Fixed error in tests with bam index.

ivanek · Nov 2, 2023 · 866a84b · 866a84b
1 parent c566d51
commit 866a84b
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
@@ -57,7 +57,8 @@ sam <- c(
 )
 samfile <- tempfile(fileext = ".sam")
 cat(paste(sam, collapse = "\n"), file = samfile)
-bamfile <- Rsamtools::asBam(samfile, indexDestination = TRUE)
+bamfile <- Rsamtools::asBam(samfile, indexDestination = FALSE)
+Rsamtools::indexBam(bamfile)
 
 ## FASTA
 fastafile <- system.file("extdata/test.fa", package = "Gviz")

diff --git a/tests/testthat/test_Gviz.R b/tests/testthat/test_Gviz.R
@@ -110,7 +110,8 @@ test_that("import of alignments from BAM file works", {
 
     unlink(paste(bamfile, "bai", sep = "."))
     expect_error(.import.bam.alignments(bamfile, GRanges("chr1", IRanges(189891401, 189894000))), "Unable to find index for BAM file")
-    bamfile <- Rsamtools::asBam(samfile, indexDestination = TRUE, overwrite = TRUE)
+    bamfile <- Rsamtools::asBam(samfile, indexDestination = FALSE, overwrite = TRUE)
+    Rsamtools::indexBam(bamfile)
 
     expect_identical(.import.bam.alignments(bamfile, GRanges("chr1", IRanges(189891401, 189894000))), bamgr)
     expect_identical(.import.bam.alignments(bamfile, GRanges("chr2", IRanges(1, 2))), empty)