generation.sh

@@ -21,4 +21,3 @@ prefix="curesim_"
 
 Rscript src/repertoire.r "$sequences" "$sequencing_runs"
 java -jar tools/CuReSim.jar -m "$read_mean_size" -sd "$read_variance_size" -f "$data_directory$filename$fasta" -o "$data_directory$prefix$filename$fastq"
-rm "$data_directory/log.txt"

src/repertoire.r

@@ -14,9 +14,9 @@ amplify_rows <- function(data, column, factor) {
   if (column == "sequence") {
     dna_string <- Biostrings::DNAStringSet(data)
     reverse_complement <- Biostrings::reverseComplement(dna_string)
-    return(rep(reverse_complement, factor))
+    return(Biostrings::DNAStringSet(rep(reverse_complement, factor)))
   }
-  return(rep(data, factor))
+  return(as.character(rep(data, factor)))
 }
 
 save_data <- function(data, name) {