tso tmb trace: do not parse cols as logicals

umccr · Oct 6, 2024 · f4b210a · f4b210a
1 parent 4f701b6
commit f4b210a
Show file tree

Hide file tree

Showing 3 changed files with 5 additions and 4 deletions.
diff --git a/R/tso.R b/R/tso.R
@@ -301,8 +301,8 @@ tso_tmbt_read <- function(x) {
     VariantType = "c", CosmicIDs = "c", MaxCosmicCount = "d",
     AlleleCountsGnomadExome = "d", AlleleCountsGnomadGenome = "d",
     AlleleCounts1000Genomes = "d", MaxDatabaseAlleleCounts = "d",
-    GermlineFilterDatabase = "l", GermlineFilterProxi = "l",
-    CodingVariant = "l", Nonsynonymous = "l", IncludedInTMBNumerator = "l"
+    GermlineFilterDatabase = "c", GermlineFilterProxi = "c",
+    CodingVariant = "c", Nonsynonymous = "c", IncludedInTMBNumerator = "c"
   )
   # cttso v2 has introduced a few extra columns
   ct2 <- list(

diff --git a/man/MultiqcFile.Rd b/man/MultiqcFile.Rd
diff --git a/tests/testthat/test-roxytest-testexamples-multiqc.R b/tests/testthat/test-roxytest-testexamples-multiqc.R
@@ -2,7 +2,7 @@
 
 # File R/multiqc.R: @testexamples
 
-test_that("Function multiqc_date_fmt() @ L348", {
+test_that("Function multiqc_date_fmt() @ L360", {
 
   cdate <- "2023-04-07, 09:09 UTC"
   (res1 <- multiqc_date_fmt(cdate))