def test_autobin(self):
"""The 'autobin' command."""
bam_fname = "formats/na12878-chrM-Y-trunc.bam"
target_bed = "formats/my-targets.bed"
targets = tabio.read(target_bed, 'bed')
access_bed = "../data/access-5k-mappable.hg19.bed"
accessible = tabio.read(access_bed, 'bed').filter(chromosome='chrY')
for method in ('amplicon', 'wgs', 'hybrid'):
(cov, bs), _ = autobin.do_autobin(bam_fname, method,
targets=targets,
access=accessible)
self.assertGreater(cov, 0)
self.assertGreater(bs, 0)
def test_autobin(self):
"""The 'autobin' command."""
bam_fname = "formats/na12878-chrM-Y-trunc.bam"
target_bed = "formats/my-targets.bed"
targets = tabio.read(target_bed, 'bed')
access_bed = "../data/access-5k-mappable.hg19.bed"
accessible = tabio.read(access_bed, 'bed').filter(chromosome='chrY')
for method in ('amplicon', 'wgs', 'hybrid'):
(cov, bs), _ = autobin.do_autobin(bam_fname, method,
targets=targets,
access=accessible)
self.assertGreater(cov, 0)
self.assertGreater(bs, 0)
