diff --git a/DESCRIPTION b/DESCRIPTION index 37106ef..201c34a 100644 --- 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 index de24abd..9b16f23 100644 --- 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 index b6aa2a4..b806e96 100644 --- 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 index cb1fbb6..1901c0d 100644 --- 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, . @@ -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 index e2093a7..75e223a 100644 --- 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, . 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}, }