vectorise find_isoform bam existance check

mritchielab · Jul 31, 2023 · 23320f0 · 23320f0
1 parent d094dae
commit 23320f0
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/R/find_isoform.R b/R/find_isoform.R
@@ -85,8 +85,8 @@ find_isoform_bambu <- function(annotation, genome_fa, genome_bam, outdir, config
 #' @importFrom reticulate import_from_path
 #' @importFrom Rsamtools indexFa
 find_isoform_flames <- function(annotation, genome_fa, genome_bam, outdir, config) {
- if (!file.exists(paste0(genome_bam, ".bai"))) {
- stop(c("Cannot find corresponding bam file ", genome_bam, ".bai. Cancelling find_isoform."))
+ if (!all(file.exists(paste0(genome_bam, ".bai")))) {
+ stop(c("Cannot find corresponding bam file(s) ", paste0(genome_bam, ".bai"), ". Cancelling find_isoform."))
  }
  isoform_annotation <- file.path(outdir, "isoform_annotated.gff3")
  tss_stat <- file.path(outdir, "tss_tes.bedgraph")