Option to skip/ignore out-of-order tags.

[lightning.git] / tilelib.go

diff --git a/tilelib.go b/tilelib.go
index 7b90810242335fd6ac7ff0a906b9f923d262b26d..339bc215e3e5a82704b03ba81f93d0f8377e70d7 100644 (file)
--- a/tilelib.go
+++ b/tilelib.go
@@ -39,6 +39,7 @@ func (tseq tileSeq) Variants() []tileVariantID {
 }
 
 type tileLibrary struct {
+       skipOOO bool
        taglib  *tagLibrary
        variant [][][blake2b.Size256]byte
        // count [][]int
@@ -72,6 +73,12 @@ func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader) (tileSeq,
                }
                todo <- jobT{seqlabel, fasta}
        }()
+       type foundtag struct {
+               pos    int
+               tagid  tagID
+               taglen int
+       }
+       found := make([]foundtag, 2000000)
        path := make([]tileLibRef, 2000000)
        totalPathLen := 0
        skippedSequences := 0
@@ -83,19 +90,33 @@ func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader) (tileSeq,
                        continue
                }
                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})
+               })
                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}
+               for i, f := range found {
+                       if tilelib.skipOOO {
+                               if f.tagid < last.tagid+1 {
+                                       // e.g., last=B, this=A
+                                       continue
+                               }
+                               if f.tagid > last.tagid+1 && i+1 < len(found) && found[i+1].tagid <= f.tagid {
+                                       // e.g., last=A, this=C, next=B
+                                       continue
+                               }
                        }
-                       tilestart = pos
-                       tiletagid = id
-               })
-               if tiletagid >= 0 {
-                       path = append(path, tilelib.getRef(tiletagid, job.fasta[tilestart:]))
+                       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