fix typos

R/get_data_matrix_from_bams.R

@@ -16,7 +16,7 @@
 #' \item{"otherC"}{methylation states of all other cytosines which do not fall into above categories.}
 #' \item{"allC"}{methylation states of all cytosines combined.}
 #' }
-#' @param alignerUsed \code{character} that defines which aligner was used to generate BAM files. Currently supported aligners are QuasR, Bismark and BISQUIT.
+#' @param alignerUsed \code{character} that defines which aligner was used to generate BAM files. Currently supported aligners are QuasR, Bismark and BISCUIT.
 #' @param collapseBySample \code{logical} indicating whether to collapse counts for bam files with same \code{samplenames}. If \code{FALSE} prefix \code{s} followed by index is added to \code{samplenames}.
 #' @param remove_nonunique \code{logical} if \code{TRUE} only unique fragments are analyzed. Uniqueness is defined by fragments start, end and methylation states of all cytosines. 
 #' @param clip_until_nbg \code{integer} controlling clipping partial footprints at both ends of fragments. Namely, protected states are erased from each end until \code{clip_until_nbg} unprotected states are met.
@@ -53,7 +53,7 @@ get_data_matrix_from_bams <- function(bamfiles,
 																			regions,
 																			genome,
 																			whichContext = c("GCH","WCG","bisC","otherC", "allC"),
-																			alignerUsed = c("QuasR","Bismark","BISQUIT"),
+																			alignerUsed = c("QuasR","Bismark","BISCUIT"),
 																			collapseBySample = TRUE,
 																			remove_nonunique = TRUE,
 																			clip_until_nbg  = 1L,

src/fetch_data_from_bam.cpp

@@ -39,11 +39,11 @@ bool fetch_data_from_bam(const string& bamfile,
 	case Bismark:
 	  collectRegionData = &collectRegionData_QsBism;
 	  break;
-	case BISQUIT:
+	case BISCUIT:
 	  collectRegionData = &collectRegionData_Bisq;
 	  break;
 	default:
-	  Rcpp::stop("Only alignments generated by QuasR, Bismark or BISQUIT can be analyzed\n");
+	  Rcpp::stop("Only alignments generated by QuasR, Bismark or BISCUIT can be analyzed\n");
 	}
 
 	// call corresponding retrieval function to store alignments in region
@@ -198,7 +198,7 @@ static int collectRegionData_QsBism(const bam1_t *hit, void *data) {
 
 
 
-// bam_fetch callback function for methyl calling and data storing for BAMs produced by BISQUIT
+// bam_fetch callback function for methyl calling and data storing for BAMs produced by BISCUIT
 static int collectRegionData_Bisq(const bam1_t *hit, void *data) { 
 
   static obj_pnts *pdata = NULL;
@@ -237,7 +237,7 @@ static int collectRegionData_Bisq(const bam1_t *hit, void *data) {
     }
 
   } else {
-    Rcpp::Rcout << "No YD tag found. Either BAM file is corrupted or generated not by BISQUIT." << std::endl;
+    Rcpp::Rcout << "No YD tag found. Either BAM file is corrupted or generated not by BISCUIT." << std::endl;
   }
 
 

src/fetch_data_from_bam.h

@@ -46,7 +46,7 @@ bool fetch_data_from_bam(const string& bamfile,
 // bam_fetch callback function for bam_fetch for data retrieval from BAM files produced by QuasR and Bismark
 static int collectRegionData_QsBism(const bam1_t *hit, void *data);
 
-// bam_fetch callback function for bam_fetch for data retrieval from BAM files produced by BISQUIT
+// bam_fetch callback function for bam_fetch for data retrieval from BAM files produced by BISCUIT
 static int collectRegionData_Bisq(const bam1_t *hit, void *data);
 
 

src/functions_export_rcpp.cpp

@@ -41,10 +41,10 @@ Rcpp::List fetch_data_matrix_from_bams_cpp(const Rcpp::CharacterVector& whichCon
     aligner = QuasR;
   else if(alignerUsed_ == "Bismark")
     aligner = Bismark;
-  else if(alignerUsed_ == "BISQUIT")
-    aligner = BISQUIT;
+  else if(alignerUsed_ == "BISCUIT")
+    aligner = BISCUIT;
   else
-    Rcpp::stop("Only alignments generated by QuasR, Bismark or BISQUIT can be analyzed\n");
+    Rcpp::stop("Only alignments generated by QuasR, Bismark or BISCUIT can be analyzed\n");
 
 
   vector<string > infiles_ = Rcpp::as<vector<string > >(infiles);

src/utils_globvars.h

@@ -22,7 +22,7 @@ enum fragMapType{GCH, WCG, bisC, otherC,
 // enumerator for aligners for which we have function implemented
 enum alignerType{QuasR,
                  Bismark,
-                 BISQUIT
+                 BISCUIT
 };