import (
"bufio"
"bytes"
+ "encoding/gob"
"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 {
- taglib *tagLibrary
- variant [][][blake2b.Size256]byte
+ includeNoCalls bool
+ skipOOO bool
+ taglib *tagLibrary
+ variant [][][blake2b.Size256]byte
// count [][]int
// seq map[[blake2b.Size]byte][]byte
variants int
+ // if non-nil, write out any tile variants added while tiling
+ encoder *gob.Encoder
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 || strings.Contains(job.label, "_") {
+ if len(job.fasta) == 0 {
+ continue
+ } else if strings.Contains(job.label, "_") {
+ skippedSequences++
continue
}
- log.Printf("%s %s tiling", filelabel, job.label)
+ 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})
+ })
+ totalFoundTags += len(found)
+
+ skipped := 0
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(job.fasta, func(id tagID, pos, taglen int) {
- if tilestart >= 0 {
- path = append(path, tilelib.getRef(tiletagid, job.fasta[tilestart:pos+taglen]))
+ 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]
}
- tilestart = pos
- tiletagid = id
- })
- if tiletagid >= 0 {
- path = append(path, tilelib.getRef(tiletagid, job.fasta[tilestart:]))
+ skipped = len(found) - len(keep)
+ found = found[:len(keep)]
+ }
+ 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.Printf("%s %s tiled with path len %d", filelabel, job.label, len(path))
+ 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()
}
// 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}
+ if !tilelib.includeNoCalls {
+ 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[[blake2b.Size]byte][]byte{}
// }
seqhash := blake2b.Sum256(seq)
for i, varhash := range tilelib.variant[tag] {
if varhash == seqhash {
+ tilelib.mtx.Unlock()
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]))}
+ ret := tileLibRef{tag: tag, variant: tileVariantID(len(tilelib.variant[tag]))}
+ tilelib.mtx.Unlock()
+
+ if tilelib.encoder != nil {
+ tilelib.encoder.Encode(LibraryEntry{
+ TileVariants: []TileVariant{{
+ Tag: tag,
+ Blake2b: seqhash,
+ Sequence: seq,
+ }},
+ })
+ }
+ return ret
}
projects / lightning.git / blobdiff