def test_merge(self):
cmdline = SamtoolsMergeCommandline(samtools_exe)
cmdline.set_parameter("input_bam", [self.bamfile1, self.bamfile2])
cmdline.set_parameter("out_bam", self.outbamfile)
cmdline.set_parameter("f", True) # Overwrite out.bam if it exists
stdout, stderr = cmdline()
self.assertFalse(
stderr,
"Samtools merge failed:\n%s\nStderr:%s" % (cmdline, stderr))
self.assertTrue(os.path.exists(self.outbamfile))
def test_merge(self):
cmdline = SamtoolsMergeCommandline(samtools_exe)
cmdline.set_parameter("input_bam", [self.bamfile1, self.bamfile2])
cmdline.set_parameter("out_bam", self.outbamfile)
cmdline.set_parameter("f", True) # Overwrite out.bam if it exists
stdout, stderr = cmdline()
self.assertFalse(stderr, "Samtools merge failed:\n%s\nStderr:%s" % (cmdline, stderr))
self.assertTrue(os.path.exists(self.outbamfile))
def test_merge(self):
cmdline = SamtoolsMergeCommandline(samtools_exe)
cmdline.set_parameter("input_bam", [self.bamfile1, self.bamfile2])
cmdline.set_parameter("out_bam", self.outbamfile)
cmdline.set_parameter("f", True) # Overwrite out.bam if it exists
stdout, stderr = cmdline()
# Worked up to v1.2, then there was a regression failing with message
# but as of v1.3 expect a warning: [W::bam_merge_core2] No @HD tag found.
self.assertTrue(not stderr or stderr.strip() == "[W::bam_merge_core2] No @HD tag found.",
"Samtools merge failed:\n%s\nStderr:%s"
% (cmdline, stderr))
self.assertTrue(os.path.exists(self.outbamfile))
def test_merge(self):
cmdline = SamtoolsMergeCommandline(samtools_exe)
cmdline.set_parameter("input_bam", [self.bamfile1, self.bamfile2])
cmdline.set_parameter("out_bam", self.outbamfile)
cmdline.set_parameter("f", True) # Overwrite out.bam if it exists
stdout, stderr = cmdline()
# Worked up to v1.2, then there was a regression failing with message
# but as of v1.3 expect a warning: [W::bam_merge_core2] No @HD tag found.
self.assertTrue(not stderr or stderr.strip() == "[W::bam_merge_core2] No @HD tag found.",
"Samtools merge failed:\n%s\nStderr:%s"
% (cmdline, stderr))
self.assertTrue(os.path.exists(self.outbamfile))
