Less verbose logging.

[lightning.git] / tilelib.go

diff --git a/tilelib.go b/tilelib.go
index 51f5fdc574d473c5b95ad6ad65c32f0fc5c113d7..7b90810242335fd6ac7ff0a906b9f923d262b26d 100644 (file)
--- a/tilelib.go
+++ b/tilelib.go
@@ -4,13 +4,14 @@ import (
        "bufio"
        "bytes"
        "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
@@ -19,9 +20,27 @@ type tileLibRef struct {
 
 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 [][][blake2b.Size]byte
+       variant [][][blake2b.Size256]byte
        // count [][]int
        // seq map[[blake2b.Size]byte][]byte
        variants int
@@ -46,24 +65,30 @@ func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader) (tileSeq,
                        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}
        }()
+       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.Printf("%s %s tiling", filelabel, job.label)
-               var path []tileLibRef
+               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(job.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, job.fasta[tilestart:pos]))
+                               path = append(path, tilelib.getRef(tiletagid, job.fasta[tilestart:pos+taglen]))
                        }
                        tilestart = pos
                        tiletagid = id
@@ -71,9 +96,13 @@ func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader) (tileSeq,
                if tiletagid >= 0 {
                        path = append(path, tilelib.getRef(tiletagid, job.fasta[tilestart:]))
                }
-               ret[job.label] = path
-               log.Printf("%s %s tiled with path len %d", filelabel, job.label, len(path))
+               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)
        }
+       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()
 }
 
@@ -99,18 +128,9 @@ func (tilelib *tileLibrary) getRef(tag tagID, seq []byte) tileLibRef {
        //      tilelib.seq = map[[blake2b.Size]byte][]byte{}
        // }
        if tilelib.variant == nil {
-               tilelib.variant = make([][][blake2b.Size]byte, tilelib.taglib.Len())
-       }
-       hash, err := blake2b.New(32, nil)
-       if err != nil {
-               panic(err)
-       }
-       _, err = hash.Write(seq)
-       if err != nil {
-               panic(err)
+               tilelib.variant = make([][][blake2b.Size256]byte, tilelib.taglib.Len())
        }
-       var seqhash [blake2b.Size]byte
-       copy(seqhash[:], hash.Sum(nil))
+       seqhash := blake2b.Sum256(seq)
        for i, varhash := range tilelib.variant[tag] {
                if varhash == seqhash {
                        return tileLibRef{tag: tag, variant: tileVariantID(i + 1)}