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, int, int) {
+ maxtag := 0
+ for _, refs := range tseq {
+ for _, ref := range refs {
+ if maxtag < int(ref.tag) {
+ maxtag = int(ref.tag)
+ }
+ }
+ }
+ vars := make([]tileVariantID, maxtag+1)
+ var kept, dropped int
+ for _, refs := range tseq {
+ for _, ref := range refs {
+ if vars[int(ref.tag)] != 0 {
+ dropped++
+ } else {
+ kept++
+ }
+ vars[int(ref.tag)] = ref.variant
+ }
+ }
+ return vars, kept, dropped
+}
+
type tileLibrary struct {
+ skipOOO bool
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
}
var seqlabel string
for scanner.Scan() {
buf := scanner.Bytes()
- if len(buf) == 0 || buf[0] == '>' {
+ if len(buf) > 0 && buf[0] == '>' {
todo <- jobT{seqlabel, fasta}
seqlabel, fasta = string(buf[1:]), nil
- log.Printf("%s %s reading fasta", filelabel, seqlabel)
+ 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
+ }
+ found := make([]foundtag, 2000000)
+ path := make([]tileLibRef, 2000000)
+ totalFoundTags := 0
+ totalPathLen := 0
+ skippedSequences := 0
for job := range todo {
if len(job.fasta) == 0 {
continue
+ } else if strings.Contains(job.label, "_") {
+ skippedSequences++
+ continue
}
- log.Printf("%s %s tiling", filelabel, job.label)
- var path []tileLibRef
- tilestart := -1 // position in fasta of tile that ends here
- tiletagid := tagID(-1) // tag id starting tile that ends here
- tilelib.taglib.FindAll(job.fasta, func(id tagID, pos int) {
- if tilestart >= 0 {
- path = append(path, tilelib.getRef(tiletagid, job.fasta[tilestart:pos]))
- }
- tilestart = pos
- tiletagid = id
+ log.Debugf("%s %s tiling", filelabel, job.label)
+
+ found = found[:0]
+ tilelib.taglib.FindAll(job.fasta, func(tagid tagID, pos, taglen int) {
+ found = append(found, foundtag{pos: pos, tagid: tagid, taglen: taglen})
})
- if tiletagid >= 0 {
- path = append(path, tilelib.getRef(tiletagid, job.fasta[tilestart:]))
+ totalFoundTags += len(found)
+
+ skipped := 0
+ path = path[:0]
+ last := foundtag{tagid: -1}
+ if tilelib.skipOOO {
+ 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)]
}
- ret[job.label] = path
- log.Printf("%s %s tiled with path len %d", filelabel, job.label, len(path))
+ 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]))
+ }
+ last = f
+ }
+ if last.taglen > 0 {
+ path = append(path, tilelib.getRef(last.tagid, job.fasta[last.pos:]))
+ }
+
+ 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)
+ 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()
}
+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