--- a +++ b/deepvariant/dv_vcf_constants_test.py @@ -0,0 +1,65 @@ +# Copyright 2017 Google LLC. +# +# Redistribution and use in source and binary forms, with or without +# modification, are permitted provided that the following conditions +# are met: +# +# 1. Redistributions of source code must retain the above copyright notice, +# this list of conditions and the following disclaimer. +# +# 2. Redistributions in binary form must reproduce the above copyright +# notice, this list of conditions and the following disclaimer in the +# documentation and/or other materials provided with the distribution. +# +# 3. Neither the name of the copyright holder nor the names of its +# contributors may be used to endorse or promote products derived from this +# software without specific prior written permission. +# +# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE +# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +# POSSIBILITY OF SUCH DAMAGE. +"""Tests for deepvariant .dv_vcf_constants.""" + +from absl.testing import absltest +from absl.testing import parameterized +from third_party.nucleus.protos import reference_pb2 +from deepvariant import dv_vcf_constants + + +class DvVcfConstantsTest(parameterized.TestCase): + + @parameterized.parameters( + dict(contigs=[], sample_names=[]), + dict( + contigs=[reference_pb2.ContigInfo(name='chr1')], + sample_names=['single_sample'], + ), + dict( + contigs=[ + reference_pb2.ContigInfo(name='1'), + reference_pb2.ContigInfo(name='2'), + ], + sample_names=['multiple', 'samples'], + ), + ) + def test_deepvariant_header(self, contigs, sample_names): + header = dv_vcf_constants.deepvariant_header( + contigs=contigs, sample_names=sample_names + ) + self.assertCountEqual(header.contigs, contigs) + self.assertCountEqual(header.sample_names, sample_names) + self.assertGreater(len(header.filters), 0) + self.assertGreater(len(header.infos), 0) + self.assertGreater(len(header.formats), 0) + + +if __name__ == '__main__': + absltest.main()