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Fixes for issues 21/22 #23

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Sep 5, 2023
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Fixes for issues 21/22 #23

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92 changes: 52 additions & 40 deletions include/genomics/printer.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -130,8 +130,14 @@ namespace genomics {
break;
auto pos = std::get<0>(t);
auto match = std::get<1>(t);
std::string match_sequence = complement(match.sequence);
// Note that we cannot simply take k.pam as the PAM
// because the match may well have been found using
// an alternate PAM. The relevant PAM to consider for
// CFD calculations is found at the end of the match.
std::string pam = match_sequence.substr(20, 3);

if (match.mismatches == 0)
if ((match.mismatches == 0) && (pam.substr(1, 2) == "GG"))
perfect_match = true;

coordinates c;
Expand All @@ -140,12 +146,6 @@ namespace genomics {
if (c.chr.name == "") continue;
v.push_back(pos);

auto match_sequence = complement(match.sequence);
// Note that we cannot simply take k.pam as the PAM
// because the match may well have been found using
// an alternate PAM. The relevant PAM to consider for
// CFD calculations is found at the end of the match.
auto pam = match_sequence.substr(20, 3);
cfd_sum += calculate_cfd(k.sequence, match_sequence, pam);

n_off_targets++;
Expand Down Expand Up @@ -181,6 +181,17 @@ namespace genomics {
os << ",specificity" << std::endl;
}

template <class t_wt, uint32_t t_dens, uint32_t t_inv_dens>
std::string get_csv_line_nomatch(const genome_index<t_wt, t_dens, t_inv_dens>& gi,
const kmer& k, bool start, bool complete) {

std::string csvline(k.id);
std::string sequence = start ? k.pam + k.sequence : k.sequence + k.pam;
csvline += "," + sequence + ",NA,NA,NA,0,1.0"; // sequence, chrom, pos, strand, distance, specificity
if (complete) csvline += ",NA,NA,NA"; // match sequence, rna bulges, dna bulges;
return csvline;
}

template <class t_wt, uint32_t t_dens, uint32_t t_inv_dens>
std::string get_csv_line(const genome_index<t_wt, t_dens, t_inv_dens>& gi,
const kmer& k, bool start, match m,
Expand Down Expand Up @@ -233,34 +244,45 @@ namespace genomics {

float cfd_sum = 0.0;
bool perfect_match = false;
bool no_match_no_offtargets = true;
std::vector<std::string> off_targets_lines;

for (uint64_t d = 0; d < off_targets.size(); d++) {
for (int64_t i = 0; i < off_targets[d].size(); i++) {
no_match_no_offtargets = false;
if ((max_off_targets != -1) && (i >= max_off_targets)) break;

const auto& off_target = off_targets[d][i];
int64_t off_target_abs_coords = std::get<0>(off_target);
match match = std::get<1>(off_target);
if (match.mismatches == 0)
std::string match_sequence = complement(match.sequence);
// Note that we cannot simply take k.pam as the PAM
// because the match may well have been found using
// an alternate PAM. The relevant PAM to consider for
// CFD calculations is found at the end of the match.
std::string pam = match_sequence.substr(20, 3);

if ((match.mismatches == 0) && (pam.substr(1, 2) == "GG"))
perfect_match = true;

std::string csvline = get_csv_line(gi, k, start, match, off_target_abs_coords, complete);
if (csvline != "") {
off_targets_lines.push_back(csvline);
auto match_sequence = complement(match.sequence);
// Note that we cannot simply take k.pam as the PAM
// because the match may well have been found using
// an alternate PAM. The relevant PAM to consider for
// CFD calculations is found at the end of the match.
cfd_sum += calculate_cfd(k.sequence, match_sequence, match_sequence.substr(20, 3));
cfd_sum += calculate_cfd(k.sequence, match_sequence, pam);
}
}
}

// Each off-target will have the same specificity value - add at the end of each line
float specificity = 0.0;
if (!perfect_match) cfd_sum += 1;
if (cfd_sum > 0) specificity = 1/cfd_sum;
for (auto line: off_targets_lines) {
csvlines += line + "," + std::to_string(specificity) + "\n";
if (no_match_no_offtargets) {
csvlines += get_csv_line_nomatch(gi, k, start, complete) + "\n";
} else {
// Each off-target will have the same specificity value - add at the end of each line
float specificity = 0.0;
if (!perfect_match) cfd_sum += 1;
if (cfd_sum > 0) specificity = 1 / cfd_sum;
for (auto line: off_targets_lines) {
csvlines += line + "," + std::to_string(specificity) + "\n";
}
}

return csvlines;
Expand Down Expand Up @@ -290,30 +312,20 @@ namespace genomics {
}

samline += "\t*"; // SAM:QUAL

bool no_off_targets = true;
for (const auto& v : off_targets) {
if (!v.empty()) {
no_off_targets = false;
break;
}

// store off-target counts in tag
for (uint64_t k = 0; k < off_targets.size(); k++) {
samline += "\tk" + std::to_string(k) + ":i:" + std::to_string(off_targets[k].size());
}

if (!no_off_targets) {
// store off-target counts in tag
for (uint64_t k = 0; k < off_targets.size(); k++) {
samline += "\tk" + std::to_string(k) + ":i:" + std::to_string(off_targets[k].size());
}

std::string offtarget_hex;
float specificity;
tie(offtarget_hex, specificity) = off_target_fields(k, gi.gs, off_targets, max_off_targets);
std::string offtarget_hex;
float specificity;
tie(offtarget_hex, specificity) = off_target_fields(k, gi.gs, off_targets, max_off_targets);

if (complete) {
samline += "\tof:H:" + offtarget_hex;
}
samline += "\tsp:f:" + std::to_string(specificity);
if (complete) {
samline += "\tof:H:" + offtarget_hex;
}
samline += "\tsp:f:" + std::to_string(specificity);

return samline;
}
Expand Down
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