+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
package lightning
import (
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 {
}
defer input.Close()
}
- return tilelib.TileFasta(infile, input, cmd.matchChromosome)
+ return tilelib.TileFasta(infile, input, cmd.matchChromosome, isRef)
}
func (cmd *importer) loadTagLibrary() (*tagLibrary, 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()
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()
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
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
}