Exemple #1
0
 def test1_2(self):
     input_vcf = self.starling_vcf
     class_name = type(self).__name__
     test_name = sys._getframe().f_code.co_name
     output_vcf = os.path.join(self.OUTPUT_FOLDER,
                               "%s.%s.vcf" % (class_name, test_name))
     config = {
         "input_vcf": input_vcf,
         "output_vcf": output_vcf,
         "variant_caller": STRELKA_VARIANT_CALLER,
         "selection_method": SELECTION_METHOD_AF,
         "equality_mode": INCLUDE_ALTERNATE,
         "sample_idx": "0",
         "sample_name": "sample",
         "sort_vcf": False,
         "sort_threads": -2,
         "temp_folder": ""
     }
     try:
         print 1
         vcf_dedup_runner = VcfDedupRunner(config)
         print 2
         vcf_dedup_runner.run()
         print 3
         self.assertTrue(False)
         print 4
     except:
         self.assertTrue(True)
Exemple #2
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 def test1_7(self):
     input_vcf = self.generic2
     class_name = type(self).__name__
     test_name = sys._getframe().f_code.co_name
     output_vcf = os.path.join(self.OUTPUT_FOLDER,
                               "%s.%s.vcf" % (class_name, test_name))
     config = {
         "input_vcf": input_vcf,
         "output_vcf": output_vcf,
         "variant_caller": GENERIC_VARIANT_CALLER,
         "selection_method": SELECTION_METHOD_AF,
         "equality_mode": INCLUDE_ALTERNATE,
         "sort_vcf": True,
         "sort_threads": 1,
         "temp_folder": ""
     }
     vcf_dedup_runner = VcfDedupRunner(config)
     vcf_dedup_runner.run()
     del vcf_dedup_runner
Exemple #3
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 def test1_8(self):
     input_vcf = self.strelka_vcf
     class_name = type(self).__name__
     test_name = sys._getframe().f_code.co_name
     output_vcf = os.path.join(self.OUTPUT_FOLDER,
                               "%s.%s.vcf" % (class_name, test_name))
     config = {
         "input_vcf": input_vcf,
         "output_vcf": output_vcf,
         "variant_caller": STARLING_VARIANT_CALLER,
         "selection_method": SELECTION_METHOD_AF,
         "equality_mode": INCLUDE_ALTERNATE,
         "sort_vcf": True,
         "sort_threads": 1,
         "temp_folder": ""
     }
     try:
         vcf_dedup_runner = VcfDedupRunner(config)
         vcf_dedup_runner.run()
         self.assertTrue(False)
     except:
         self.assertTrue(True)