"encoding/gob"
"fmt"
"io"
+ "regexp"
+ "runtime"
+ "sort"
"strings"
"sync"
}
type tileLibrary struct {
- includeNoCalls bool
- skipOOO bool
+ retainNoCalls bool
+ skipOOO bool
+ retainTileSequences bool
+
taglib *tagLibrary
variant [][][blake2b.Size256]byte
refseqs map[string]map[string][]tileLibRef
+ compactGenomes map[string][]tileVariantID
// count [][]int
- // seq map[[blake2b.Size]byte][]byte
+ seq map[[blake2b.Size256]byte][]byte
variants int
// if non-nil, write out any tile variants added while tiling
encoder *gob.Encoder
var wg sync.WaitGroup
errs := make(chan error, 1)
for _, cg := range cgs {
- name, variants := cg.Name, cg.Variants
wg.Add(1)
+ cg := cg
go func() {
defer wg.Done()
- for i, variant := range variants {
+ for i, variant := range cg.Variants {
if len(errs) > 0 {
return
}
tag := tagID(i / 2)
newvariant, ok := variantmap[tileLibRef{Tag: tag, Variant: variant}]
if !ok {
- err := fmt.Errorf("oops: genome %q has variant %d for tag %d, but that variant was not in its library", name, variant, tag)
+ err := fmt.Errorf("oops: genome %q has variant %d for tag %d, but that variant was not in its library", cg.Name, variant, tag)
select {
case errs <- err:
default:
}
return
}
- log.Tracef("loadCompactGenomes: cg %s tag %d variant %d => %d", name, tag, variant, newvariant)
- variants[i] = newvariant
+ log.Tracef("loadCompactGenomes: cg %s tag %d variant %d => %d", cg.Name, tag, variant, newvariant)
+ cg.Variants[i] = newvariant
}
if onLoadGenome != nil {
onLoadGenome(cg)
return
}
}
+ if tilelib.compactGenomes != nil {
+ tilelib.mtx.Lock()
+ defer tilelib.mtx.Unlock()
+ tilelib.compactGenomes[cg.Name] = cg.Variants
+ }
}()
}
wg.Wait()
for _, cseq := range cseqs {
for _, tseq := range cseq.TileSequences {
for i, libref := range tseq {
+ if libref.Variant == 0 {
+ // No variant (e.g., import
+ // dropped tiles with
+ // no-calls) = no translation.
+ continue
+ }
v, ok := variantmap[libref]
if !ok {
return fmt.Errorf("oops: CompactSequence %q has variant %d for tag %d, but that variant was not in its library", cseq.Name, libref.Variant, libref.Tag)
// match.
//
// If onLoadGenome is non-nil, call it on each CompactGenome entry.
-func (tilelib *tileLibrary) LoadGob(ctx context.Context, rdr io.Reader, onLoadGenome func(CompactGenome)) error {
+func (tilelib *tileLibrary) LoadGob(ctx context.Context, rdr io.Reader, gz bool, onLoadGenome func(CompactGenome)) error {
cgs := []CompactGenome{}
cseqs := []CompactSequence{}
variantmap := map[tileLibRef]tileVariantID{}
- err := DecodeLibrary(rdr, func(ent *LibraryEntry) error {
+ err := DecodeLibrary(rdr, gz, func(ent *LibraryEntry) error {
if ctx.Err() != nil {
return ctx.Err()
}
return nil
}
-func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader) (tileSeq, error) {
+type importStats struct {
+ InputFile string
+ InputLabel string
+ InputLength int
+ InputCoverage int
+ TileCoverage int
+ PathLength int
+ DroppedOutOfOrderTiles int
+}
+
+func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader, matchChromosome *regexp.Regexp) (tileSeq, []importStats, error) {
ret := tileSeq{}
type jobT struct {
label string
buf := scanner.Bytes()
if len(buf) > 0 && buf[0] == '>' {
todo <- jobT{seqlabel, fasta}
- seqlabel, fasta = string(buf[1:]), nil
+ seqlabel, fasta = strings.SplitN(string(buf[1:]), " ", 2)[0], nil
log.Debugf("%s %s reading fasta", filelabel, seqlabel)
} else {
fasta = append(fasta, bytes.ToLower(buf)...)
totalFoundTags := 0
totalPathLen := 0
skippedSequences := 0
+ stats := make([]importStats, 0, len(todo))
for job := range todo {
if len(job.fasta) == 0 {
continue
- } else if strings.Contains(job.label, "_") {
+ } else if !matchChromosome.MatchString(job.label) {
skippedSequences++
continue
}
})
totalFoundTags += len(found)
+ basesOut := 0
skipped := 0
path = path[:0]
last := foundtag{tagid: -1}
}
for i, f := range found {
log.Tracef("%s %s found[%d] == %#v", filelabel, job.label, i, f)
- if last.taglen > 0 {
- path = append(path, tilelib.getRef(last.tagid, job.fasta[last.pos:f.pos+f.taglen]))
+ if last.tagid < 0 {
+ // first tag in sequence
+ last = foundtag{tagid: f.tagid}
+ continue
+ }
+ libref := tilelib.getRef(last.tagid, job.fasta[last.pos:f.pos+f.taglen])
+ path = append(path, libref)
+ if libref.Variant > 0 {
+ // Count output coverage from
+ // the end of the previous tag
+ // (if any) to the end of the
+ // current tag, IOW don't
+ // double-count coverage for
+ // the previous tag.
+ basesOut += countBases(job.fasta[last.pos+last.taglen : f.pos+f.taglen])
} else {
- f.pos = 0
+ // If we dropped this tile
+ // (because !retainNoCalls),
+ // set taglen=0 so the
+ // overlapping tag is counted
+ // toward coverage on the
+ // following tile.
+ f.taglen = 0
}
last = f
}
- if last.taglen > 0 {
- path = append(path, tilelib.getRef(last.tagid, job.fasta[last.pos:]))
- } else {
+ if last.tagid < 0 {
log.Warnf("%s %s no tags found", filelabel, job.label)
+ } else {
+ libref := tilelib.getRef(last.tagid, job.fasta[last.pos:])
+ path = append(path, libref)
+ if libref.Variant > 0 {
+ basesOut += countBases(job.fasta[last.pos+last.taglen:])
+ }
}
pathcopy := make([]tileLibRef, len(path))
copy(pathcopy, path)
ret[job.label] = pathcopy
- log.Debugf("%s %s tiled with path len %d, skipped %d", filelabel, job.label, len(path), skipped)
+
+ basesIn := countBases(job.fasta)
+ log.Infof("%s %s fasta in %d coverage in %d coverage out %d path len %d skipped %d", filelabel, job.label, len(job.fasta), basesIn, basesOut, len(path), skipped)
+ stats = append(stats, importStats{
+ InputFile: filelabel,
+ InputLabel: job.label,
+ InputLength: len(job.fasta),
+ InputCoverage: basesIn,
+ TileCoverage: basesOut,
+ PathLength: len(path),
+ DroppedOutOfOrderTiles: skipped,
+ })
+
totalPathLen += len(path)
}
- log.Printf("%s tiled with total path len %d in %d sequences (skipped %d sequences with '_' in name, skipped %d out-of-order tags)", filelabel, totalPathLen, len(ret), skippedSequences, totalFoundTags-totalPathLen)
- return ret, scanner.Err()
+ 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()
}
func (tilelib *tileLibrary) Len() int {
// 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 {
- if !tilelib.includeNoCalls {
+ dropSeq := false
+ if !tilelib.retainNoCalls {
for _, b := range seq {
if b != 'a' && b != 'c' && b != 'g' && b != 't' {
- // return "tile not found" if seq has any
- // no-calls
- return tileLibRef{Tag: tag}
+ dropSeq = true
+ break
}
}
}
tilelib.mtx.Lock()
- // if tilelib.seq == nil {
- // tilelib.seq = map[[blake2b.Size]byte][]byte{}
- // }
if tilelib.variant == nil && tilelib.taglib != nil {
tilelib.variant = make([][][blake2b.Size256]byte, tilelib.taglib.Len())
}
}
tilelib.variants++
tilelib.variant[tag] = append(tilelib.variant[tag], seqhash)
- // tilelib.seq[seqhash] = append([]byte(nil), seq...)
+ if tilelib.retainTileSequences && !dropSeq {
+ if tilelib.seq == nil {
+ tilelib.seq = map[[blake2b.Size256]byte][]byte{}
+ }
+ tilelib.seq[seqhash] = append([]byte(nil), seq...)
+ }
variant := tileVariantID(len(tilelib.variant[tag]))
tilelib.mtx.Unlock()
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,
Variant: variant,
Blake2b: seqhash,
- Sequence: seq,
+ Sequence: saveSeq,
}},
})
}
return tileLibRef{Tag: tag, Variant: variant}
}
+
+func (tilelib *tileLibrary) TileVariantSequence(libref tileLibRef) []byte {
+ if libref.Variant == 0 || len(tilelib.variant) <= int(libref.Tag) || len(tilelib.variant[libref.Tag]) < int(libref.Variant) {
+ return nil
+ }
+ return tilelib.seq[tilelib.variant[libref.Tag][libref.Variant-1]]
+}
+
+// Tidy deletes unreferenced tile variants and renumbers variants so
+// more common variants have smaller IDs.
+func (tilelib *tileLibrary) Tidy() {
+ log.Print("Tidy: compute inref")
+ inref := map[tileLibRef]bool{}
+ for _, refseq := range tilelib.refseqs {
+ for _, librefs := range refseq {
+ for _, libref := range librefs {
+ inref[libref] = true
+ }
+ }
+ }
+ log.Print("Tidy: compute remap")
+ remap := make([][]tileVariantID, len(tilelib.variant))
+ throttle := throttle{Max: runtime.NumCPU() + 1}
+ for tag, oldvariants := range tilelib.variant {
+ tag, oldvariants := tagID(tag), oldvariants
+ if tag%10000 == 0 {
+ log.Printf("Tidy: tag %d", tag)
+ }
+ throttle.Acquire()
+ go func() {
+ defer throttle.Release()
+ uses := make([]int, len(oldvariants))
+ for _, cg := range tilelib.compactGenomes {
+ for phase := 0; phase < 2; phase++ {
+ cgi := int(tag)*2 + phase
+ if cgi < len(cg) && cg[cgi] > 0 {
+ uses[cg[cgi]-1]++
+ }
+ }
+ }
+
+ // Compute desired order of variants:
+ // neworder[x] == index in oldvariants that
+ // should move to position x.
+ neworder := make([]int, len(oldvariants))
+ for i := range neworder {
+ neworder[i] = i
+ }
+ sort.Slice(neworder, func(i, j int) bool {
+ if cmp := uses[neworder[i]] - uses[neworder[j]]; cmp != 0 {
+ return cmp > 0
+ } else {
+ return bytes.Compare(oldvariants[neworder[i]][:], oldvariants[neworder[j]][:]) < 0
+ }
+ })
+
+ // Replace tilelib.variants[tag] with a new
+ // re-ordered slice of hashes, and make a
+ // mapping from old to new variant IDs.
+ remaptag := make([]tileVariantID, len(oldvariants)+1)
+ newvariants := make([][blake2b.Size256]byte, 0, len(neworder))
+ for _, oldi := range neworder {
+ if uses[oldi] > 0 || inref[tileLibRef{Tag: tag, Variant: tileVariantID(oldi + 1)}] {
+ newvariants = append(newvariants, oldvariants[oldi])
+ remaptag[oldi+1] = tileVariantID(len(newvariants))
+ }
+ }
+ tilelib.variant[tag] = newvariants
+ remap[tag] = remaptag
+ }()
+ }
+ throttle.Wait()
+
+ // Apply remap to genomes and reference sequences, so they
+ // refer to the same tile variants using the changed IDs.
+ log.Print("Tidy: apply remap")
+ for _, cg := range tilelib.compactGenomes {
+ for idx, variant := range cg {
+ cg[idx] = remap[tagID(idx/2)][variant]
+ }
+ }
+ for _, refcs := range tilelib.refseqs {
+ for _, refseq := range refcs {
+ for i, tv := range refseq {
+ refseq[i].Variant = remap[tv.Tag][tv.Variant]
+ }
+ }
+ }
+ log.Print("Tidy: done")
+}
+
+func countBases(seq []byte) int {
+ n := 0
+ for _, c := range seq {
+ if isbase[c] {
+ n++
+ }
+ }
+ return n
+}