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import math
import numpy as np
class Constants:
MAX_QV = 60
# (identical) cutoffs for RQ and QV for "High-Fidelity" reads
HIFI_QV = 20
HIFI_RQ = 0.99
def accuracy_as_phred_qv(accuracy, max_qv=Constants.MAX_QV):
"""
Convert fractional accuracy to Phred QV: 0.999 --> 30
returns: float or numpy array
"""
if isinstance(accuracy, (float, int)):
assert 0 <= accuracy <= 1.0
if accuracy == 1:
return max_qv
return -10 * math.log10(1 - accuracy)
else:
if isinstance(accuracy, (tuple, list)):
accuracy = np.array(accuracy)
error_rate = 1.0 - accuracy
min_error_rate = 10 ** (-max_qv / 10.0)
zero_error = error_rate < min_error_rate
error_rate[zero_error] = min_error_rate
return -10 * np.log10(error_rate)
def phred_qv_as_accuracy(qv):
if qv == 0:
return 0
elif qv < 0:
raise ValueError("Negative Phred scores not allowed")
else:
return 1.0 - 10**(-qv/10)
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