From 09dcb4db1d094a385357f88bb368e4e0471a905b Mon Sep 17 00:00:00 2001
From: Andre <andre_sim@gis.a-star.edu.sg>
Date: Tue, 29 Oct 2024 15:25:27 +0800
Subject: [PATCH] remove commas

---
 R/bambu.R | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/R/bambu.R b/R/bambu.R
index cd9e3a66..34d9a166 100644
--- a/R/bambu.R
+++ b/R/bambu.R
@@ -146,18 +146,18 @@ bambu <- function(reads, annotations = NULL, genome = NULL, NDR = NULL,
         lowMemory = TRUE
     }
     if(mode == "multiplexed"){
-        if(is.null(demultiplex)) demultiplex = TRUE,
-        cleanReads = TRUE,
-        opt.em = list(degradationBias = FALSE),
+        if(is.null(demultiplex)) demultiplex = TRUE
+        cleanReads = TRUE
+        opt.em = list(degradationBias = FALSE)
         quant = FALSE
     }
     if(mode == "fusion"){
-        NDR = 1,
+        NDR = 1
         fusionMode = TRUE
     }
     if(mode == "debug"){
-        verbose = TRUE,
-        trackReads = TRUE,
+        verbose = TRUE
+        trackReads = TRUE
         returnDistTable = TRUE
     }
     if(is.null(annotations)) { annotations = GRangesList()