def test_calmd(self): """Test for samtools calmd""" cmdline = SamtoolsCalmdCommandline(samtools_exe) cmdline.set_parameter("reference", self.reference) cmdline.set_parameter("input_bam", self.bamfile1) ## If there is no index file for the reference ## samtools calmd creates one at the time of calling if os.path.exists(self.referenceindexfile): #print("exists") stderr_calmd_expected = "" else: #print("doesnt exist") stderr_calmd_expected = "[fai_load] build FASTA index.\n" stdout, stderr = cmdline() self.assertEqual(stderr, stderr_calmd_expected)
def test_calmd(self): """Test for samtools calmd.""" self.create_fasta_index() cmdline = SamtoolsCalmdCommandline(samtools_exe) cmdline.set_parameter("reference", self.reference) cmdline.set_parameter("input_bam", self.bamfile1) # If there is no index file for the reference # samtools calmd creates one at the time of calling if os.path.exists(self.referenceindexfile): # print("exists") stderr_calmd_expected = "" else: # print("doesnt exist") stderr_calmd_expected = "[fai_load] build FASTA index.\n" stdout, stderr = cmdline() self.assertEqual(stderr, stderr_calmd_expected)