Export HGVS.

[lightning.git] / import.go

diff --git a/import.go b/import.go
index 860ac3eb7af691a2dc750815e4bf89cee1b7b566..71ab688e989f19bc597b77527090dd6e8b1100e6 100644 (file)
--- a/import.go
+++ b/import.go
@@ -317,12 +317,20 @@ func (cmd *importer) tileInputs(tilelib *tileLibrary, infiles []string) error {
                                log.Printf("%s starting", infile)
                                defer log.Printf("%s done", infile)
                                tseqs, err := cmd.tileFasta(tilelib, infile)
-                               var kept, dropped int
-                               variants[0], kept, dropped = tseqs.Variants()
-                               variants[1] = variants[0]
-                               log.Printf("%s found %d unique tags plus %d repeats", infile, kept, dropped)
-                               return err
+                               if err != nil {
+                                       return err
+                               }
+                               totlen := 0
+                               for _, tseq := range tseqs {
+                                       totlen += len(tseq)
+                               }
+                               log.Printf("%s tiled %d seqs, total len %d", infile, len(tseqs), totlen)
+                               return cmd.encoder.Encode(LibraryEntry{
+                                       CompactSequences: []CompactSequence{{Name: infile, TileSequences: tseqs}},
+                               })
                        }
+                       // Don't write out a CompactGenomes entry
+                       continue
                } else if vcfFilenameRe.MatchString(infile) {
                        for phase := 0; phase < 2; phase++ {
                                phase := phase
@@ -347,20 +355,8 @@ func (cmd *importer) tileInputs(tilelib *tileLibrary, infiles []string) error {
                        if len(errs) > 0 {
                                return
                        }
-                       ntags := len(variants[0])
-                       if ntags < len(variants[1]) {
-                               ntags = len(variants[1])
-                       }
-                       flat := make([]tileVariantID, ntags*2)
-                       for i := 0; i < ntags; i++ {
-                               for hap := 0; hap < 2; hap++ {
-                                       if i < len(variants[hap]) {
-                                               flat[i*2+hap] = variants[hap][i]
-                                       }
-                               }
-                       }
                        err := cmd.encoder.Encode(LibraryEntry{
-                               CompactGenomes: []CompactGenome{{Name: infile, Variants: flat}},
+                               CompactGenomes: []CompactGenome{{Name: infile, Variants: flatten(variants)}},
                        })
                        if err != nil {
                                select {
@@ -450,3 +446,21 @@ func (cmd *importer) tileGVCF(tilelib *tileLibrary, infile string, phase int) (t
        }
        return
 }
+
+func flatten(variants [][]tileVariantID) []tileVariantID {
+       ntags := 0
+       for _, v := range variants {
+               if ntags < len(v) {
+                       ntags = len(v)
+               }
+       }
+       flat := make([]tileVariantID, ntags*2)
+       for i := 0; i < ntags; i++ {
+               for hap := 0; hap < 2; hap++ {
+                       if i < len(variants[hap]) {
+                               flat[i*2+hap] = variants[hap][i]
+                       }
+               }
+       }
+       return flat
+}