Kill other children and exit early if one child process fails.

[lightning.git] / tilelib.go

diff --git a/tilelib.go b/tilelib.go
index cfe91fb49f5fccecd9f43d4d9770f03c57cb083d..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
@@ -19,6 +20,24 @@ 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.Size256]byte
@@ -46,19 +65,25 @@ 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, taglen int) {
@@ -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()
 }