version bump

Author: mikelove

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: plyranges
 Type: Package
 Title: A fluent interface for manipulating GenomicRanges
-Version: 1.27.6
+Version: 1.31.1
 Authors@R: c(
       person("Stuart", "Lee", role = c("aut"), 
              comment = c(ORCID = "0000-0003-1179-8436")),
@@ -31,7 +31,7 @@ Imports:
   tidyselect (>= 1.0.0),
   rtracklayer,
   GenomicAlignments,
-  GenomeInfoDb,
+  Seqinfo,
   Rsamtools,
   S4Vectors (>= 0.23.10),
   utils

NAMESPACE

@@ -342,16 +342,6 @@ importFrom(BiocGenerics,unique)
 importFrom(BiocGenerics,unlist)
 importFrom(BiocGenerics,which)
 importFrom(BiocGenerics,width)
-importFrom(GenomeInfoDb,"seqinfo<-")
-importFrom(GenomeInfoDb,"seqlevels<-")
-importFrom(GenomeInfoDb,"seqnames<-")
-importFrom(GenomeInfoDb,Seqinfo)
-importFrom(GenomeInfoDb,genome)
-importFrom(GenomeInfoDb,isCircular)
-importFrom(GenomeInfoDb,seqinfo)
-importFrom(GenomeInfoDb,seqlengths)
-importFrom(GenomeInfoDb,seqlevels)
-importFrom(GenomeInfoDb,seqnames)
 importFrom(GenomicAlignments,extractAlignmentRangesOnReference)
 importFrom(GenomicAlignments,readGAlignmentPairs)
 importFrom(GenomicAlignments,readGAlignments)
@@ -414,6 +404,16 @@ importFrom(S4Vectors,runValue)
 importFrom(S4Vectors,splitAsList)
 importFrom(S4Vectors,subjectHits)
 importFrom(S4Vectors,zipup)
+importFrom(Seqinfo,"seqinfo<-")
+importFrom(Seqinfo,"seqlevels<-")
+importFrom(Seqinfo,"seqnames<-")
+importFrom(Seqinfo,Seqinfo)
+importFrom(Seqinfo,genome)
+importFrom(Seqinfo,isCircular)
+importFrom(Seqinfo,seqinfo)
+importFrom(Seqinfo,seqlengths)
+importFrom(Seqinfo,seqlevels)
+importFrom(Seqinfo,seqnames)
 importFrom(dplyr,arrange)
 importFrom(dplyr,bind_cols)
 importFrom(dplyr,bind_rows)

R/io-bed.R

@@ -46,7 +46,7 @@ norm_args_reader <- function(genome_info) {
 #' @return A GRanges object
 #'
 #' @importFrom rtracklayer import.bed
-#' @importFrom GenomeInfoDb seqinfo
+#' @importFrom Seqinfo seqinfo
 #' @importFrom methods is
 #' @seealso \code{rtracklayer::\link[rtracklayer:BEDFile-class]{BEDFile()}}
 #'

R/io-bigwig.R

@@ -26,7 +26,7 @@ read_bigwig <- function(file, genome_info = NULL, overlap_ranges = NULL) {
     if (is(genome_info, "GRanges")) {
       seq_info <- seqinfo(genome_info)
     } else if (is.character(genome_info)) {
-      seq_info <- GenomeInfoDb::Seqinfo(genome = genome_info)
+      seq_info <- Seqinfo::Seqinfo(genome = genome_info)
     }
   } else {
       seq_info <- NULL

R/io-gff.R

@@ -28,7 +28,7 @@ norm_args_reader_gff <- function(genome_info) {
 #' @return A GRanges object
 #'
 #' @importFrom rtracklayer import.gff
-#' @importFrom GenomeInfoDb seqinfo
+#' @importFrom Seqinfo seqinfo
 #' @seealso \code{rtracklayer::\link[rtracklayer:GFFFile-class]{GFFFile()}}
 #' @export
 #' @rdname io-gff-read

R/ranges-construct.R

@@ -19,7 +19,7 @@
 #' @importFrom rlang quos eval_tidy
 #' @importFrom S4Vectors mcols metadata mcols<- metadata<-
 #' @importFrom BiocGenerics start end width strand score start<- end<- width<- score<- strand<-
-#' @importFrom GenomeInfoDb seqnames seqnames<- seqinfo<-
+#' @importFrom Seqinfo seqnames seqnames<- seqinfo<-
 #' @importFrom IRanges IRanges
 #' @importFrom GenomicRanges GRanges granges
 #' @rdname ranges-construct

R/ranges-genomeinfo.R

@@ -30,8 +30,8 @@ genome_info <- function(genome = NULL, seqnames = NULL, seqlengths = NULL, is_ci
 #' annotations to an existing Ranges object use `set_genome_info`. To retrieve
 #' an annotation as a Ranges object use `get_genome_info`.
 #'
-#' @importFrom GenomeInfoDb Seqinfo seqnames seqlengths isCircular genome seqinfo
-#' @seealso [GenomeInfoDb::Seqinfo()]
+#' @importFrom Seqinfo Seqinfo seqnames seqlengths isCircular genome seqinfo
+#' @seealso [Seqinfo::Seqinfo()]
 #' @examples
 #' x <- genome_info(genome = "toy",
 #'                  seqnames = letters[1:4],

R/ranges-overlap-joins-outer.R

@@ -86,7 +86,7 @@ add_na_seqlevels <- function(x) {
 }
 
 #' @importFrom S4Vectors queryLength decode
-#' @importFrom GenomeInfoDb seqlevels seqlevels<-
+#' @importFrom Seqinfo seqlevels seqlevels<-
 #' @rdname overlap-joins
 #' @export
 join_overlap_left <- function(x, y, maxgap, minoverlap, suffix = c(".x", ".y")) {