Revert "Add steps for saving annotation db"

This reverts commit 36cbb2b.

analyses/focal-cn-file-preparation/01-prepare-cn-file.R

@@ -127,16 +127,6 @@ if (!dir.exists(results_dir)) {
   dir.create(results_dir)
 }
 
-# this is the output of GenomicFeatures::makeTxDbFromGFF
-# TODO: possibly update this when the GTF file gets included in the data
-#       download; may also remove the --gtf_file option and hardcode it?
-annotation_directory <- file.path(root_dir,
-                                  "analyses",
-                                  "focal-cn-file-preparation",
-                                  "annotation_files")
-annotation_file <- file.path(annotation_directory,
-                             "txdb_from_gencode.v27.gtf.db")
-
 #### Format CNV file and overlap with hg38 genome annotations ------------------
 
 # we want to standardize the formats between the two methods here and drop
@@ -177,19 +167,11 @@ cnv_no_xy_gr <- cnv_no_xy %>%
   GenomicRanges::makeGRangesFromDataFrame(keep.extra.columns = TRUE,
                                           starts.in.df.are.0based = FALSE)
 
-if (!file.exists(annotation_file)) {
-  # Define the annotations for the hg38 genome
-  txdb <- GenomicFeatures::makeTxDbFromGFF(
-    file = opt$gtf_file,
-    format = "gtf"
-  )
-  # can do this even if the directory exists
-  dir.create(annotation_directory, showWarnings = FALSE)
-  # write this to file to save time next time
-  AnnotationDbi::saveDb(txdb, annotation_file)
-} else {
-  txdb <- AnnotationDbi::loadDb(annotation_file)
-}
+# Define the annotations for the hg38 genome
+txdb <- GenomicFeatures::makeTxDbFromGFF(
+  file = opt$gtf_file,
+  format = "gtf"
+)
 
 # if the chromosome filter is on, then we will only look at exons on chr 1:22
 if (chrom_filter) {