def __init__(self, bamfile, desc = None, step = 1e6, out = sys.stderr):
self._bam = None
self._out = out
self._desc = desc
self._step = step
self._count = 0
self._last_count = 0
self._last_time = time.time()
self._start_time = self._last_time
self._last_fract = -1.0
self._total = 0.0
self._counts = []
if bamfile and bamfile.header.get("HD", {}).get("SO", "NA") == "coordinate":
self._bam = bamfile
self._total = float(sum(bamfile.lengths)) or 1.0
self._counts.append(0)
self._counts.extend(cumsum(bamfile.lengths))
def __init__(self, bamfile, desc=None, step=1e6, out=sys.stderr):
self._bam = None
self._out = out
self._desc = desc
self._step = step
self._count = 0
self._last_count = 0
self._last_time = time.time()
self._start_time = self._last_time
self._last_fract = -1.0
self._total = 0.0
self._counts = []
if bamfile and bamfile.header.get("HD", {}).get("SO",
"NA") == "coordinate":
self._bam = bamfile
self._total = float(sum(bamfile.lengths)) or 1.0
self._counts.append(0)
self._counts.extend(cumsum(bamfile.lengths))
def test_cumsum__initial():
assert_equal(list(utils.cumsum(range(5), -10)), [-10, -9, -7, -4, 0])
def test_cumsum__float():
assert_equal(list(utils.cumsum((1.0, 2.0, 3.0))), [1.0, 3.0, 6.0])
def test_cumsum__integers():
assert_equal(list(utils.cumsum(range(-4, 5))),
[-4, -7, -9, -10, -10, -9, -7, -4, 0])
def test_cumsum__empty():
assert_equal(list(utils.cumsum([])), [])
def test_cumsum__initial():
assert_equal(list(utils.cumsum(range(5), -10)), [-10, -9, -7, -4, 0])
def test_cumsum__float():
assert_equal(list(utils.cumsum((1.0, 2.0, 3.0))), [1.0, 3.0, 6.0])
def test_cumsum__integers():
assert_equal(list(utils.cumsum(range(-4, 5))), [-4, -7, -9, -10, -10, -9, -7, -4, 0])
def test_cumsum__empty():
assert_equal(list(utils.cumsum([])), [])
