From 48520780b23419e04f6a26d6a0a848f341252907 Mon Sep 17 00:00:00 2001
From: J Wokaty <jwokaty@users.noreply.github.com>
Date: Mon, 26 Aug 2024 10:13:25 -0400
Subject: [PATCH] Fix indent

---
 R/bedbaser.R                   | 15 +++++++++------
 R/utils.R                      | 16 +++++++++-------
 tests/testthat/test-bedbaser.R |  6 ++++--
 vignettes/bedbaser.Rmd         |  6 ++++--
 4 files changed, 26 insertions(+), 17 deletions(-)

diff --git a/R/bedbaser.R b/R/bedbaser.R
index 60cb3d3..a27cba4 100644
--- a/R/bedbaser.R
+++ b/R/bedbaser.R
@@ -57,7 +57,7 @@ BEDbase <- function() {
 }
 
 #' Display API
-#' 
+#'
 #' @param x BEDbase object
 #' @param ... other options
 #' @param .deprecated (default FALSE) if deprecated
@@ -76,7 +76,8 @@ setMethod(
     "operations", "BEDbase",
     function(x, ..., .deprecated = FALSE) {
         callNextMethod(x, ..., .deprecated = .deprecated)
-    })
+    }
+)
 
 #' Get the example BED file or BEDset with metadata
 #'
@@ -172,8 +173,9 @@ bb_metadata <- function(api, id, full = FALSE) {
 #' bb_list_beds(api)
 #'
 #' @export
-bb_list_beds <- function(api, genome = NULL, bed_type = NULL, limit = 1000,
-    offset = 0) {
+bb_list_beds <- function(
+        api, genome = NULL, bed_type = NULL, limit = 1000,
+        offset = 0) {
     rsp <- api$list_beds_v1_bed_list_get(
         genome = genome, bed_type = bed_type,
         limit = limit, offset = offset
@@ -323,8 +325,9 @@ bb_bed_text_search <- function(api, query, limit = 10, offset = 0) {
 #' bb_to_granges(api, ex_bed$id)
 #'
 #' @export
-bb_to_granges <- function(api, bed_id, file_type = "bed", extra_cols = NULL,
-    quietly = TRUE) {
+bb_to_granges <- function(
+        api, bed_id, file_type = "bed", extra_cols = NULL,
+        quietly = TRUE) {
     stopifnot(file_type %in% c("bed", "bigbed"))
     metadata <- bb_metadata(api, bed_id, TRUE)
     file_path <- .get_file(metadata, file_type, "http", quietly)
diff --git a/R/utils.R b/R/utils.R
index 381abf0..8182573 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -39,8 +39,9 @@
 #' .get_file(md, "bed", "http")
 #'
 #' @noRd
-.get_file <- function(metadata, file_type = c("bed", "bigbed"),
-    access_type = c("s3", "http"), quietly = TRUE) {
+.get_file <- function(
+        metadata, file_type = c("bed", "bigbed"),
+        access_type = c("s3", "http"), quietly = TRUE) {
     file_details <- .format_metadata_files(metadata$files) |>
         filter(
             name == paste(file_type, "file", sep = "_"),
@@ -121,8 +122,9 @@
 #' .bed_file_to_granges(file_path, md)
 #'
 #' @noRd
-.bed_file_to_granges <- function(file_path, metadata, extra_cols = NULL,
-    quietly = TRUE) {
+.bed_file_to_granges <- function(
+        file_path, metadata, extra_cols = NULL,
+        quietly = TRUE) {
     bed_format <- gsub("peak", "Peak", metadata$bed_format)
     nums <- str_replace(metadata$bed_type, "bed", "") |>
         str_split_1("\\+") |>
@@ -140,9 +142,9 @@
             extra_cols <- .get_extra_cols(file_path, nums[1], nums[2])
         }
         import(file_path,
-               format = "bed",
-               extraCols = extra_cols,
-               genome = metadata$genome_alias
+            format = "bed",
+            extraCols = extra_cols,
+            genome = metadata$genome_alias
         )
     } else {
         import(file_path, format = bed_format, genome = metadata$genome_alias)
diff --git a/tests/testthat/test-bedbaser.R b/tests/testthat/test-bedbaser.R
index 30e5641..8497106 100644
--- a/tests/testthat/test-bedbaser.R
+++ b/tests/testthat/test-bedbaser.R
@@ -102,8 +102,10 @@ test_that("bb_to_granges returns a GRanges object given a bigBed file", {
         gro <- bb_to_granges(api, ex_bed$id, "bigbed")
         expect_equal("GRanges", class(gro)[1])
     } else {
-        expect_warning(rlang::warn("This feature does not work on Windows."),
-                       bb_to_granges(api, ex_bed$id, "bigbed"))
+        expect_warning(
+            rlang::warn("This feature does not work on Windows."),
+            bb_to_granges(api, ex_bed$id, "bigbed")
+        )
     }
 })
 
diff --git a/vignettes/bedbaser.Rmd b/vignettes/bedbaser.Rmd
index a9ee3f7..830951b 100644
--- a/vignettes/bedbaser.Rmd
+++ b/vignettes/bedbaser.Rmd
@@ -191,8 +191,10 @@ Download the
 [chain file](https://hgdownload.cse.ucsc.edu/downloads.html#liftover) from UCSC.
 
 ```{r convertCoordinates_getTheChain, message=FALSE}
-chain_url <- paste0("https://hgdownload.cse.ucsc.edu/goldenPath/mm10/liftOver/",
-                    "mm10ToMm39.over.chain.gz")
+chain_url <- paste0(
+    "https://hgdownload.cse.ucsc.edu/goldenPath/mm10/liftOver/",
+    "mm10ToMm39.over.chain.gz"
+)
 tmpdir <- tempdir()
 gz <- file.path(tmpdir, "mm10ToMm39.over.chain.gz")
 download.file(chain_url, gz)