InputLabel string
InputLength int
InputCoverage int
- TileCoverage int
PathLength int
DroppedOutOfOrderTiles int
}
todo <- jobT{seqlabel, fasta}
}()
type foundtag struct {
- pos int
- tagid tagID
- taglen int
+ pos int
+ tagid tagID
}
found := make([]foundtag, 2000000)
path := make([]tileLibRef, 2000000)
totalFoundTags := 0
totalPathLen := 0
skippedSequences := 0
+ taglen := tilelib.taglib.TagLen()
var stats []importStats
for job := range todo {
if len(job.fasta) == 0 {
found = found[:0]
tilelib.taglib.FindAll(job.fasta, func(tagid tagID, pos, taglen int) {
- found = append(found, foundtag{pos: pos, tagid: tagid, taglen: taglen})
+ found = append(found, foundtag{pos: pos, tagid: tagid})
})
totalFoundTags += len(found)
+ if len(found) == 0 {
+ log.Warnf("%s %s no tags found", filelabel, job.label)
+ }
- basesOut := 0
skipped := 0
- path = path[:0]
- last := foundtag{tagid: -1}
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)
found = found[:len(keep)]
}
+
+ log.Infof("%s %s getting %d librefs", filelabel, job.label, len(found))
+ throttle := &throttle{Max: runtime.NumCPU()}
+ path = path[:len(found)]
for i, f := range found {
- log.Tracef("%s %s found[%d] == %#v", filelabel, job.label, i, f)
- 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 {
- // 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.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:])
- }
+ 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])
+ }()
}
+ throttle.Wait()
+
+ log.Infof("%s %s copying path", filelabel, job.label)
pathcopy := make([]tileLibRef, len(path))
copy(pathcopy, path)
ret[job.label] = pathcopy
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)
+ log.Infof("%s %s fasta in %d coverage in %d path len %d skipped-out-of-order %d", filelabel, job.label, len(job.fasta), basesIn, 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,
})
}
}
seqhash := blake2b.Sum256(seq)
+ var vlock sync.Locker
+
tilelib.mtx.RLock()
- if int(tag) < len(tilelib.variant) {
+ if len(tilelib.vlock) > int(tag) {
+ vlock = tilelib.vlock[tag]
+ }
+ tilelib.mtx.RUnlock()
+
+ if vlock != nil {
+ vlock.Lock()
for i, varhash := range tilelib.variant[tag] {
if varhash == seqhash {
- tilelib.mtx.RUnlock()
+ vlock.Unlock()
return tileLibRef{Tag: tag, Variant: tileVariantID(i + 1)}
}
}
- }
- var vlock sync.Locker
- if len(tilelib.vlock) > int(tag) {
- vlock = tilelib.vlock[tag]
- }
- tilelib.mtx.RUnlock()
- if vlock == nil {
+ vlock.Unlock()
+ } else {
tilelib.mtx.Lock()
if tilelib.variant == nil && tilelib.taglib != nil {
tilelib.variant = make([][][blake2b.Size256]byte, tilelib.taglib.Len())
tilelib.vlock = make([]sync.Locker, tilelib.taglib.Len())
for i := range tilelib.vlock {
- tilelib.vlock[i] = &sync.Mutex{}
+ tilelib.vlock[i] = new(sync.Mutex)
}
}
if int(tag) >= len(tilelib.variant) {
- oldlen := len(tilelib.variant)
+ oldlen := len(tilelib.vlock)
+ for i := 0; i < oldlen; i++ {
+ tilelib.vlock[i].Lock()
+ }
// If we haven't seen the tag library yet (as
// in a merge), tilelib.taglib.Len() is
// zero. We can still behave correctly, we
- // just need to expand the tilelib.variant
- // slice as needed.
+ // just need to expand the tilelib.variant and
+ // tilelib.vlock slices as needed.
if int(tag) >= cap(tilelib.variant) {
// Allocate 2x capacity.
newslice := make([][][blake2b.Size256]byte, int(tag)+1, (int(tag)+1)*2)
tilelib.variant = tilelib.variant[:int(tag)+1]
tilelib.vlock = tilelib.vlock[:int(tag)+1]
}
- for i := oldlen; i < len(tilelib.variant); i++ {
- tilelib.vlock[i] = &sync.Mutex{}
+ for i := oldlen; i < len(tilelib.vlock); i++ {
+ tilelib.vlock[i] = new(sync.Mutex)
+ }
+ for i := 0; i < oldlen; i++ {
+ tilelib.vlock[i].Unlock()
}
}
vlock = tilelib.vlock[tag]
tilelib.mtx.Unlock()
}
- tilelib.mtx.RLock()
vlock.Lock()
for i, varhash := range tilelib.variant[tag] {
if varhash == seqhash {
vlock.Unlock()
- tilelib.mtx.RUnlock()
return tileLibRef{Tag: tag, Variant: tileVariantID(i + 1)}
}
}
atomic.AddInt64(&tilelib.variants, 1)
tilelib.variant[tag] = append(tilelib.variant[tag], seqhash)
+ variant := tileVariantID(len(tilelib.variant[tag]))
+ vlock.Unlock()
+
if tilelib.retainTileSequences && !dropSeq {
+ tilelib.mtx.Lock()
if tilelib.seq == nil {
tilelib.seq = map[[blake2b.Size256]byte][]byte{}
}
tilelib.seq[seqhash] = append([]byte(nil), seq...)
+ tilelib.mtx.Unlock()
}
- variant := tileVariantID(len(tilelib.variant[tag]))
- vlock.Unlock()
- tilelib.mtx.RUnlock()
if tilelib.encoder != nil {
saveSeq := seq
projects / lightning.git / blobdiff