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Fix test failure from defunct cigarRangesAlongReferenceSpace() #125

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Merged
kriemo merged 1 commit into from
Sep 16, 2026
Merged

Fix test failure from defunct cigarRangesAlongReferenceSpace() #125

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3 changes: 2 additions & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,8 @@ Suggests:
AnnotationHub,
covr,
raerdata,
txdbmaker
txdbmaker,
cigarillo
LinkingTo:
Rhtslib
SystemRequirements:
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4 changes: 2 additions & 2 deletions tests/testthat/test_pileup_sites.R
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Expand Up @@ -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]
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