def test_pileup_query_qualities_are_equal(self):
samtools_result = build_query_qualities_with_samtoolspipe(self.fn)
pysam_result = build_query_qualities_with_pysam(self.fn)
pysam_result = [
[chr(min(126, x + 33)) for x in l] for l in pysam_result]
self.assertEqual("".join(flatten_nested_list(pysam_result)),
"".join(flatten_nested_list(samtools_result)))
def test_pileup_mapping_qualities_are_equal(self):
samtools_result = PileupTestUtils.build_mapping_qualities_with_samtoolspipe(
self.fn)
pysam_result = PileupTestUtils.build_mapping_qualities_with_pysam(
self.fn)
# convert to chars
pysam_result = [[chr(min(126, x + 33)) for x in l]
for l in pysam_result]
self.assertEqual("".join(flatten_nested_list(pysam_result)),
"".join(flatten_nested_list(samtools_result)))
def test_build_query_bases_with_reference_from_bam_with_samtoolspysam(benchmark):
result = benchmark(build_query_bases_with_samtoolspysam,
os.path.join(BAM_DATADIR, "ex2.bam"),
"-f", os.path.join(BAM_DATADIR, "ex1.fa"))
assert len("".join(flatten_nested_list(result))) == 115924
def test_build_query_bases_with_reference_from_bam_with_pysam(benchmark):
with pysam.FastaFile(os.path.join(BAM_DATADIR, "ex1.fa")) as fasta:
result = benchmark(build_query_bases_with_pysam,
os.path.join(BAM_DATADIR, "ex2.bam"),
fastafile=fasta)
assert len("".join(flatten_nested_list(result))) == 115924
def test_build_query_bases_from_bam_with_pysam(benchmark):
result = benchmark(build_query_bases_with_pysam,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert len("".join(flatten_nested_list(result))) == 116308
def test_build_query_bases_from_bam_with_pysam_pileups(benchmark):
# note that there is no overlap detection here
result = benchmark(build_query_bases_with_pysam_pileups,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert len("".join(flatten_nested_list(result))) == 107241
