# Copyright (c) 2015 Boocock James <james.boocock@otago.ac.nz>
# Author: Boocock James <james.boocock@otago.ac.nz>
# 
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# this software and associated documentation files (the "Software"), to deal in
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# the Software, and to permit persons to whom the Software is furnished to do so,
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# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
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from fine_mapping_pipeline.finemap.finemap import run_finemap, remove_surrogates, _write_matrix, _write_zscores 
import logging 
logging.basicConfig(level=logging.INFO)

def test_remove_surrogate(tmpdir):
    input_matrix = 'tests/finemap_data/test.matrix'
    input_zscore = 'tests/finemap_data/test.Z'
    surrogates_out = 'tests/finemap_data/out.surro'
    (matrix, zscores) = remove_surrogates(input_matrix,input_zscore, surrogates_out)
    _write_matrix(matrix, "tests/finemap_data/out.matrix")
    assert 1 == 2
    _write_zscores(zscores, "tests/finemap_data/out.zscores")