-package main
+package lightning
import (
"bufio"
"encoding/gob"
"fmt"
"io"
+ "regexp"
"runtime"
"sort"
"strings"
"sync"
+ "sync/atomic"
log "github.com/sirupsen/logrus"
"golang.org/x/crypto/blake2b"
compactGenomes map[string][]tileVariantID
// count [][]int
seq map[[blake2b.Size256]byte][]byte
- variants int
+ variants int64
// if non-nil, write out any tile variants added while tiling
encoder *gob.Encoder
- mtx sync.Mutex
+ mtx sync.RWMutex
+ vlock []sync.Locker
}
func (tilelib *tileLibrary) loadTagSet(newtagset [][]byte) error {
InputLabel string
InputLength int
InputCoverage int
- TileCoverage int
PathLength int
DroppedOutOfOrderTiles int
}
-func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader) (tileSeq, []importStats, error) {
+func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader, matchChromosome *regexp.Regexp) (tileSeq, []importStats, error) {
ret := tileSeq{}
type jobT struct {
label string
fasta []byte
}
- todo := make(chan jobT)
+ todo := make(chan jobT, 1)
scanner := bufio.NewScanner(rdr)
go func() {
defer close(todo)
for scanner.Scan() {
buf := scanner.Bytes()
if len(buf) > 0 && buf[0] == '>' {
- todo <- jobT{seqlabel, fasta}
- seqlabel, fasta = strings.SplitN(string(buf[1:]), " ", 2)[0], nil
+ 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
- taglen int
+ pos int
+ tagid tagID
}
found := make([]foundtag, 2000000)
path := make([]tileLibRef, 2000000)
totalFoundTags := 0
totalPathLen := 0
skippedSequences := 0
- stats := make([]importStats, 0, len(todo))
+ taglen := tilelib.taglib.TagLen()
+ var stats []importStats
for job := range todo {
if len(job.fasta) == 0 {
continue
- } else if strings.Contains(job.label, "_") {
+ } else if !matchChromosome.MatchString(job.label) {
skippedSequences++
continue
}
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)]
+ var lowquality int64
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])
+ if countBases(job.fasta[startpos:endpos]) != endpos-startpos {
+ atomic.AddInt64(&lowquality, 1)
+ }
+ }()
}
+ 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 low-quality %d skipped-out-of-order %d", filelabel, job.label, len(job.fasta), basesIn, len(path), lowquality, 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)
+ 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 {
- tilelib.mtx.Lock()
- defer tilelib.mtx.Unlock()
- return tilelib.variants
+func (tilelib *tileLibrary) Len() int64 {
+ return atomic.LoadInt64(&tilelib.variants)
}
// Return a tileLibRef for a tile with the given tag and sequence,
}
}
}
- tilelib.mtx.Lock()
- if tilelib.variant == nil && tilelib.taglib != nil {
- tilelib.variant = make([][][blake2b.Size256]byte, tilelib.taglib.Len())
+ seqhash := blake2b.Sum256(seq)
+ var vlock sync.Locker
+
+ tilelib.mtx.RLock()
+ if len(tilelib.vlock) > int(tag) {
+ vlock = tilelib.vlock[tag]
}
- if int(tag) >= len(tilelib.variant) {
- // 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.
- if int(tag) >= cap(tilelib.variant) {
- // Allocate 2x capacity.
- newslice := make([][][blake2b.Size256]byte, int(tag)+1, (int(tag)+1)*2)
- copy(newslice, tilelib.variant)
- tilelib.variant = newslice[:int(tag)+1]
- } else {
- // Use previously allocated capacity, avoiding
- // copy.
- tilelib.variant = tilelib.variant[:int(tag)+1]
+ tilelib.mtx.RUnlock()
+
+ if vlock != nil {
+ vlock.Lock()
+ for i, varhash := range tilelib.variant[tag] {
+ if varhash == seqhash {
+ vlock.Unlock()
+ return tileLibRef{Tag: tag, Variant: tileVariantID(i + 1)}
+ }
+ }
+ 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] = new(sync.Mutex)
+ }
+ }
+ if int(tag) >= 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 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)
+ copy(newslice, tilelib.variant)
+ tilelib.variant = newslice[:int(tag)+1]
+ newvlock := make([]sync.Locker, int(tag)+1, (int(tag)+1)*2)
+ copy(newvlock, tilelib.vlock)
+ tilelib.vlock = newvlock[:int(tag)+1]
+ } else {
+ // Use previously allocated capacity,
+ // avoiding copy.
+ tilelib.variant = tilelib.variant[:int(tag)+1]
+ tilelib.vlock = tilelib.vlock[:int(tag)+1]
+ }
+ 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()
}
- seqhash := blake2b.Sum256(seq)
+
+ vlock.Lock()
for i, varhash := range tilelib.variant[tag] {
if varhash == seqhash {
- tilelib.mtx.Unlock()
+ vlock.Unlock()
return tileLibRef{Tag: tag, Variant: tileVariantID(i + 1)}
}
}
- tilelib.variants++
+ 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]))
- tilelib.mtx.Unlock()
if tilelib.encoder != nil {
saveSeq := seq
throttle := throttle{Max: runtime.NumCPU() + 1}
for tag, oldvariants := range tilelib.variant {
tag, oldvariants := tagID(tag), oldvariants
- if tag%10000 == 0 {
+ if tag%1000000 == 0 {
log.Printf("Tidy: tag %d", tag)
}
throttle.Acquire()
}
})
- // Replace tilelib.variants[tag] with a new
+ // Replace tilelib.variant[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)
projects / lightning.git / blobdiff