Code cleanup

epigen · Jan 4, 2024 · f054fce · f054fce
1 parent d6bd692
commit f054fce
Showing 1 changed file with 2 additions and 12 deletions.
diff --git a/R/filtering.R b/R/filtering.R
@@ -634,22 +634,12 @@ rnb.step.snp.removal <- function(rnb.set, report) {
 	if (rnb.getOption("logging") && logger.isinitialized() == FALSE) {
 		logger.start(fname = NA) # initialize console logger
 	}
-	logger.info("#############")
-	logger.info(rnb.set@assembly)
-	print("HERE")
-	is.hg38 <- ifelse(rnb.set@assembly == "hg38", TRUE, FALSE)
 	result <- rnb.step.snp.removal.internal(class(rnb.set), integer(), report,
-		annotation(rnb.set, add.names = TRUE), is.hg38)
+		annotation(rnb.set, add.names = TRUE))
 	return(list(dataset = remove.sites(rnb.set, result$filtered), report = result$report))
 }
 
-rnb.step.snp.removal.internal <- function(dataset.class, sites2ignore, report, anno.table, is.hg38) {
-	## TODO: Improve for hg38 annotation.
-	if (is.hg38) {
-		logger.info("HG38 *********************")
-	} else {
-		logger.info("HG19 **************") ## ??
-	}
+rnb.step.snp.removal.internal <- function(dataset.class, sites2ignore, report, anno.table) {
 	logger.start("Removal of SNP-enriched Sites")
 	snp <- rnb.getOption("filtering.snp")
 	is.infinium <- !(dataset.class %in% c("RnBiseqSet", "RnBSet"))