feat: bfc fix

nahid18 · Sep 24, 2023 · 418c410 · 418c410
1 parent eff4a9a
commit 418c410
Show file tree

Hide file tree

Showing 5 changed files with 11 additions and 6 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: easylift
 Title: An R package to perform genomic liftover
-Version: 0.99.1
+Version: 0.99.2
 Date: 2023-09-25
 Authors@R: 
     c(

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+# easylift 0.99.1
+
+* Updated the code and documentation to reflect the changes suggested by the Bioconductor team.
+
+
 # easylift 0.99.0
 
 * Submitted to Bioconductor
diff --git a/R/easylift.R b/R/easylift.R
@@ -65,7 +65,7 @@ easylift <- function(x, to, chain) {
     trychainfile <- paste0(genome(x), "To", capTo, ".over.chain")
     q <- bfcquery(bfc, trychainfile)
     if (nrow(q) >= 1) {
-      chain <- bfc[[q$rid[2]]]
+      chain <- bfc[[q$rid[1]]]
     } else {
       stop(
         "Chain file not specified and not found in BiocFileCache. Look for a chain file named '",

diff --git a/README.Rmd b/README.Rmd
@@ -71,7 +71,7 @@ easylift(gr, "hg38")
 To cite package ‘easylift’ in publications use:
 
   Al Nahid A, Love M (2023). _easylift: An R package to perform
-  genomic liftover_. R package version 0.99.0,
+  genomic liftover_. R package version 0.99.2,
   <https://github.com/nahid18/easylift>.
 
 
@@ -82,7 +82,7 @@ A BibTeX entry for LaTeX users is
     title = {easylift: An R package to perform genomic liftover},
     author = {Abdullah Al Nahid and Michael Love},
     year = {2023},
-    note = {R package version 0.99.1},
+    note = {R package version 0.99.2},
     url = {https://github.com/nahid18/easylift},
   }
 ```

diff --git a/README.md b/README.md
@@ -69,7 +69,7 @@ easylift(gr, "hg38")
 To cite package ‘easylift’ in publications use:
 
 Al Nahid A, Love M (2023). *easylift: An R package to perform genomic
-liftover*. R package version 0.99.0,
+liftover*. R package version 0.99.2,
 <https://github.com/nahid18/easylift>.
 
 A BibTeX entry for LaTeX users is
@@ -78,7 +78,7 @@ A BibTeX entry for LaTeX users is
         title = {easylift: An R package to perform genomic liftover},
         author = {Abdullah Al Nahid and Michael Love},
         year = {2023},
-        note = {R package version 0.99.1},
+        note = {R package version 0.99.2},
         url = {https://github.com/nahid18/easylift},
       }