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))