def test_coverage(self):
"""The 'coverage' command."""
# fa = 'formats/chrM-Y-trunc.hg19.fa'
bed = 'formats/my-targets.bed'
bam = 'formats/na12878-chrM-Y-trunc.bam'
for by_count in (False, True):
for min_mapq in (0, 30):
for nprocs in (1, 2):
cna = commands.do_coverage(bed, bam,
by_count=by_count,
min_mapq=min_mapq,
processes=nprocs)
self.assertEqual(len(cna), 4)
self.assertTrue((cna.log2 != 0).any())
self.assertGreater(cna.log2.nunique(), 1)
def test_coverage(self):
"""The 'coverage' command."""
# fa = 'formats/chrM-Y-trunc.hg19.fa'
bed = 'formats/my-targets.bed'
bam = 'formats/na12878-chrM-Y-trunc.bam'
for by_count in (False, True):
for min_mapq in (0, 30):
for nprocs in (1, 2):
cna = commands.do_coverage(bed, bam,
by_count=by_count,
min_mapq=min_mapq,
processes=nprocs)
self.assertEqual(len(cna), 4)
self.assertTrue((cna.log2 != 0).any())
self.assertGreater(cna.log2.nunique(), 1)