def log_realigned_reads(self, region, reads):
"""Logs, if enabled, the realigned reads for region."""
if self.enabled and self.config.emit_realigned_reads:
path = self._file_for_region(region, self.realigned_reads_filename)
with genomics_io.make_read_writer(path) as writer:
for read in reads:
writer.write(read)
def test_make_read_writer_tfrecords(self):
outfile = test_utils.test_tmpfile('test.tfrecord')
writer = genomics_io.make_read_writer(outfile=outfile)
# Test that the writer is a context manager and that we can write a read to
# it.
with writer:
writer.write(self.read1)
writer.write(self.read2)
# Our output should have exactly one read in it.
self.assertEqual([self.read1, self.read2],
list(
io_utils.read_tfrecords(outfile,
proto=reads_pb2.Read)))
def test_make_read_writer_bam_fails_with_not_implemented_error(self):
with self.assertRaises(NotImplementedError):
genomics_io.make_read_writer('test.bam', contigs=self.contigs)
def test_make_read_writer_bam_fails_without_contigs(self):
with self.assertRaisesRegexp(ValueError, 'contigs'):
genomics_io.make_read_writer('test.bam')