From e316ebe37013210ce8e525397c6bdf64c6e5ffae Mon Sep 17 00:00:00 2001
From: lingminhao <lingminhao31@gmail.com>
Date: Thu, 6 Feb 2025 14:26:15 +0800
Subject: [PATCH] fix bug about CompressedCharacterList

---
 R/bambu.R | 14 ++++----------
 1 file changed, 4 insertions(+), 10 deletions(-)

diff --git a/R/bambu.R b/R/bambu.R
index a42ae236..17902f87 100644
--- a/R/bambu.R
+++ b/R/bambu.R
@@ -265,8 +265,6 @@ bambu <- function(reads, annotations = NULL, genome = NULL, NDR = NULL,
         ColNames <- c()
         for(i in seq_along(quantData)){
             quantData_i <- quantData[[i]]
-            #load in the barcode clustering from file if provided
-            iter <- seq_len(ncol(metadata(quantData_i)$countMatrix)) # iter is integer
             if(!is.null(clusters)){
                 if(class(clusters[[i]])!="CompressedCharacterList"){ # !is.list(clusters) is FALSE for CompressedCharacterList 
                     clusterMaps <- NULL
@@ -285,14 +283,9 @@ bambu <- function(reads, annotations = NULL, genome = NULL, NDR = NULL,
                     rm(clusterMap)
                     iter <- clustering
 
-                } else{ #if clusters is a list
-                    if(length(quantData)>1){
-                        iter <- clusters[[i]] #lowMemory mode
-                    }else{
-                        iter <- clusters#do.call(c,clusters)
-                    }
+                } else{
+                  iter <- clusters[[i]]
                 }
-            }
             countsSeCompressed <- bplapply(iter, FUN = function(j){ # previous i changed to j to avoid duplicated assignment 
                 #i = iter[i %in% colnames(metadata(quantData_i)$countMatrix)] #bug, after assignment, i become emptyprint(i)
                 countMatrix <- unname(metadata(quantData_i)$countMatrix[,j]) # same here 
@@ -332,4 +325,5 @@ bambu <- function(reads, annotations = NULL, genome = NULL, NDR = NULL,
         colnames(countsSe) <- ColData[,1]
         return(countsSe)
     }
-}
+  }
+}
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