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Minor typo fixes #176

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Minor typo fixes #176

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b2bf11d
Fixing typos in methSeg.R
robsyme Feb 5, 2020
9a6fc32
Update methylDBFunctions.R
robsyme Feb 5, 2020
3a7bf1a
Update tabix.functions.R
robsyme Feb 5, 2020
7a1f574
Update methCall.cpp
robsyme Feb 5, 2020
ed7c5d7
Merge branch 'master' into robsyme-typopatch-1
alexg9010 May 20, 2020
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6 changes: 3 additions & 3 deletions R/methSeg.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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.")

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3 changes: 2 additions & 1 deletion R/methylDBFunctions.R
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@@ -1,10 +1,11 @@
# Helper Functions ---------------------------------------------------


#' @noRd
## function checks wether 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) ) {
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2 changes: 1 addition & 1 deletion R/tabix.functions.R
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/methCall.cpp
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Expand Up @@ -953,7 +953,7 @@ int process_bam ( std::string &input,
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
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