8000 Merge adjacent CIGAR operations by AndreaGuarracino · Pull Request #365 · waveygang/wfmash · GitHub
[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to content

Merge adjacent CIGAR operations #365

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 1 commit into from
Jun 6, 2025
Merged

Merge adjacent CIGAR operations #365

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
34 changes: 32 additions & 2 deletions src/common/wflign/src/wflign.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -205,6 +205,36 @@ void do_biwfa_alignment(
return short_cigar;
};

// Helper function to merge adjacent CIGAR operations at concatenation point
auto merge_adjacent_ops = [](const std::string& cigar1, const std::string& cigar2) -> std::string {
if (cigar1.empty()) return cigar2;
if (cigar2.empty()) return cigar1;

// Find the last operation in cigar1
size_t pos1 = cigar1.length() - 1;
while (pos1 > 0 && !std::isdigit(cigar1[pos1])) pos1--;
char op1 = cigar1.back();
size_t start1 = cigar1.rfind(std::isdigit(cigar1[pos1]) ? cigar1[pos1] : ' ');
while (start1 > 0 && std::isdigit(cigar1[start1-1])) start1--;
int count1 = std::stoi(cigar1.substr(start1, pos1 - start1 + 1));

// Find the first operation in cigar2
size_t pos2 = 0;
while (pos2 < cigar2.length() && std::isdigit(cigar2[pos2])) pos2++;
if (pos2 >= cigar2.length()) return cigar1 + cigar2;
char op2 = cigar2[pos2];
int count2 = std::stoi(cigar2.substr(0, pos2));

// If operations match, merge them
if (op1 == op2) {
return cigar1.substr(0, start1) +
std::to_string(count1 + count2) + op1 +
cigar2.substr(pos2 + 1);
}

return cigar1 + cigar2;
};

// Perform head patching
{
u_int64_t query_eroded = 0;
Expand Down Expand Up @@ -282,7 +312,7 @@ void do_biwfa_alignment(
head_cigar_short = erode_short_matches_in_cigar(head_cigar_short, 3);

// Remove the eroded part from the beginning of main_cigar
main_cigar = head_cigar_short + main_cigar.substr(erode_end_pos);
main_cigar = merge_adjacent_ops(head_cigar_short, main_cigar.substr(erode_end_pos));
}
}
}
Expand Down Expand Up @@ -380,7 +410,7 @@ void do_biwfa_alignment(
}

// Combine the truncated main CIGAR with the tail CIGAR
main_cigar = truncated_cigar + tail_cigar_short;
main_cigar = merge_adjacent_ops(truncated_cigar, tail_cigar_short);
}
}
}
Expand Down
0