Bug fix for issue #37

Bug identified by @zyqfrog10 in the way position indices are tracked
in the internal function bumphunt(). Previously, the order of the
`chrs` vector containing chromosome names did not necessarily match
the order of the names in the cumulative index table when chrM was
included and listed last. This commit
introduces a fix by removing the `as.character` call when building
the cumulative sum table, which was reordering the names alphabetically.
It also adds a check that the order of these two items is identical,
and if not will throw an error to prevent this type of bug from
persisting.

DESCRIPTION

@@ -2,7 +2,7 @@ Package: dmrseq
 Type: Package
 Title: Detection and inference of differentially methylated regions 
  from Whole Genome Bisulfite Sequencing 
-Version: 1.7.0
+Version: 1.7.1
 Authors@R: c(person("Keegan", "Korthauer", role = c("cre", "aut"), 
  email = "[email protected]", 
  comment = c(ORCID = "0000-0002-4565-1654")),

R/helper_functions.R

@@ -312,13 +312,20 @@ bumphunt <- function(bs,
  }
 
  chrs <- unique(seqnames(bs))
- chrlengths <- cumsum(table(as.character(seqnames(bs))))
- for (j in seq_len(length(chrs)-1)) {
- ch <- chrs[[j+1]]
- tab$indexStart[tab$chr %in% ch] <- tab$indexStart[tab$chr %in% ch] +
- chrlengths[names(chrlengths) == chrs[j]]
- tab$indexEnd[tab$chr %in% ch] <- tab$indexEnd[tab$chr %in% ch] +
- chrlengths[names(chrlengths) == chrs[j]] 
+ chrlengths <- cumsum(table(seqnames(bs)))
+ # Add a check to make sure chr order lines up with 
+ # cumulative sum table
+ if (chrs == names(chrlengths)){
+ for (j in seq_len(length(chrs)-1)) {
+ ch <- chrs[[j+1]]
+ tab$indexStart[tab$chr %in% ch] <- tab$indexStart[tab$chr %in% ch] +
+ chrlengths[names(chrlengths) == chrs[j]]
+ tab$indexEnd[tab$chr %in% ch] <- tab$indexEnd[tab$chr %in% ch] +
+ chrlengths[names(chrlengths) == chrs[j]] 
+ }
+ }else{
+ stop("Chromosome order could not be reliably determined. ",
+ "Please use the 'sort' function before running dmrseq")
  }
  }