--- ./ClinCNV-1.18.3.orig/trios/helpersTrio.R   2023-09-20 17:10:20.410302000 +0100
+++ ./ClinCNV-1.18.3/trios/helpersTrio.R        2023-09-20 17:11:41.828440000 +0100
@@ -29,8 +29,15 @@
         vectorOfGeneNames = c(vectorOfGeneNames, unlist(strsplit(genesThatHasToBeSeparated[i], split=",")))
       }
       vectorOfGeneNamesTrimmed = c()
-      for (elem in vectorOfGeneNames) {
-        vectorOfGeneNamesTrimmed = c(vectorOfGeneNamesTrimmed,trimws(elem) )
+      if (length(vectorOfGeneNames) > 0) {
+        for (elem in vectorOfGeneNames) {
+          vectorOfGeneNamesTrimmed = c(vectorOfGeneNamesTrimmed,trimws(elem) )
+        }
+      }
+      if (length(vectorOfGeneNamesTrimmed) > 0) {
+        annotationGenes <- paste(unique(vectorOfGeneNamesTrimmed), collapse=",")
+      } else {
+        annotationGenes = "na"
       }
       annotationGenes <- paste(unique(vectorOfGeneNamesTrimmed), collapse=",")
       CNVtoOut <- matrix(c(chrom, toyBedFile[found_CNVs[s,2],2], toyBedFile[found_CNVs[s,3],3],
@@ -96,4 +103,4 @@
     }
   }
   return(cnvsToOutput)
-}
\ No newline at end of file
+}