remove the min.primarySecondaryDistStartEnd2 from opt.discovery since this is not used in transcript discovery

Author: SuiYue-2308

R/bambu.R

@@ -34,11 +34,8 @@
 #'     annotation to be assigned to the same gene id, defaults to 10bp}
 #'     \item{min.primarySecondaryDist}{specifying the minimum number of distance 
 #'     threshold, defaults to 5bp}
-#'     \item{min.primarySecondaryDistStartEnd1}{specifying the minimum number 
+#'     \item{min.primarySecondaryDistStartEnd1}{specifying the minimum number
 #'     of distance threshold, used for extending annotation, defaults to 5bp}
-#'     \item{min.primarySecondaryDistStartEnd2}{specifying the minimum number 
-#'     of distance threshold, used for estimating distance to annotation, 
-#'     defaults to 5bp}
 #'     \item{min.txScore.multiExon}{specifying the minimum transcript level 
 #'     threshold for multi-exon transcripts during sample combining, 
 #'     defaults to 0}
@@ -183,6 +180,8 @@ bambu <- function(reads, annotations = NULL, genome = NULL, NDR = NULL,
     }
     if(lowMemory)
         message("lowMemory has been deprecated and split into processByChromosome and processByBam. Please see Documentation")
+    if(!is.null(opt.discovery[["min.primarySecondaryDistStartEnd2"]]))
+        message("min.primarySecondaryDistStartEnd2 has been moved to opt.rcAssignment. Please pass this parameter via opt.rcAssignment instead.")
     if(is.null(annotations)){ 
         annotations <- GRangesList()
     } else {

R/bambu_utilityFunctions.R

@@ -26,7 +26,6 @@ setDiscoveryParameters <- function(discoveryParameters){
         min.exonOverlap = 10,
         min.primarySecondaryDist = 5,
         min.primarySecondaryDistStartEnd1 = 5, # for creating new annotations
-        min.primarySecondaryDistStartEnd2 = 5, # for read assignment
         min.txScore.multiExon = 0,
         min.txScore.singleExon = 1,
         fitReadClassModel = TRUE,