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)