def test_sort(self): cmdline = SamtoolsSortCommandline(samtools_exe) cmdline.set_parameter("input_bam", self.bamfile1) cmdline.set_parameter("out_prefix", "SamBam/out") stdout, stderr = cmdline() self.assertFalse( stderr, "Samtools sort failed:\n%s\nStderr:%s" % (cmdline, stderr))
def test_sort(self): cmdline = SamtoolsSortCommandline(samtools_exe) cmdline.set_parameter("input_bam", self.bamfile1) cmdline.set_parameter("out_prefix", "SamBam/out") try: stdout, stderr = cmdline() except ApplicationError as err: if "[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files" in str(err): # TODO: The samtools sort API changed... return else: raise self.assertFalse(stderr, "Samtools sort failed:\n%s\nStderr:%s" % (cmdline, stderr))