old_contents: from unittest import TestCase
  
  from atlas.schema import VariantCall
  from atlas.schema import Variant
  
  from atlas.pheno.amr import TBPredictor
  
  
  class AMRPredictTest(TestCase):
  
      def setUp(self):
          self.variant_snp = Variant.create(start=0, end=1, reference_bases="A",
                                            alternate_bases=["T"])
  
          self.predictor = TBPredictor(variant_calls={},
                                       called_genes={})
  
      def teardown(self):
          pass
  
      def test_wt_vars(self):
          call = VariantCall.create(
              variant=self.variant_snp,
              genotype=[
                  0,
                  1],
              genotype_likelihoods=[
                  0.1,
                  0.9,
                  0.12],
              info={
                  "contamination_depths": [],
                  "coverage": {
                      "alternate": {
                          "percent_coverage": 100.0,
                          "median_depth": 15,
                          "min_depth": 2},
                      "reference": {
                          "percent_coverage": 100.0,
                          "median_depth": 139,
                          "min_depth": 128}},
                  "expected_depths": [152]})
  
          assert self.predictor._coverage_greater_than_threshold(call, [""]) == False
  
new_contents: from unittest import TestCase
  
  from atlas.schema import VariantCall
  from atlas.schema import Variant
  
  from atlas.pheno.amr import TBPredictor
  
  
  class AMRPredictTest(TestCase):
  
      def setUp(self):
          self.variant_snp = Variant.create(start=0, end=1, reference_bases="A",
                                            alternate_bases=["T"])
  
          self.predictor = TBPredictor(variant_calls={},
                                       called_genes={})
  
      def teardown(self):
          pass
  
      def test_wt_vars(self):
          call = VariantCall.create(
              variant=self.variant_snp,
              genotype=[
                  0,
                  1],
              genotype_likelihoods=[
                  0.1,
                  0.9,
                  0.12],
              info={
                  "contamination_depths": [],
                  "coverage": {
                      "alternate": {
                          "percent_coverage": 100.0,
                          "median_depth": 15,
                          "min_depth": 2},
                      "reference": {
                          "percent_coverage": 100.0,
                          "median_depth": 139,
                          "min_depth": 128}},
                  "expected_depths": [152]})
  
          assert self.predictor._coverage_greater_than_threshold(call, [
                                                                 ""]) == False
  
subject: fix amr test