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))
