def het_lik(self, variant_probe_coverage):
if variant_probe_coverage.alternate_percent_coverage < 100 or variant_probe_coverage.reference_percent_coverage < 100:
return MIN_LLK
else:
het_liks = []
for expected_depth in self.expected_depths:
het_liks.append(
log_lik_R_S_coverage(
variant_probe_coverage.alternate_median_depth,
variant_probe_coverage.reference_median_depth,
expected_depth * self.minor_freq,
expected_depth * (1 - self.minor_freq)))
return max(het_liks)
def hom_alt_lik(self, variant_probe_coverage):
if variant_probe_coverage.alternate_percent_coverage < 100 * \
percent_coverage_from_expected_coverage(max(self.expected_depths)):
return MIN_LLK
else:
hom_alt_liks = []
# Either alt+cov or alt_covg + contam_covg
for expected_depth in self.expected_depths:
hom_alt_liks.append(
log_lik_R_S_coverage(
variant_probe_coverage.alternate_median_depth,
variant_probe_coverage.reference_median_depth,
expected_depth, expected_depth * self.error_rate / 3))
for contamination in self.contamination_depths:
hom_alt_liks.append(
log_lik_R_S_coverage(
variant_probe_coverage.alternate_median_depth,
variant_probe_coverage.reference_median_depth,
expected_depth + contamination,
(expected_depth + contamination) *
self.error_rate / 3))
return max(hom_alt_liks)