changing CovStats outfile ending

michaelgruenstaeudl · Feb 6, 2024 · beff502 · beff502
1 parent 6efad5c
commit beff502
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/R/PACVr.R b/R/PACVr.R
@@ -104,7 +104,7 @@ PACVr.quadripRegions <- function(gbkData,
                                  gbkDataDF,
                                  isIRCheck) {
   if (isIRCheck) {
-    logger::log_info('Parsing the different genome regions')
+    logger::log_info('Parsing the quadripartite genome structure')
     quadripRegions <- PACVr.parseQuadripRegions(gbkData,
                                                 gbkDataDF)
   } else {

diff --git a/R/helpers.R b/R/helpers.R
@@ -340,21 +340,21 @@ writeTables <- function(regions, bamFile, genes, dir, sample_name) {
     # Writing values to output table
     write.table(
       ir_genes,
-      paste(dir, .Platform$file.sep, sample_name["sample_name"], "_coverage.genes.bed", sep = ""),
+      paste(dir, .Platform$file.sep, sample_name["sample_name"], "_coverage.genes.tsv", sep = ""),
       row.names = FALSE,
       quote = FALSE,
       sep = "\t"
     )
     write.table(
       ir_regions,
-      paste(dir, .Platform$file.sep, sample_name["sample_name"], "_coverage.regions.bed", sep = ""),
+      paste(dir, .Platform$file.sep, sample_name["sample_name"], "_coverage.regions.tsv", sep = ""),
       row.names = FALSE,
       quote = FALSE,
       sep = "\t"
     )
     write.table(
       ir_noncoding,
-      paste(dir, .Platform$file.sep, sample_name["sample_name"], "_coverage.noncoding.bed", sep = ""),
+      paste(dir, .Platform$file.sep, sample_name["sample_name"], "_coverage.noncoding.tsv", sep = ""),
       row.names = FALSE,
       quote = FALSE,
       sep = "\t"