From 59b02c04d1cdb665a0de436956d4b8211f8d8ca9 Mon Sep 17 00:00:00 2001
From: js2264 <jacquesserizay@gmail.com>
Date: Wed, 19 Jun 2024 10:15:01 +0200
Subject: [PATCH] fix: tests for pair_granges

---
 NAMESPACE               |  1 +
 R/pair-granges.R        |  2 +-
 R/reexports-plyranges.R |  1 +
 tests/testthat.R        | 20 ++++++++++----------
 4 files changed, 13 insertions(+), 11 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index b47c66d..25b39ac 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -240,6 +240,7 @@ importFrom(plyranges,anchor_5p)
 importFrom(plyranges,anchor_center)
 importFrom(plyranges,anchor_end)
 importFrom(plyranges,anchor_start)
+importFrom(plyranges,as_granges)
 importFrom(plyranges,count_overlaps)
 importFrom(plyranges,count_overlaps_directed)
 importFrom(plyranges,filter_by_non_overlaps)
diff --git a/R/pair-granges.R b/R/pair-granges.R
index 10722b1..5e37468 100644
--- a/R/pair-granges.R
+++ b/R/pair-granges.R
@@ -27,6 +27,6 @@
 pair_granges <- function(x) {
 
     combs <- combn(length(x), 2)
-    InteractionSet::GInteractions(combs[1,], combs[2,], gr)
+    InteractionSet::GInteractions(combs[1,], combs[2,], x)
 
 }
diff --git a/R/reexports-plyranges.R b/R/reexports-plyranges.R
index c820878..d2cb6e2 100644
--- a/R/reexports-plyranges.R
+++ b/R/reexports-plyranges.R
@@ -1,4 +1,5 @@
 #' @rdname reexports
+#' @importFrom plyranges as_granges
 #' @importFrom plyranges anchor
 #' @export
 plyranges::anchor
diff --git a/tests/testthat.R b/tests/testthat.R
index f858f15..5c3cde7 100644
--- a/tests/testthat.R
+++ b/tests/testthat.R
@@ -10,15 +10,15 @@ library(testthat)
 library(plyinteractions)
 
 gi <- read.table(text = "
-        chr1 11 20 chr1 21 30 + +
-        chr1 11 20 chr1 51 55 + +
-        chr1 11 30 chr1 51 55 - -
-        chr1 11 30 chr2 51 60 - -",
-        col.names = c(
-        "seqnames1", "start1", "end1", 
-        "seqnames2", "start2", "end2", "strand1", "strand2")
-    ) |> 
-        as_ginteractions() |> 
-        mutate(score = runif(4), type = c('cis', 'cis', 'cis', 'trans'))
+    chr1 11 20 chr1 21 30 + +
+    chr1 11 20 chr1 51 55 + +
+    chr1 11 30 chr1 51 55 - -
+    chr1 11 30 chr2 51 60 - -",
+    col.names = c(
+    "seqnames1", "start1", "end1", 
+    "seqnames2", "start2", "end2", "strand1", "strand2")
+) |> 
+    as_ginteractions() |> 
+    mutate(score = runif(4), type = c('cis', 'cis', 'cis', 'trans'))
 
 test_check("plyinteractions")