Merge pull request #146 from GoekeLab/bambu-devel

update annotationFunction to test txdb object first Former-commit-id: 7e3cdae
GoekeLab · Jul 28, 2020 · 0458b3b · 0458b3b
2 parents baa55d6 + 87b4a0e
commit 0458b3b
Showing 1 changed file with 6 additions and 3 deletions.
diff --git a/R/annotationFunctions.R b/R/annotationFunctions.R
@@ -12,9 +12,6 @@
 #'  package = "bambu")
 #'  gr <- prepareAnnotationsFrom(x = gtf.file)
 prepareAnnotations <- function(x) {
-  if(grepl(".gtf",x)){
-    return(prepareAnnotationsFromGTF(x))
-  }
   if(class(x) == "TxDb"){
     exonsByTx = exonsBy(txdb,by='tx', use.names=TRUE)
     if(any(duplicated(names(exonsByTx)))) {
@@ -37,8 +34,14 @@ prepareAnnotations <- function(x) {
     minEqClasses <- getMinimumEqClassByTx(exonsByTx)
     mcols(exonsByTx)$eqClass <- minEqClasses$eqClass[match(names(exonsByTx),minEqClasses$queryTxId)]
     return(exonsByTx)
+  }else{
+    if(grepl(".gtf",x)){
+      return(prepareAnnotationsFromGTF(x))
+    }
+
   }
 
+
 }