"encoding/gob"
"fmt"
"io"
+ "math/rand"
"os"
"regexp"
"runtime"
retainNoCalls bool
skipOOO bool
retainTileSequences bool
+ useDups bool
taglib *tagLibrary
variant [][][blake2b.Size256]byte
variants int64
// if non-nil, write out any tile variants added while tiling
encoder *gob.Encoder
+ // set Ref flag when writing new variants to encoder
+ encodeRef bool
+
+ onAddTileVariant func(libref tileLibRef, hash [blake2b.Size256]byte, seq []byte) error
+ onAddGenome func(CompactGenome) error
+ onAddRefseq func(CompactSequence) error
mtx sync.RWMutex
vlock []sync.Locker
for _, tv := range tvs {
// Assign a new variant ID (unique across all inputs)
// for each input variant.
- variantmap[tileLibRef{Tag: tv.Tag, Variant: tv.Variant}] = tilelib.getRef(tv.Tag, tv.Sequence).Variant
+ variantmap[tileLibRef{Tag: tv.Tag, Variant: tv.Variant}] = tilelib.getRef(tv.Tag, tv.Sequence, tv.Ref).Variant
}
return nil
}
-func (tilelib *tileLibrary) loadCompactGenomes(cgs []CompactGenome, variantmap map[tileLibRef]tileVariantID, onLoadGenome func(CompactGenome)) error {
+func (tilelib *tileLibrary) loadCompactGenomes(cgs []CompactGenome, variantmap map[tileLibRef]tileVariantID) error {
log.Debugf("loadCompactGenomes: %d", len(cgs))
var wg sync.WaitGroup
errs := make(chan error, 1)
// log.Tracef("loadCompactGenomes: cg %s tag %d variant %d => %d", cg.Name, tag, variant, newvariant)
cg.Variants[i] = newvariant
}
- if onLoadGenome != nil {
- onLoadGenome(cg)
+ if tilelib.onAddGenome != nil {
+ err := tilelib.onAddGenome(cg)
+ if err != nil {
+ select {
+ case errs <- err:
+ default:
+ }
+ return
+ }
}
if tilelib.encoder != nil {
err := tilelib.encoder.Encode(LibraryEntry{
return err
}
}
+ if tilelib.onAddRefseq != nil {
+ err := tilelib.onAddRefseq(cseq)
+ if err != nil {
+ return err
+ }
+ }
log.Infof("loadCompactSequences: checking %s done", cseq.Name)
}
tilelib.mtx.Lock()
return nil
}
-func (tilelib *tileLibrary) LoadDir(ctx context.Context, path string, onLoadGenome func(CompactGenome)) error {
+func allFiles(path string, re *regexp.Regexp) ([]string, error) {
var files []string
- var walk func(string) error
- walk = func(path string) error {
- f, err := open(path)
- if err != nil {
- return err
- }
- defer f.Close()
- fis, err := f.Readdir(-1)
- if err != nil {
- files = append(files, path)
- return nil
- }
- for _, fi := range fis {
- if fi.Name() == "." || fi.Name() == ".." {
- continue
- } else if child := path + "/" + fi.Name(); fi.IsDir() {
- err = walk(child)
- if err != nil {
- return err
- }
- } else if strings.HasSuffix(child, ".gob") || strings.HasSuffix(child, ".gob.gz") {
- files = append(files, child)
+ f, err := open(path)
+ if err != nil {
+ return nil, err
+ }
+ defer f.Close()
+ fis, err := f.Readdir(-1)
+ if err != nil {
+ return []string{path}, nil
+ }
+ for _, fi := range fis {
+ if fi.Name() == "." || fi.Name() == ".." {
+ continue
+ } else if child := path + "/" + fi.Name(); fi.IsDir() {
+ add, err := allFiles(child, re)
+ if err != nil {
+ return nil, err
}
+ files = append(files, add...)
+ } else if re == nil || re.MatchString(child) {
+ files = append(files, child)
}
- return nil
}
+ sort.Strings(files)
+ return files, nil
+}
+
+var matchGobFile = regexp.MustCompile(`\.gob(\.gz)?$`)
+
+func (tilelib *tileLibrary) LoadDir(ctx context.Context, path string) error {
log.Infof("LoadDir: walk dir %s", path)
- err := walk(path)
+ files, err := allFiles(path, matchGobFile)
if err != nil {
return err
}
mtx.Unlock()
}
for _, tv := range ent.TileVariants {
- variantmap[tileLibRef{Tag: tv.Tag, Variant: tv.Variant}] = tilelib.getRef(tv.Tag, tv.Sequence).Variant
+ variantmap[tileLibRef{Tag: tv.Tag, Variant: tv.Variant}] = tilelib.getRef(tv.Tag, tv.Sequence, tv.Ref).Variant
}
cgs = append(cgs, ent.CompactGenomes...)
cseqs = append(cseqs, ent.CompactSequences...)
for _, cgs := range allcgs {
flatcgs = append(flatcgs, cgs...)
}
- err = tilelib.loadCompactGenomes(flatcgs, allvariantmap, onLoadGenome)
+ err = tilelib.loadCompactGenomes(flatcgs, allvariantmap)
if err != nil {
return err
}
// Load library data from rdr. Tile variants might be renumbered in
// the process; in that case, genomes variants will be renumbered to
// match.
-//
-// If onLoadGenome is non-nil, call it on each CompactGenome entry.
-func (tilelib *tileLibrary) LoadGob(ctx context.Context, rdr io.Reader, gz bool, onLoadGenome func(CompactGenome)) error {
+func (tilelib *tileLibrary) LoadGob(ctx context.Context, rdr io.Reader, gz bool) error {
cgs := []CompactGenome{}
cseqs := []CompactSequence{}
variantmap := map[tileLibRef]tileVariantID{}
if ctx.Err() != nil {
return ctx.Err()
}
- err = tilelib.loadCompactGenomes(cgs, variantmap, onLoadGenome)
+ err = tilelib.loadCompactGenomes(cgs, variantmap)
if err != nil {
return err
}
}
type importStats struct {
- InputFile string
- InputLabel string
- InputLength int
- InputCoverage int
- PathLength int
- DroppedOutOfOrderTiles int
+ InputFile string
+ InputLabel string
+ InputLength int
+ InputCoverage int
+ PathLength int
+ DroppedRepeatedTags int
+ DroppedOutOfOrderTags int
}
-func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader, matchChromosome *regexp.Regexp) (tileSeq, []importStats, error) {
+func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader, matchChromosome *regexp.Regexp, isRef bool) (tileSeq, []importStats, error) {
ret := tileSeq{}
- type jobT struct {
- label string
- fasta []byte
- }
- todo := make(chan jobT, 1)
- scanner := bufio.NewScanner(rdr)
- go func() {
- defer close(todo)
- var fasta []byte
- var seqlabel string
- for scanner.Scan() {
- buf := scanner.Bytes()
- if len(buf) > 0 && buf[0] == '>' {
- todo <- jobT{seqlabel, append([]byte(nil), fasta...)}
- seqlabel, fasta = strings.SplitN(string(buf[1:]), " ", 2)[0], fasta[:0]
- log.Debugf("%s %s reading fasta", filelabel, seqlabel)
- } else {
- fasta = append(fasta, bytes.ToLower(buf)...)
- }
- }
- todo <- jobT{seqlabel, fasta}
- }()
type foundtag struct {
pos int
tagid tagID
skippedSequences := 0
taglen := tilelib.taglib.TagLen()
var stats []importStats
- for job := range todo {
- if len(job.fasta) == 0 {
- continue
- } else if !matchChromosome.MatchString(job.label) {
+
+ in := bufio.NewReader(rdr)
+readall:
+ for {
+ var seqlabel string
+ // Advance to next '>', then
+ // read seqlabel up to \r?\n
+ readseqlabel:
+ for seqlabelStarted := false; ; {
+ rune, _, err := in.ReadRune()
+ if err == io.EOF {
+ break readall
+ } else if err != nil {
+ return nil, nil, err
+ }
+ switch {
+ case rune == '\r':
+ case seqlabelStarted && rune == '\n':
+ break readseqlabel
+ case seqlabelStarted:
+ seqlabel += string(rune)
+ case rune == '>':
+ seqlabelStarted = true
+ default:
+ }
+ }
+ log.Debugf("%s %s reading fasta", filelabel, seqlabel)
+ if !matchChromosome.MatchString(seqlabel) {
skippedSequences++
continue
}
- log.Debugf("%s %s tiling", filelabel, job.label)
+ log.Debugf("%s %s tiling", filelabel, seqlabel)
+ fasta := bytes.NewBuffer(nil)
found = found[:0]
- tilelib.taglib.FindAll(job.fasta, func(tagid tagID, pos, taglen int) {
+ err := tilelib.taglib.FindAll(in, fasta, func(tagid tagID, pos, taglen int) {
found = append(found, foundtag{pos: pos, tagid: tagid})
})
+ if err != nil {
+ return nil, nil, err
+ }
totalFoundTags += len(found)
if len(found) == 0 {
- log.Warnf("%s %s no tags found", filelabel, job.label)
+ log.Warnf("%s %s no tags found", filelabel, seqlabel)
}
- skipped := 0
+ droppedDup := 0
+ if !tilelib.useDups {
+ // Remove any tags that appeared more than once
+ dup := map[tagID]bool{}
+ for _, ft := range found {
+ _, dup[ft.tagid] = dup[ft.tagid]
+ }
+ dst := 0
+ for _, ft := range found {
+ if !dup[ft.tagid] {
+ found[dst] = ft
+ dst++
+ }
+ }
+ droppedDup = len(found) - dst
+ log.Infof("%s %s dropping %d non-unique tags", filelabel, seqlabel, droppedDup)
+ found = found[:dst]
+ }
+
+ droppedOOO := 0
if tilelib.skipOOO {
- log.Infof("%s %s keeping longest increasing subsequence", filelabel, job.label)
keep := longestIncreasingSubsequence(len(found), func(i int) int { return int(found[i].tagid) })
for i, x := range keep {
found[i] = found[x]
}
- skipped = len(found) - len(keep)
+ droppedOOO = len(found) - len(keep)
+ log.Infof("%s %s dropping %d out-of-order tags", filelabel, seqlabel, droppedOOO)
found = found[:len(keep)]
}
- log.Infof("%s %s getting %d librefs", filelabel, job.label, len(found))
- throttle := &throttle{Max: runtime.NumCPU()}
+ log.Infof("%s %s getting %d librefs", filelabel, seqlabel, len(found))
path = path[:len(found)]
var lowquality int64
- for i, f := range found {
- i, f := i, f
- throttle.Acquire()
- go func() {
- defer throttle.Release()
- var startpos, endpos int
- if i == 0 {
- startpos = 0
- } else {
- startpos = f.pos
- }
- if i == len(found)-1 {
- endpos = len(job.fasta)
- } else {
- endpos = found[i+1].pos + taglen
- }
- path[i] = tilelib.getRef(f.tagid, job.fasta[startpos:endpos])
- if countBases(job.fasta[startpos:endpos]) != endpos-startpos {
- atomic.AddInt64(&lowquality, 1)
- }
- }()
+ // Visit each element of found, but start at a random
+ // index, to reduce the likelihood of lock contention
+ // when importing many samples concurrently.
+ startpoint := rand.Int() % len(found)
+ for offset := range found {
+ i := startpoint + offset
+ if i >= len(found) {
+ i -= len(found)
+ }
+ f := found[i]
+ var startpos, endpos int
+ if i == 0 {
+ startpos = 0
+ } else {
+ startpos = f.pos
+ }
+ if i == len(found)-1 {
+ endpos = fasta.Len()
+ } else {
+ endpos = found[i+1].pos + taglen
+ }
+ path[i] = tilelib.getRef(f.tagid, fasta.Bytes()[startpos:endpos], isRef)
+ if countBases(fasta.Bytes()[startpos:endpos]) != endpos-startpos {
+ lowquality++
+ }
}
- throttle.Wait()
- log.Infof("%s %s copying path", filelabel, job.label)
+ log.Infof("%s %s copying path", filelabel, seqlabel)
pathcopy := make([]tileLibRef, len(path))
copy(pathcopy, path)
- ret[job.label] = pathcopy
+ ret[seqlabel] = pathcopy
- basesIn := countBases(job.fasta)
- log.Infof("%s %s fasta in %d coverage in %d path len %d low-quality %d skipped-out-of-order %d", filelabel, job.label, len(job.fasta), basesIn, len(path), lowquality, skipped)
+ basesIn := countBases(fasta.Bytes())
+ log.Infof("%s %s fasta in %d coverage in %d path len %d low-quality %d", filelabel, seqlabel, fasta.Len(), basesIn, len(path), lowquality)
stats = append(stats, importStats{
- InputFile: filelabel,
- InputLabel: job.label,
- InputLength: len(job.fasta),
- InputCoverage: basesIn,
- PathLength: len(path),
- DroppedOutOfOrderTiles: skipped,
+ InputFile: filelabel,
+ InputLabel: seqlabel,
+ InputLength: fasta.Len(),
+ InputCoverage: basesIn,
+ PathLength: len(path),
+ DroppedOutOfOrderTags: droppedOOO,
+ DroppedRepeatedTags: droppedDup,
})
totalPathLen += len(path)
}
log.Printf("%s tiled with total path len %d in %d sequences (skipped %d sequences that did not match chromosome regexp, skipped %d out-of-order tags)", filelabel, totalPathLen, len(ret), skippedSequences, totalFoundTags-totalPathLen)
- return ret, stats, scanner.Err()
+ return ret, stats, nil
}
func (tilelib *tileLibrary) Len() int64 {
// Return a tileLibRef for a tile with the given tag and sequence,
// adding the sequence to the library if needed.
-func (tilelib *tileLibrary) getRef(tag tagID, seq []byte) tileLibRef {
+func (tilelib *tileLibrary) getRef(tag tagID, seq []byte, usedByRef bool) tileLibRef {
dropSeq := false
if !tilelib.retainNoCalls {
for _, b := range seq {
locker.Unlock()
}
+ saveSeq := seq
+ if dropSeq {
+ // Save the hash, but not the sequence
+ saveSeq = nil
+ }
if tilelib.encoder != nil {
- saveSeq := seq
- if dropSeq {
- // Save the hash, but not the sequence
- saveSeq = nil
- }
tilelib.encoder.Encode(LibraryEntry{
TileVariants: []TileVariant{{
Tag: tag,
+ Ref: usedByRef,
Variant: variant,
Blake2b: seqhash,
Sequence: saveSeq,
}},
})
}
+ if tilelib.onAddTileVariant != nil {
+ tilelib.onAddTileVariant(tileLibRef{tag, variant}, seqhash, saveSeq)
+ }
return tileLibRef{Tag: tag, Variant: variant}
}
projects / lightning.git / blobdiff