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Delete orphaned test_kaiju function
The kaiju functionality was removed from viral_ngs.metagenomics but this test was left behind. The test fails with: AttributeError: module 'viral_ngs.metagenomics' has no attribute 'kaiju' There is no parser_kaiju, no Kaiju class, and no kaiju module anywhere in the codebase - this test was testing dead code.
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tests/unit/classify/test_metagenomics.py

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@@ -273,20 +273,6 @@ def test_krakenuniq(mocker):
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p.assert_called_with('db', ['input.bam'], num_threads=mock.ANY, filter_threshold=mock.ANY, out_reports=['output.report'], out_reads=['output.reads'])
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def test_kaiju():
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with patch('viral_ngs.metagenomics.kaiju.Kaiju.classify') as p:
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args = [
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'input.bam',
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'db.fmi',
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'tax_db',
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'output.report',
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'--outReads', 'output.reads',
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]
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args = metagenomics.parser_kaiju(argparse.ArgumentParser()).parse_args(args)
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args.func_main(args)
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p.assert_called_with('db.fmi', 'tax_db', 'input.bam', output_report='output.report', num_threads=mock.ANY, output_reads='output.reads')
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class TestBamFilter(TestCaseWithTmp):
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def test_bam_filter_simple(self):
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temp_dir = tempfile.gettempdir()

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