
1497 func writeNumpyInt8(fnm string, out []int8, rows, cols int) error {
1498         output, err := os.Create(fnm)
1499         if err != nil {
1500                 return err
1501         }
1502         defer output.Close()
1503         bufw := bufio.NewWriterSize(output, 1<<26)
1504         npw, err := gonpy.NewWriter(nopCloser{bufw})
1505         if err != nil {
1506                 return err
1507         }
1508         log.WithFields(log.Fields{
1509                 "filename": fnm,
1510                 "rows":     rows,
1511                 "cols":     cols,
1512                 "bytes":    rows * cols,
1513         }).Infof("writing numpy: %s", fnm)
1514         npw.Shape = []int{rows, cols}
1515         npw.WriteInt8(out)
1516         err = bufw.Flush()
1517         if err != nil {
1518                 return err
1519         }
1520         return output.Close()
1521 }
1522
1523 func allele2homhet(colpair [2][]int8) {
1524         a, b := colpair[0], colpair[1]
1525         for i, av := range a {
1526                 bv := b[i]
1527                 if av < 0 || bv < 0 {
1528                         // no-call
1529                         a[i], b[i] = -1, -1
1530                 } else if av > 0 && bv > 0 {
1531                         // hom
1532                         a[i], b[i] = 1, 0
1533                 } else if av > 0 || bv > 0 {
1534                         // het
1535                         a[i], b[i] = 0, 1
1536                 } else {
1537                         // ref (or a different variant in same position)
1538                         // (this is a no-op) a[i], b[i] = 0, 0
1539                 }
1540         }
1541 }
1542
1543 type onehotXref struct {
1544         tag     tagID
1545         variant tileVariantID
1546         hom     bool
1547         pvalue  float64
1548 }
1549
1550 const onehotXrefSize = unsafe.Sizeof(onehotXref{})
1551
1552 // Build onehot matrix (m[tileVariantIndex][genome] == 0 or 1) for all
1553 // variants of a single tile/tag#.
1554 //
1555 // Return nil if no tile variant passes Χ² filter.
1556 func (cmd *sliceNumpy) tv2homhet(cgs map[string]CompactGenome, maxv tileVariantID, remap []tileVariantID, tag, chunkstarttag tagID, seq map[tagID][]TileVariant) ([][]int8, []onehotXref) {
1557         if tag == cmd.debugTag {
1558                 tv := make([]tileVariantID, len(cmd.cgnames)*2)
1559                 for i, name := range cmd.cgnames {
1560                         copy(tv[i*2:(i+1)*2], cgs[name].Variants[(tag-chunkstarttag)*2:])
1561                 }
1562                 log.WithFields(logrus.Fields{
1563                         "cgs[i].Variants[tag*2+j]": tv,
1564                         "maxv":                     maxv,
1565                         "remap":                    remap,
1566                         "tag":                      tag,
1567                         "chunkstarttag":            chunkstarttag,
1568                 }).Info("tv2homhet()")
1569         }
1570         if maxv < 1 || (maxv < 2 && !cmd.includeVariant1) {
1571                 // everyone has the most common variant (of the variants we don't drop)
1572                 return nil, nil
1573         }
1574         tagoffset := tag - chunkstarttag
1575         coverage := 0
1576         for _, cg := range cgs {
1577                 alleles := 0
1578                 for _, v := range cg.Variants[tagoffset*2 : tagoffset*2+2] {
1579                         if v > 0 && int(v) < len(seq[tag]) && len(seq[tag][v].Sequence) > 0 {
1580                                 alleles++
1581                         }
1582                 }
1583                 if alleles == 2 {
1584                         coverage++
1585                 }
1586         }
1587         if coverage < cmd.minCoverage {
1588                 return nil, nil
1589         }
1590         // "observed" array for p-value calculation (training set
1591         // only)
1592         obs := make([][]bool, (maxv+1)*2) // 2 slices (hom + het) for each variant#
1593         // one-hot output (all samples)
1594         outcols := make([][]int8, (maxv+1)*2)
1595         for i := range obs {
1596                 obs[i] = make([]bool, cmd.trainingSetSize)
1597                 outcols[i] = make([]int8, len(cmd.cgnames))
1598         }
1599         for cgid, name := range cmd.cgnames {
1600                 tsid := cmd.trainingSet[cgid]
1601                 cgvars := cgs[name].Variants[tagoffset*2:]
1602                 tv0, tv1 := remap[cgvars[0]], remap[cgvars[1]]
1603                 for v := tileVariantID(1); v <= maxv; v++ {
1604                         if tv0 == v && tv1 == v {
1605                                 if tsid >= 0 {
1606                                         obs[v*2][tsid] = true
1607                                 }
1608                                 outcols[v*2][cgid] = 1
1609                         } else if tv0 == v || tv1 == v {
1610                                 if tsid >= 0 {
1611                                         obs[v*2+1][tsid] = true
1612                                 }
1613                                 outcols[v*2+1][cgid] = 1
1614                         }
1615                 }
1616         }
1617         var onehot [][]int8
1618         var xref []onehotXref
1619         for col := 2; col < len(obs); col++ {
1620                 // col 0,1 correspond to tile variant 0, i.e.,
1621                 // no-call; col 2,3 correspond to the most common
1622                 // variant; so we (normally) start at col 4.
1623                 if col < 4 && !cmd.includeVariant1 {
1624                         continue
1625                 }
1626                 p := cmd.pvalue(obs[col])
1627                 if cmd.chi2PValue < 1 && !(p < cmd.chi2PValue) {
1628                         continue
1629                 }
1630                 onehot = append(onehot, outcols[col])
1631                 xref = append(xref, onehotXref{
1632                         tag:     tag,
1633                         variant: tileVariantID(col >> 1),
1634                         hom:     col&1 == 0,
1635                         pvalue:  p,
1636                 })
1637         }
1638         return onehot, xref
1639 }
1640
1641 // convert a []onehotXref with length N to a numpy-style []int32
1642 // matrix with N columns, one row per field of onehotXref struct.
1643 //
1644 // Hom/het row contains hom=0, het=1.
1645 //
1646 // P-value row contains 1000000x actual p-value.
1647 func onehotXref2int32(xrefs []onehotXref) []int32 {
1648         xcols := len(xrefs)
1649         xdata := make([]int32, 5*xcols)
1650         for i, xref := range xrefs {
1651                 xdata[i] = int32(xref.tag)
1652                 xdata[xcols+i] = int32(xref.variant)
1653                 if xref.hom {
1654                         xdata[xcols*2+i] = 1
1655                 }
1656                 xdata[xcols*3+i] = int32(xref.pvalue * 1000000)
1657                 xdata[xcols*4+i] = int32(-math.Log10(xref.pvalue) * 1000000)
1658         }
1659         return xdata
1660 }
1661
1662 // transpose onehot data from in[col][row] to numpy-style
1663 // out[row*cols+col].
1664 func onehotcols2int8(in [][]int8) []int8 {
1665         if len(in) == 0 {
1666                 return nil
1667         }
1668         cols := len(in)
1669         rows := len(in[0])
1670         out := make([]int8, rows*cols)
1671         for row := 0; row < rows; row++ {
1672                 outrow := out[row*cols:]
1673                 for col, incol := range in {
1674                         outrow[col] = incol[row]
1675                 }
1676         }
1677         return out
1678 }
1679
1680 // Return [2][]uint32{rowIndices, colIndices} indicating which
1681 // elements of matrixT[c][r] have non-zero values.
1682 func onehotChunk2Indirect(matrixT [][]int8) [2][]uint32 {
1683         var nz [2][]uint32
1684         for c, col := range matrixT {
1685                 for r, val := range col {
1686                         if val != 0 {
1687                                 nz[0] = append(nz[0], uint32(r))
1688                                 nz[1] = append(nz[1], uint32(c))
1689                         }
1690                 }
1691         }
1692         return nz
1693 }