Ran github actions

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: transmogR
 Type: Package
 Title: Modify a set of reference sequences using a set of variants
-Version: 0.99.3
+Version: 0.99.5
 Authors@R: person("Stevie", "Pederson", 
     email = "stephen.pederson.au@gmail.com", 
     role = c("aut", "cre"),

R/helpers.R

@@ -8,11 +8,16 @@
     ## Deal with NAs
     alts <- mcols(var)[[alt_col]]
     if (is(alts, "XStringSetList")) alts <- as.character(unlist(alts))
+    if (length(alts) != length(var))
+        stop("Some alternate alleles have been specified with multiple values")
     is_na <- is.na(alts)
     if (any(is_na)) message("NA values found in ", alt_col, ". Removing...")
     var <- var[!is_na]
     if (all(is_na) & length(is_na) > 0) stop("All NA values in ", alt_col)
 
+    if (any(nchar(alts) == 0))
+        stop("Please set Deletions so that width(REF) > 1 and width(ALT) > 0")
+
     ## Check Non-IUPAC alt alleles
     iupac <- paste(names(IUPAC_CODE_MAP), collapse = "")
     pat <- paste0("^[", iupac, "]+$")

tests/testthat/test_helpers.R

@@ -1,6 +1,8 @@
 test_that(".checkAlts behaves correctly", {
     gr <- GenomicRanges::GRanges("chr1:1")
     gr$ALT <- ""
+    expect_error(.checkAlts(gr, "ALT"), "Please set Deletions.+")
+    gr$ALT <- "x"
     expect_error(.checkAlts(gr, "ALT"), "Non-IUPAC.+")
 
     gr$ALT <- NA
@@ -31,7 +33,7 @@ test_that(".makeIntersectionArgs behaves correctly",{
     types <- c(
         mapping = "call", counts = "logical", bar_number_threshold = "numeric",
         text_colors = "call", text = "call", text_mapping = "call", mode = "character",
-        position = "call", fill = "character"
+        position = "call", width = "numeric", fill = "character"
     )
     expect_equal(vapply(new, \(x) is(x)[[1]], character(1)), types)
     expect_true(new$bar_number_threshold == 1)