def test_all_stepper(self):
refs = force_str(
samtools_mpileup("-f", self.fastafilename, "-A", "-B",
self.samfilename)).splitlines(True)
iterator = self.samfile.pileup(stepper="all", fastafile=self.fastafile)
self.check_equal(refs, iterator)
def test_samtools_stepper_redo_baq(self):
refs = force_str(
samtools_mpileup("-f", self.fastafilename, "--redo-BAQ",
self.samfilename)).splitlines(True)
iterator = self.samfile.pileup(stepper="samtools",
fastafile=self.fastafile,
redo_baq=True)
self.check_equal(refs, iterator)
def test_samtools_stepper_ignore_orphans(self):
refs = force_str(
samtools_mpileup("-f", self.fastafilename, "--count-orphans",
self.samfilename)).splitlines(True)
iterator = self.samfile.pileup(stepper="samtools",
fastafile=self.fastafile,
ignore_orphans=False)
self.check_equal(refs, iterator)
def test_samtools_stepper_base_quality_threshold(self):
refs = force_str(
samtools_mpileup("-f", self.fastafilename, "--min-BQ", "20",
self.samfilename)).splitlines(True)
iterator = self.samfile.pileup(stepper="samtools",
fastafile=self.fastafile,
min_base_quality=20)
self.check_equal(refs, iterator)