From b2bf11dc31de8efca2d67a9946056743049677bb Mon Sep 17 00:00:00 2001 From: Robert Syme Date: Wed, 5 Feb 2020 11:05:26 -0500 Subject: [PATCH 1/4] Fixing typos in methSeg.R Just changing 'wether' to 'whether'. --- R/methSeg.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/R/methSeg.R b/R/methSeg.R index 27f28fcd..334d810d 100644 --- a/R/methSeg.R +++ b/R/methSeg.R @@ -115,17 +115,17 @@ methSeg<-function(obj, diagnostic.plot=TRUE, join.neighbours=FALSE, # destrand strand(obj) <- "*" - ## check wether obj contains at least one metacol + ## check whether obj contains at least one metacol if(ncol(elementMetadata(obj))<1) stop("GRanges does not have any meta column.") - ## check wether obj contains is sorted by position + ## check whether obj contains is sorted by position if(is.unsorted(obj,ignore.strand=TRUE)) { obj <- sort(obj,ignore.strand=TRUE) message("Object not sorted by position, sorting now.") } - ## check wether obj contains at least two ranges else stop + ## check whether obj contains at least two ranges else stop if(length(obj)<=1) stop("segmentation requires at least two ranges.") From 9a6fc3261116836f4f4fa04e13a435d155a7775d Mon Sep 17 00:00:00 2001 From: Robert Syme Date: Wed, 5 Feb 2020 11:06:10 -0500 Subject: [PATCH 2/4] Update methylDBFunctions.R --- R/methylDBFunctions.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/methylDBFunctions.R b/R/methylDBFunctions.R index 501c9b36..61443fdd 100644 --- a/R/methylDBFunctions.R +++ b/R/methylDBFunctions.R @@ -1,9 +1,9 @@ # Helper Functions --------------------------------------------------- -## function checks wether a tabix file already exists and +## function checks whether a tabix file already exists and ## appends number if file already exists .checkTabixFileExists <- function(tabixfile) { - message("\nchecking wether tabix file already exists:") + message("\nchecking whether tabix file already exists:") tabixfile <- paste0(tabixfile,".bgz") message(tabixfile) if(file.exists(tabixfile) ) { From 3a7bf1a11730dc2cd3068d708f031b12b786e139 Mon Sep 17 00:00:00 2001 From: Robert Syme Date: Wed, 5 Feb 2020 11:06:46 -0500 Subject: [PATCH 3/4] Update tabix.functions.R --- R/tabix.functions.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/tabix.functions.R b/R/tabix.functions.R index 6fcc325a..5c719d8f 100644 --- a/R/tabix.functions.R +++ b/R/tabix.functions.R @@ -273,7 +273,7 @@ obj2tabix <- function(obj,filename,rm.txt=TRUE){ append = TRUE) } -#' function to check wether tabix header exists +#' function to check whether tabix header exists #' and exit with message instead of error #' #' @param tbxFile tabix file From 7a1f574f5c6aeb21b72ee6937c9903e15d6e07ef Mon Sep 17 00:00:00 2001 From: Robert Syme Date: Wed, 5 Feb 2020 11:07:20 -0500 Subject: [PATCH 4/4] Update methCall.cpp --- src/methCall.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/methCall.cpp b/src/methCall.cpp index 875bce55..f65fed84 100644 --- a/src/methCall.cpp +++ b/src/methCall.cpp @@ -936,7 +936,7 @@ int process_bam ( std::string &input, std::string &CpGfile, std::string &CHHfile else if( (xr_tag == "ZGA") && (xg_tag == "ZGA") ) {strand='-';} // complementary to original bottom strand, bismark says + strand to this - // check wether read is proper paired (both mapped) + // check whether read is proper paired (both mapped) int proper_paired = (int) ((b)->core.flag&BAM_FPROPER_PAIR); // if is proper pair and no_overlap is set