fix bambu.singlecell comments and fix CB column assignment in processreads for bulk mode

Author: ch99l

R/bambu-processReads.R

@@ -70,7 +70,7 @@ bambu.processReads <- function(reads, annotations, genomeSequence,
             if(extractBarcodeUMI){
                 mcols(readGrgList[[i]])$CB <- paste0(names(reads)[i], '_', mcols(readGrgList[[i]])$CB)
             } else{
-                mcols(readGrgList[[i]])$CB <- i
+                mcols(readGrgList[[i]])$CB <- names(reads)[i]
             }
 
             mcols(readGrgList[[i]])$CB <- as.factor(mcols(readGrgList[[i]])$CB)

R/bambu.R

@@ -335,6 +335,7 @@ bambu <- function(reads, annotations = NULL, genome = NULL, NDR = NULL,
 #'     \item{dedupUMI}{Logical, whether to perform UMI-based deduplication per
 #'     barcode. Defaults to FALSE}
 #'     \item{clusters}{A named list mapping cluster names to barcode vectors,
+#'     or a path to a CSV file with \code{barcode} and \code{cluster} columns,
 #'     used for cluster-level transcript discovery. Defaults to NULL}
 #' }
 #' @inheritParams bambu