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)
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
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)