Mention undiffable variants in annotations, write -2 in hgvs matrix.

[lightning.git] / tilelib.go

diff --git a/tilelib.go b/tilelib.go
index 4ad607c1e518a667f2c7dbccb03f63a0b22f6ea8..289f8895e5ba420b00d0d449f9a916cfcaf5d4f5 100644 (file)
--- a/tilelib.go
+++ b/tilelib.go
@@ -71,6 +71,8 @@ type tileLibrary struct {
        variants       int64
        // if non-nil, write out any tile variants added while tiling
        encoder *gob.Encoder
+       // set Ref flag when writing new variants to encoder
+       encodeRef bool
 
        onAddTileVariant func(libref tileLibRef, hash [blake2b.Size256]byte, seq []byte) error
        onAddGenome      func(CompactGenome) error
@@ -120,7 +122,7 @@ func (tilelib *tileLibrary) loadTileVariants(tvs []TileVariant, variantmap map[t
        for _, tv := range tvs {
                // Assign a new variant ID (unique across all inputs)
                // for each input variant.
-               variantmap[tileLibRef{Tag: tv.Tag, Variant: tv.Variant}] = tilelib.getRef(tv.Tag, tv.Sequence).Variant
+               variantmap[tileLibRef{Tag: tv.Tag, Variant: tv.Variant}] = tilelib.getRef(tv.Tag, tv.Sequence, tv.Ref).Variant
        }
        return nil
 }
@@ -234,36 +236,36 @@ func (tilelib *tileLibrary) loadCompactSequences(cseqs []CompactSequence, varian
        return nil
 }
 
-func (tilelib *tileLibrary) LoadDir(ctx context.Context, path string) error {
+func allGobFiles(path string) ([]string, error) {
        var files []string
-       var walk func(string) error
-       walk = func(path string) error {
-               f, err := open(path)
-               if err != nil {
-                       return err
-               }
-               defer f.Close()
-               fis, err := f.Readdir(-1)
-               if err != nil {
-                       files = append(files, path)
-                       return nil
-               }
-               for _, fi := range fis {
-                       if fi.Name() == "." || fi.Name() == ".." {
-                               continue
-                       } else if child := path + "/" + fi.Name(); fi.IsDir() {
-                               err = walk(child)
-                               if err != nil {
-                                       return err
-                               }
-                       } else if strings.HasSuffix(child, ".gob") || strings.HasSuffix(child, ".gob.gz") {
-                               files = append(files, child)
+       f, err := open(path)
+       if err != nil {
+               return nil, err
+       }
+       defer f.Close()
+       fis, err := f.Readdir(-1)
+       if err != nil {
+               return []string{path}, nil
+       }
+       for _, fi := range fis {
+               if fi.Name() == "." || fi.Name() == ".." {
+                       continue
+               } else if child := path + "/" + fi.Name(); fi.IsDir() {
+                       add, err := allGobFiles(child)
+                       if err != nil {
+                               return nil, err
                        }
+                       files = append(files, add...)
+               } else if strings.HasSuffix(child, ".gob") || strings.HasSuffix(child, ".gob.gz") {
+                       files = append(files, child)
                }
-               return nil
        }
+       return files, nil
+}
+
+func (tilelib *tileLibrary) LoadDir(ctx context.Context, path string) error {
        log.Infof("LoadDir: walk dir %s", path)
-       err := walk(path)
+       files, err := allGobFiles(path)
        if err != nil {
                return err
        }
@@ -307,7 +309,7 @@ func (tilelib *tileLibrary) LoadDir(ctx context.Context, path string) error {
                                        mtx.Unlock()
                                }
                                for _, tv := range ent.TileVariants {
-                                       variantmap[tileLibRef{Tag: tv.Tag, Variant: tv.Variant}] = tilelib.getRef(tv.Tag, tv.Sequence).Variant
+                                       variantmap[tileLibRef{Tag: tv.Tag, Variant: tv.Variant}] = tilelib.getRef(tv.Tag, tv.Sequence, tv.Ref).Variant
                                }
                                cgs = append(cgs, ent.CompactGenomes...)
                                cseqs = append(cseqs, ent.CompactSequences...)
@@ -546,7 +548,7 @@ type importStats struct {
        DroppedOutOfOrderTiles int
 }
 
-func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader, matchChromosome *regexp.Regexp) (tileSeq, []importStats, error) {
+func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader, matchChromosome *regexp.Regexp, isRef bool) (tileSeq, []importStats, error) {
        ret := tileSeq{}
        type jobT struct {
                label string
@@ -630,7 +632,7 @@ func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader, matchChro
                                } else {
                                        endpos = found[i+1].pos + taglen
                                }
-                               path[i] = tilelib.getRef(f.tagid, job.fasta[startpos:endpos])
+                               path[i] = tilelib.getRef(f.tagid, job.fasta[startpos:endpos], isRef)
                                if countBases(job.fasta[startpos:endpos]) != endpos-startpos {
                                        atomic.AddInt64(&lowquality, 1)
                                }
@@ -667,7 +669,7 @@ func (tilelib *tileLibrary) Len() int64 {
 
 // 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 {
+func (tilelib *tileLibrary) getRef(tag tagID, seq []byte, usedByRef bool) tileLibRef {
        dropSeq := false
        if !tilelib.retainNoCalls {
                for _, b := range seq {
@@ -788,6 +790,7 @@ func (tilelib *tileLibrary) getRef(tag tagID, seq []byte) tileLibRef {
                tilelib.encoder.Encode(LibraryEntry{
                        TileVariants: []TileVariant{{
                                Tag:      tag,
+                               Ref:      usedByRef,
                                Variant:  variant,
                                Blake2b:  seqhash,
                                Sequence: saveSeq,