def test_set_meta_presorted():
b = Bam()
with get_dataset('1.bam') as dataset:
b.set_meta(dataset=dataset)
assert dataset.metadata.sort_order == 'coordinate'
bam_file = pysam.AlignmentFile(dataset.file_name, mode='rb',
index_filename=dataset.metadata.bam_index.file_name)
assert bam_file.has_index() is True
def test_set_meta_presorted():
b = Bam()
with get_dataset('1.bam') as dataset:
b.set_meta(dataset=dataset)
assert dataset.metadata.sort_order == 'coordinate'
bam_file = pysam.AlignmentFile(dataset.file_name, mode='rb',
index_filename=dataset.metadata.bam_index.file_name)
assert bam_file.has_index() is True
def test_set_meta_header_info():
"""
check if information from the bam header is set
as metadata
"""
b = Bam()
with get_dataset('bam_from_sam.bam') as dataset:
b.set_meta(dataset=dataset)
assert dataset.metadata.bam_header == {'HD': {'VN': '1.3', 'SO': 'coordinate'}, 'SQ': [{'SN': 'ref', 'LN': 45}, {'SN': 'ref2', 'LN': 40}]}
assert dataset.metadata.reference_names == ['ref', 'ref2']