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Fix infinite loop in fragment length distribution estimation #51

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Jun 5, 2023
Merged

Fix infinite loop in fragment length distribution estimation #51

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44 changes: 36 additions & 8 deletions src/fragment_length_dist.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -172,6 +172,12 @@ FragmentLengthDist::FragmentLengthDist(const vector<uint32_t> & frag_length_coun
cerr << "\talpha " << alpha << endl;
#endif

// in practice, the MOM estimate of alpha often starts way too large, this is a
// heuristic to speed up convergence
if (abs(alpha) > 1000.0 * sigma) {
alpha = (alpha > 0.0 ? 1.0 : -1.0) * 1000.0 * sigma;
}

// alternatingly optimize alpha and mu until convergence (sigma can
// be computed analytically)
auto log_likelihood = [&](double mu, double sigma, double alpha) {
Expand All @@ -196,20 +202,32 @@ FragmentLengthDist::FragmentLengthDist(const vector<uint32_t> & frag_length_coun
double prev_alpha = alpha + 2.0 * tol;
int max_iters = 100;
int iter_num = 0;
const double factor = 1.3; // less than 1 + phi so that we guarantee non infinity at the boundaries
while (iter_num < max_iters &&
(abs(prev_mu - mu) >= tol || abs(prev_alpha - alpha) >= tol)) {


++iter_num;
prev_mu = mu;
prev_alpha = alpha;
double ll = alpha_log_likelihood(alpha);
// find an interval that contains a local maximum
double left_radius = 1.0, right_radius = 1.0;
while (alpha_log_likelihood(alpha - left_radius) >= ll) {
left_radius *= 2.0;
double rad_ll = alpha_log_likelihood(alpha - left_radius);
while (rad_ll >= ll && !isinf(rad_ll)) {
if (isinf(left_radius * factor)) {
break;
}
left_radius *= factor;
rad_ll = alpha_log_likelihood(alpha - left_radius);
}
while (alpha_log_likelihood(alpha + right_radius) >= ll) {
right_radius *= 2.0;
rad_ll = alpha_log_likelihood(alpha + right_radius);
while (rad_ll >= ll && !isinf(rad_ll)) {
if (isinf(right_radius * factor)) {
break;
}
right_radius *= factor;
rad_ll = alpha_log_likelihood(alpha + left_radius);
}
// maximize likelihood for alpha
alpha = Utils::golden_section_search<double>(alpha_log_likelihood,
Expand All @@ -219,11 +237,21 @@ FragmentLengthDist::FragmentLengthDist(const vector<uint32_t> & frag_length_coun
ll = mu_log_likelihood(mu);
left_radius = 1.0;
right_radius = 1.0;
while (mu_log_likelihood(alpha - left_radius) >= ll) {
left_radius *= 2.0;
rad_ll = mu_log_likelihood(mu - left_radius);
while (rad_ll >= ll && !isinf(rad_ll)) {
if (isinf(left_radius * factor)) {
break;
}
left_radius *= factor;
rad_ll = mu_log_likelihood(mu - left_radius);
}
while (mu_log_likelihood(alpha + right_radius) >= ll) {
right_radius *= 2.0;
rad_ll = mu_log_likelihood(mu + right_radius);
while (rad_ll >= ll && !isinf(rad_ll)) {
if (isinf(right_radius * factor)) {
break;
}
right_radius *= factor;
rad_ll = mu_log_likelihood(mu + right_radius);
}
mu = Utils::golden_section_search<double>(mu_log_likelihood,
mu - left_radius, mu + right_radius, tol / 4.0);
Expand Down