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"""Benchmarking module for AlignedSegment functionality"""
import os
import array
import pysam
from TestUtils import BAM_DATADIR
def set_binary_tag():
read = pysam.AlignedSegment()
read.set_tag('FZ', array.array('H', range(1000)))
return len(read.get_tag('FZ'))
def read_binary_tag(fn):
with pysam.AlignmentFile(fn) as inf:
read = next(inf.fetch())
return len(read.get_tag('FZ'))
def test_set_binary_tag(benchmark):
result = benchmark(set_binary_tag)
assert result == 1000
def test_read_binary_tag(benchmark):
result = benchmark(read_binary_tag, os.path.join(
BAM_DATADIR, "example_btag.bam"))
assert result == 260
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