Fix panic on blank line in fasta.

[lightning.git] / tilelib.go

diff --git a/tilelib.go b/tilelib.go
index 5b4b30754c689f2b09a2c7012e31cfb0462a9e68..49f5169665bbd19f433cf1d2da63a9313d7fde94 100644 (file)
--- a/tilelib.go
+++ b/tilelib.go
@@ -69,7 +69,7 @@ func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader) (tileSeq,
                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.Debugf("%s %s reading fasta", filelabel, seqlabel)
@@ -104,23 +104,19 @@ func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader) (tileSeq,
                })
                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)]
+               }
                for i, f := range found {
                        log.Tracef("%s %s found[%d] == %#v", filelabel, job.label, i, f)
-                       if tilelib.skipOOO {
-                               if f.tagid < last.tagid+1 {
-                                       log.Debugf("%s %s skipped out-of-order tag %d (found at %d) because it appears after tag %d (found at %d)", filelabel, job.label, f.tagid, f.pos, last.tagid, last.pos)
-                                       continue
-                               }
-                               if f.tagid > last.tagid+1 && // accepting this tag would mean skipping some tags
-                                       i+1 < len(found) && // there is a "next" found tag after this one
-                                       found[i+1].tagid > last.tagid && // next found tag is usable (we haven't already passed it in accepted sequence)
-                                       found[i+1].tagid <= f.tagid { // next found tag is expected before this one (so we can't use both)
-                                       log.Debugf("%s %s skipped out-of-order tag %d (found at %d) because it appears between tag %d (found at %d) and %d (found at %d)", filelabel, job.label, f.tagid, f.pos, last.tagid, last.pos, found[i+1].tagid, found[i+1].pos)
-                                       continue
-                               }
-                       }
                        if last.taglen > 0 {
                                path = append(path, tilelib.getRef(last.tagid, job.fasta[last.pos:f.pos+f.taglen]))
                        }
@@ -133,7 +129,7 @@ func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader) (tileSeq,
                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), len(found)-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)