Save all ref tile data in slice 0.

[lightning.git] / import.go

diff --git a/import.go b/import.go
index 79537347ee6f3fa6dfd32f69df00455cb456f477..2f1a268511c0e1cc709a2e43656788e5116c9e1c 100644 (file)
--- a/import.go
+++ b/import.go
@@ -234,7 +234,7 @@ func (cmd *importer) runBatches(stdout io.Writer, inputs []string) error {
        return nil
 }
 
-func (cmd *importer) tileFasta(tilelib *tileLibrary, infile string) (tileSeq, []importStats, error) {
+func (cmd *importer) tileFasta(tilelib *tileLibrary, infile string, isRef bool) (tileSeq, []importStats, error) {
        var input io.ReadCloser
        input, err := open(infile)
        if err != nil {
@@ -249,7 +249,7 @@ func (cmd *importer) tileFasta(tilelib *tileLibrary, infile string) (tileSeq, []
                }
                defer input.Close()
        }
-       return tilelib.TileFasta(infile, input, cmd.matchChromosome)
+       return tilelib.TileFasta(infile, input, cmd.matchChromosome, isRef)
 }
 
 func (cmd *importer) loadTagLibrary() (*tagLibrary, error) {
@@ -349,7 +349,7 @@ func (cmd *importer) tileInputs(tilelib *tileLibrary, infiles []string) error {
                                defer phases.Done()
                                log.Printf("%s starting", infile)
                                defer log.Printf("%s done", infile)
-                               tseqs, stats, err := cmd.tileFasta(tilelib, infile)
+                               tseqs, stats, err := cmd.tileFasta(tilelib, infile, false)
                                allstats[idx*2] = stats
                                var kept, dropped int
                                variants[0], kept, dropped = tseqs.Variants()
@@ -361,7 +361,7 @@ func (cmd *importer) tileInputs(tilelib *tileLibrary, infiles []string) error {
                                defer phases.Done()
                                log.Printf("%s starting", infile2)
                                defer log.Printf("%s done", infile2)
-                               tseqs, stats, err := cmd.tileFasta(tilelib, infile2)
+                               tseqs, stats, err := cmd.tileFasta(tilelib, infile2, false)
                                allstats[idx*2+1] = stats
                                var kept, dropped int
                                variants[1], kept, dropped = tseqs.Variants()
@@ -374,7 +374,7 @@ func (cmd *importer) tileInputs(tilelib *tileLibrary, infiles []string) error {
                                defer phases.Done()
                                log.Printf("%s starting", infile)
                                defer log.Printf("%s done", infile)
-                               tseqs, stats, err := cmd.tileFasta(tilelib, infile)
+                               tseqs, stats, err := cmd.tileFasta(tilelib, infile, true)
                                allstats[idx*2] = stats
                                if err != nil {
                                        return err
@@ -540,7 +540,7 @@ func (cmd *importer) tileGVCF(tilelib *tileLibrary, infile string, phase int) (t
                return
        }
        defer consensus.Wait()
-       tileseq, stats, err = tilelib.TileFasta(fmt.Sprintf("%s phase %d", infile, phase+1), stdout, cmd.matchChromosome)
+       tileseq, stats, err = tilelib.TileFasta(fmt.Sprintf("%s phase %d", infile, phase+1), stdout, cmd.matchChromosome, false)
        if err != nil {
                return
        }