import (
"bufio"
"bytes"
- "crypto/md5"
"io"
- "log"
+ "strings"
"sync"
+
+ log "github.com/sirupsen/logrus"
+ "golang.org/x/crypto/blake2b"
)
-type tileVariantID int32 // 1-based
+type tileVariantID uint16 // 1-based
type tileLibRef struct {
tag tagID
type tileSeq map[string][]tileLibRef
+func (tseq tileSeq) Variants() []tileVariantID {
+ maxtag := 0
+ for _, refs := range tseq {
+ for _, ref := range refs {
+ if maxtag < int(ref.tag) {
+ maxtag = int(ref.tag)
+ }
+ }
+ }
+ vars := make([]tileVariantID, maxtag+1)
+ for _, refs := range tseq {
+ for _, ref := range refs {
+ vars[int(ref.tag)] = ref.variant
+ }
+ }
+ return vars
+}
+
type tileLibrary struct {
taglib *tagLibrary
- variant [][][md5.Size]byte
+ variant [][][blake2b.Size256]byte
// count [][]int
- // seq map[[md5.Size]byte][]byte
+ // seq map[[blake2b.Size]byte][]byte
+ variants int
mtx sync.Mutex
}
func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader) (tileSeq, error) {
ret := tileSeq{}
- var wg sync.WaitGroup
- flush := func(seqlabel string, fasta []byte) {
- defer wg.Done()
- var path []tileLibRef
- if len(fasta) == 0 {
- return
+ type jobT struct {
+ label string
+ fasta []byte
+ }
+ todo := make(chan jobT)
+ 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, fasta}
+ seqlabel, fasta = string(buf[1:]), nil
+ log.Debugf("%s %s reading fasta", filelabel, seqlabel)
+ } else {
+ fasta = append(fasta, bytes.ToLower(buf)...)
+ }
}
+ todo <- jobT{seqlabel, fasta}
+ }()
+ path := make([]tileLibRef, 2000000)
+ totalPathLen := 0
+ skippedSequences := 0
+ for job := range todo {
+ if len(job.fasta) == 0 {
+ continue
+ } else if strings.Contains(job.label, "_") {
+ skippedSequences++
+ continue
+ }
+ log.Debugf("%s %s tiling", filelabel, job.label)
+ path = path[:0]
tilestart := -1 // position in fasta of tile that ends here
tiletagid := tagID(-1) // tag id starting tile that ends here
- tilelib.taglib.FindAll(fasta, func(id tagID, pos int) {
+ tilelib.taglib.FindAll(job.fasta, func(id tagID, pos, taglen int) {
if tilestart >= 0 {
- path = append(path, tilelib.getRef(tiletagid, fasta[tilestart:pos]))
+ path = append(path, tilelib.getRef(tiletagid, job.fasta[tilestart:pos+taglen]))
}
tilestart = pos
tiletagid = id
})
if tiletagid >= 0 {
- path = append(path, tilelib.getRef(tiletagid, fasta[tilestart:]))
- }
- ret[seqlabel] = path
- log.Printf("%s %s tiled with path len %d", filelabel, seqlabel, len(path))
- }
- var fasta []byte
- var seqlabel string
- scanner := bufio.NewScanner(rdr)
- for scanner.Scan() {
- buf := scanner.Bytes()
- if len(buf) == 0 || buf[0] == '>' {
- wg.Add(1)
- go flush(seqlabel, fasta)
- fasta = nil
- seqlabel = string(buf[1:])
- } else {
- fasta = append(fasta, bytes.ToLower(buf)...)
+ path = append(path, tilelib.getRef(tiletagid, job.fasta[tilestart:]))
}
+ pathcopy := make([]tileLibRef, len(path))
+ copy(pathcopy, path)
+ ret[job.label] = pathcopy
+ log.Debugf("%s %s tiled with path len %d", filelabel, job.label, len(path))
+ totalPathLen += len(path)
}
- if err := scanner.Err(); err != nil {
- return nil, err
- }
- wg.Add(1)
- go flush(seqlabel, fasta)
- wg.Wait()
- return ret, nil
+ log.Printf("%s tiled with total path len %d in %d sequences (skipped %d sequences with '_' in name)", filelabel, totalPathLen, len(ret), skippedSequences)
+ return ret, scanner.Err()
+}
+
+func (tilelib *tileLibrary) Len() int {
+ tilelib.mtx.Lock()
+ defer tilelib.mtx.Unlock()
+ return tilelib.variants
}
// 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 {
+ 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}
+ }
+ }
tilelib.mtx.Lock()
defer tilelib.mtx.Unlock()
// if tilelib.seq == nil {
- // tilelib.seq = map[[md5.Size]byte][]byte{}
+ // tilelib.seq = map[[blake2b.Size]byte][]byte{}
// }
- if len(tilelib.variant) <= int(tag) {
- tilelib.variant = append(tilelib.variant, make([][][md5.Size]byte, int(tag)-len(tilelib.variant)+1)...)
+ if tilelib.variant == nil {
+ tilelib.variant = make([][][blake2b.Size256]byte, tilelib.taglib.Len())
}
- seqhash := md5.Sum(seq)
+ seqhash := blake2b.Sum256(seq)
for i, varhash := range tilelib.variant[tag] {
if varhash == seqhash {
return tileLibRef{tag: tag, variant: tileVariantID(i + 1)}
}
}
+ tilelib.variants++
tilelib.variant[tag] = append(tilelib.variant[tag], seqhash)
// tilelib.seq[seqhash] = append([]byte(nil), seq...)
return tileLibRef{tag: tag, variant: tileVariantID(len(tilelib.variant[tag]))}
projects / lightning.git / blobdiff