def test_index(self):
cmdline = SamtoolsIndexCommandline(samtools_exe)
cmdline.set_parameter("input_bam", self.bamfile1)
stdout, stderr = cmdline()
self.assertFalse(
stderr, f"Samtools index failed:\n{cmdline}\nStderr:{stderr}")
self.assertTrue(os.path.exists(self.bamindexfile1))
def test_index(self):
cmdline = SamtoolsIndexCommandline(samtools_exe)
cmdline.set_parameter("input_bam", self.bamfile1)
stdout, stderr = cmdline()
self.assertFalse(stderr,
"Samtools index failed:\n%s\nStderr:%s"
% (cmdline, stderr))
self.assertTrue(os.path.exists(self.bamindexfile1))
def test_index_bam(variables):
targetpath = os.path.join(variables.targetpath, 'bait')
bam_index = SamtoolsIndexCommandline(
input=os.path.join(targetpath, 'genesippr_sorted.bam'))
bam_index()
size = os.stat(os.path.join(targetpath, 'genesippr_sorted.bam.bai'))
assert size.st_size > 0
def create_bam_index(self, input_bam):
"""Create index of an input bam file."""
cmdline = SamtoolsIndexCommandline(samtools_exe)
cmdline.set_parameter("input_bam", input_bam)
stdout, stderr = cmdline()
def create_bam_index(self, input_bam):
"""Creates index of an input bam file"""
cmdline = SamtoolsIndexCommandline(samtools_exe)
cmdline.set_parameter("input_bam", input_bam)
stdout, stderr = cmdline()
