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"""Benchmarking module for AlignmentFile functionality"""
import os
import pytest
from TestUtils import BAM_DATADIR, force_str, flatten_nested_list
from AlignmentFileFetchTestUtils import *
def test_build_fetch_from_bam_with_samtoolsshell(benchmark):
result = benchmark(build_fetch_with_samtoolsshell,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert result == 3270
def test_build_fetch_from_bam_with_samtoolspipe(benchmark):
result = benchmark(build_fetch_with_samtoolspipe,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert result == 3270
def test_build_fetch_from_bam_with_pysam(benchmark):
result = benchmark(build_fetch_with_pysam,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert result == 3270
def test_build_query_sequences_from_bam_with_samtoolsshell(benchmark):
result = benchmark(build_query_sequences_with_samtoolsshell,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert len(result) == 3270
def test_build_query_sequences_from_bam_with_samtoolspipe(benchmark):
result = benchmark(build_query_sequences_with_samtoolspipe,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert len(result) == 3270
def test_build_query_sequences_from_bam_with_pysam(benchmark):
result = benchmark(build_query_sequences_with_pysam,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert len(result) == 3270
def test_build_query_qualities_from_bam_with_pysam(benchmark):
result = benchmark(build_query_qualities_with_pysam,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert len(result) == 3270
def test_build_query_sequences_from_bam_flagfilter_with_samtoolsshell(benchmark):
result = benchmark(build_query_sequences_flagfilter_with_samtoolsshell,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert len(result) == 3124
def test_build_query_sequences_from_bam_flagfilter_with_samtoolspipe(benchmark):
result = benchmark(build_query_sequences_flagfilter_with_samtoolspipe,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert len(result) == 3124
def test_build_query_sequences_from_bam_flagfilter_with_pysam(benchmark):
result = benchmark(build_query_sequences_flagfilter_with_pysam,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert len(result) == 3124
def test_build_query_sequences_from_bam_directflagfilter_with_pysam(benchmark):
result = benchmark(build_query_sequences_flagfilter_with_pysam,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert len(result) == 3124
@pytest.mark.aligned_pairs
def test_build_aligned_pairs_default_with_pysam(benchmark):
result = benchmark(build_aligned_pairs_with_pysam,
os.path.join(BAM_DATADIR, "with_md.bam"))
assert len(result) == 3235
@pytest.mark.aligned_pairs
def test_build_aligned_pairs_matchesonly_with_pysam(benchmark):
result = benchmark(build_aligned_pairs_with_pysam,
os.path.join(BAM_DATADIR, "with_md.bam"),
matches_only=True)
assert len(result) == 3235
@pytest.mark.aligned_pairs
def test_build_aligned_pairs_withseq_with_pysam(benchmark):
result = benchmark(build_aligned_pairs_with_pysam,
os.path.join(BAM_DATADIR, "with_md.bam"),
with_seq=True)
assert len(result) == 3235
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