rename unused argument

GoekeLab · Jan 26, 2025 · 596897a · 596897a · lingminhao · Jan 26, 2025
1 parent b3fed7c
commit 596897a
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/R/prepareDataFromBam.R b/R/prepareDataFromBam.R
@@ -71,8 +71,8 @@ prepareDataFromBam <- function(bamFile, yieldSize = NULL, verbose = FALSE,
         if(cleanReads){
             softClip5Prime <- clipFunction(cigarData = GenomicAlignments::cigar(alignmentInfo), grep_pattern = '^(\\d*)[S].*', replace_pattern = '\\1')
             softClip3Prime <- clipFunction(cigarData = GenomicAlignments::cigar(alignmentInfo), grep_pattern = '.*\\D(\\d*)[S]$', replace_pattern = '\\1')
-            hardClip5Prime <- clipFunction(alignData = GenomicAlignments::cigar(alignmentInfo), grep_pattern = '^(\\d*)[H].*', replace_pattern = '\\1')
-            hardClip3Prime <- clipFunction(alignData = GenomicAlignments::cigar(alignmentInfo), grep_pattern = '.*\\D(\\d*)[H]$', replace_pattern = '\\1')
+            hardClip5Prime <- clipFunction(cigarData = GenomicAlignments::cigar(alignmentInfo), grep_pattern = '^(\\d*)[H].*', replace_pattern = '\\1')
+            hardClip3Prime <- clipFunction(cigarData = GenomicAlignments::cigar(alignmentInfo), grep_pattern = '.*\\D(\\d*)[H]$', replace_pattern = '\\1')
             # softClip5Prime <-suppressWarnings(pmax(0,as.numeric(gsub('^(\\d*)[S].*','\\1',GenomicAlignments::cigar(alignmentInfo))), na.rm=T))
             # softClip3Prime <-suppressWarnings(pmax(0,as.numeric(gsub('.*\\D(\\d*)[S]$','\\1',GenomicAlignments::cigar(alignmentInfo))), na.rm=T))
             # hardClip5Prime <-suppressWarnings(pmax(0,as.numeric(gsub('^(\\d*)[H].*','\\1',GenomicAlignments::cigar(alignmentInfo))), na.rm=T))
@@ -154,4 +154,4 @@ prepareDataFromBam <- function(bamFile, yieldSize = NULL, verbose = FALSE,
 clipFunction <- function(cigarData, grep_pattern, replace_pattern){
     return(suppressWarnings(pmax(0,as.numeric(gsub(grep_pattern,replace_pattern,
                                                    cigarData)), na.rm=T)))
-}
+}