From c6f5c72b3234fbbd9ee625e891238a1620cab63f Mon Sep 17 00:00:00 2001
From: Vicente Yepez <30469316+vyepez88@users.noreply.github.com>
Date: Thu, 15 Feb 2024 20:34:31 +0100
Subject: [PATCH] added strand to countnonSplicedReads

---
 R/countRNAseqData.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/countRNAseqData.R b/R/countRNAseqData.R
index e12a6a4a..e42184a0 100644
--- a/R/countRNAseqData.R
+++ b/R/countRNAseqData.R
@@ -864,6 +864,7 @@ countNonSplicedReads <- function(sampleID, splitCountRanges, fds,
     # unstranded case: for counting only non spliced reads we 
     # skip this information
     isPairedEnd <- pairedEnd(fds[,samples(fds) == sampleID])[[1]]
+    strand <- strandSpecific(fds[,samples(fds) == sampleID])[[1]]
     doAutosort <- isPairedEnd
     
     # check cache if available
@@ -905,7 +906,7 @@ countNonSplicedReads <- function(sampleID, splitCountRanges, fds,
             allowMultiOverlap=TRUE,
             checkFragLength=FALSE,
             minMQS=bamMapqFilter(scanBamParam(fds)),
-            strandSpecific=strandSpecific(fds),
+            strandSpecific=strand,
             
             # activating long read mode
             isLongRead=longRead,