diff --git a/DESCRIPTION b/DESCRIPTION index 4b1728e..c0f365b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -57,7 +57,8 @@ Suggests: AnnotationHub, covr, raerdata, - txdbmaker + txdbmaker, + cigarillo LinkingTo: Rhtslib SystemRequirements: diff --git a/tests/testthat/test_pileup_sites.R b/tests/testthat/test_pileup_sites.R index 82f46bb..c410aea 100644 --- a/tests/testthat/test_pileup_sites.R +++ b/tests/testthat/test_pileup_sites.R @@ -401,10 +401,10 @@ test_that("filtering for splicing events works", { test_that("filtering for indel events works", { # get sites near splicing events reads <- GenomicAlignments::readGAlignments(bamfn, use.names = T) - cig_ops <- cigarRangesAlongReferenceSpace( + cig_ops <- cigarillo::cigars_as_ranges_along_ref( cigar(reads), ops = "D", - pos = start(reads) + lmmpos = start(reads) ) refs <- seqnames(reads)[elementNROWS(cig_ops) > 0] cig_ops <- cig_ops[elementNROWS(cig_ops) > 0]