def test_find_index_cram_crai():
"""Test to find a cram index"""
# GIVEN a case with this type of alignment files
# bam_file.cram
# bam_file.cram.crai
with tempfile.TemporaryDirectory() as tmpdirname:
with tempfile.NamedTemporaryFile(dir=tmpdirname,
suffix="cram.crai") as idx:
cram_file = idx.name.replace(".crai", "")
# THEN the find_index function should return the correct index file
index = find_index(cram_file)
assert index.endswith("cram.crai")
def test_find_index_bam_bai(case_obj):
# GIVEN a case with this type of alignment files
# bam_file.bam
# bam_file.bam.bai
with tempfile.TemporaryDirectory() as tmpdirname:
with tempfile.NamedTemporaryFile(dir=tmpdirname,
suffix="bam.bai") as idx:
bam_file = idx.name.replace(".bai", "")
# THEN the find_index function should return the correct index file
index = find_index(bam_file)
assert index.endswith("bam.bai")