From 731fcdd469e71436247f80845659e33fc3e0e9cd Mon Sep 17 00:00:00 2001
From: AtaJadidAhari <atajadidahari@gmail.com>
Date: Wed, 24 Apr 2024 11:24:35 +0200
Subject: [PATCH] move strand specific error to validObject

---
 R/FraserDataSet-class.R |  6 ++++++
 R/countRNAseqData.R     | 16 +---------------
 2 files changed, 7 insertions(+), 15 deletions(-)

diff --git a/R/FraserDataSet-class.R b/R/FraserDataSet-class.R
index 2d5eb46b..2e4fc535 100644
--- a/R/FraserDataSet-class.R
+++ b/R/FraserDataSet-class.R
@@ -79,6 +79,12 @@ validateStrandSpecific <- function(object) {
                 "'colData(fds)' must be empty or contain only integers:",
                 "0L == 'no', 1L == 'yes', 2L == 'reverse'."))
     }
+    # Check mixed strand type
+    ss <- strandSpecific(object)
+    if ((any(ss == 0) && any(ss == 1)) || (any(ss == 0) && any(ss == 2))){
+      stop(paste("Error: Data contains a mix of stranded and unstranded samples.\n ",
+                 "Please consider analyzing them separately."))
+    }
     NULL
 }
 
diff --git a/R/countRNAseqData.R b/R/countRNAseqData.R
index 41888177..d228e49d 100644
--- a/R/countRNAseqData.R
+++ b/R/countRNAseqData.R
@@ -146,13 +146,6 @@ countRNAData <- function(fds, NcpuPerSample=1, minAnchor=5, recount=FALSE,
     stopifnot(is.numeric(minAnchor) & minAnchor >= 1)
     minAnchor <- as.integer(minAnchor)
     
-    # Check mixed strand type
-    ss <- strandSpecific(fds)
-    if ((any(ss == 0) && any(ss == 1)) || (any(ss == 0) && any(ss == 2))){
-        stop(paste("Data contains a mix of stranded and unstranded samples.\n ",
-                        "Please consider analyzing them separately."))
-    }
-    
     # load needed genomes if provided
     if(!(is.null(genome) | any(is.na(unique(genome))))){
         for(i in unique(genome)){
@@ -407,13 +400,6 @@ addCountsToFraserDataSet <- function(fds, splitCounts, nonSplitCounts){
     
     # check for valid fds
     validObject(fds)
-  
-    # Check mixed strand type
-    ss <- strandSpecific(fds)
-    if ((any(ss == 0) && any(ss == 1)) || (any(ss == 0) && any(ss == 2))){
-        stop(paste("Data contains a mix of stranded and unstranded samples.\n ",
-               "Please consider analyzing them separately."))
-    }
     
     # create final FRASER dataset
     fds <- new("FraserDataSet",
@@ -481,7 +467,7 @@ countSplitReads <- function(sampleID, fds, NcpuPerSample=1, genome=NULL,
     
     # check for valid fds
     validObject(fds)
-    
+  
     # check cache if available
     if(isFALSE(recount) && !is.null(cacheFile) && file.exists(cacheFile)){
         cache <- readRDS(cacheFile)