Updated call of PACVr.verboseInformation()

michaelgruenstaeudl · Feb 20, 2024 · da92809 · da92809
1 parent 7424cf3
commit da92809
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Showing 2 changed files with 8 additions and 6 deletions.
diff --git a/R/PACVr.R b/R/PACVr.R
@@ -15,9 +15,10 @@ PACVr.read.gb <- function(gbkFile) {
 PACVr.verboseInformation <- function(gbkData,
                                      bamFile,
                                      analysisSpecs,
-                                     output) {
+                                     plotSpecs) {
   sampleName <- gbkData$sampleName
-  verbosePath <- getVerbosePath(sampleName, output)
+  verbosePath <- getVerbosePath(sampleName,
+                                plotSpecs)
   printCovStats(bamFile,
                 gbkData$genes,
                 gbkData$quadripRegions,
@@ -154,7 +155,7 @@ PACVr.complete <- function(gbkFile,
     PACVr.verboseInformation(gbkData,
                              bamFile,
                              analysisSpecs,
-                             output)
+                             plotSpecs)
   }
 
   ###################################

diff --git a/R/verboseInformation.R b/R/verboseInformation.R
@@ -3,10 +3,11 @@
 #email="m_gruenstaeudl@fhsu.edu"
 #version="2024.02.08.2300"
 
-getVerbosePath <- function(sampleName, output) {
+getVerbosePath <- function(sampleName,
+                           plotSpecs) {
   # Step 1. Check ...
-  if (!is.na(output)) {
-    outDir <- dirname(output)
+  if (plotSpecs$isOutput) {
+    outDir <- dirname(plotSpecs$output)
     tmpDir <- file.path(outDir,
                         paste(sampleName["sample_name"],
                               ".tmp",