From 87b4a0e7dfc2923bbfa5c1a53a968f8b0ba03a3f Mon Sep 17 00:00:00 2001
From: cying111 <chen_ying@gis.a-star.edu.sg>
Date: Tue, 28 Jul 2020 06:02:23 +0000
Subject: [PATCH] moved the check condition for gtf one level down to test for
 txdb object first

Former-commit-id: 6a1019cfabb87b3422e5df9f85673c0c19e648d9
---
 R/annotationFunctions.R | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/R/annotationFunctions.R b/R/annotationFunctions.R
index e410a5ed..8235a164 100755
--- 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))
+    }
+    
   }
   
+  
 }