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removed debugging outputs
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@RolandFaure
RolandFaure committed Jun 12, 2024
1 parent f08092a commit 917b8ef
Showing 1 changed file with 20 additions and 58 deletions.
78 changes: 20 additions & 58 deletions scaffold.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1912,41 +1912,6 @@ void output_errors(string error_file, std::vector<SolidBridge>& solid_bridges, s

int main(int argc, char *argv[])
{

string gaf_completed2 = "tmp_last_cleanup.gaf";
string assembly_completed2 = "tmp_assembly_completed.gfa";
vector<Bridge> bridges2;
vector<Pier> piers2;
int num_well_aligned_reads_end2 = 0;
int num_partially_aligned_reads_end2 = 0;
int num_jumpings_reads_end2 = 0;
int num_undetected_duplex_reads_end2 = 0;
std::set<string> list_of_duplex_reads2;

inventoriate_bridges_and_piers(gaf_completed2, bridges2, piers2, assembly_completed2, num_well_aligned_reads_end2, num_partially_aligned_reads_end2, num_jumpings_reads_end2, num_undetected_duplex_reads_end2, list_of_duplex_reads2);
cout << "well aligned reads: " << num_well_aligned_reads_end2 << endl;
cout << "partially aligned reads: " << num_partially_aligned_reads_end2 << endl;
cout << "jumping reads: " << num_jumpings_reads_end2 << endl;
cout << "undetected duplex reads: " << num_undetected_duplex_reads_end2 << endl;

gaf_completed2 = "reads_aligned_on_assembly.gaf";
assembly_completed2 = "assembly.gfa";
num_well_aligned_reads_end2 = 0;
num_partially_aligned_reads_end2 = 0;
num_jumpings_reads_end2 = 0;
num_undetected_duplex_reads_end2 = 0;
list_of_duplex_reads2.clear();
cout << endl;
inventoriate_bridges_and_piers(gaf_completed2, bridges2, piers2, assembly_completed2, num_well_aligned_reads_end2, num_partially_aligned_reads_end2, num_jumpings_reads_end2, num_undetected_duplex_reads_end2, list_of_duplex_reads2);
cout << "well aligned reads: " << num_well_aligned_reads_end2 << endl;
cout << "partially aligned reads: " << num_partially_aligned_reads_end2 << endl;
cout << "jumping reads: " << num_jumpings_reads_end2 << endl;
cout << "undetected duplex reads: " << num_undetected_duplex_reads_end2 << endl;



exit(1);

//just check which reads are well aligned in "tmp_last_cleanup.gaf"
// int num_well_aligned_readsz = 0;
// int num_partially_aligned_readsz = 0;
Expand Down Expand Up @@ -2282,12 +2247,13 @@ int main(int argc, char *argv[])
int num_partially_aligned_reads_end = 0;
int num_jumpings_reads_end = 0;
int num_undetected_duplex_reads_end = 0;
int num_unaligned_reads_end = 0;
std::set<string> list_of_duplex_reads2;
inventoriate_bridges_and_piers(final_gaf, bridges2, piers2, assembly_completed, num_well_aligned_reads_end, num_partially_aligned_reads_end, num_jumpings_reads_end, num_undetected_duplex_reads_end, list_of_duplex_reads2);


//count the number of reads that align end-to-end, partially and not at all
count_unaligned_reads(final_gaf, input_reads, num_unaligned_reads);
count_unaligned_reads(final_gaf, input_reads, num_unaligned_reads_end);

//print the number of reads that aligned end-to-end, partially and not at all before and after
cout << "____________________________________________________________________________________________________" << endl;
Expand All @@ -2298,52 +2264,48 @@ int main(int argc, char *argv[])
for (int i = 0 ; i < 25-num_well_aligned_reads_start_str.size() ; i++){
cout << " ";
}
cout << " | " << num_well_aligned_reads;
for (int i = 0 ; i < 25-std::to_string(num_well_aligned_reads).size() ; i++){
cout << " | " << num_well_aligned_reads_end;
for (int i = 0 ; i < 25-std::to_string(num_well_aligned_reads_end).size() ; i++){
cout << " ";
}
cout << "|" << endl;

string num_undetected_duplex_reads_end_str = std::to_string(num_undetected_duplex_reads_end);
cout << "| Number of undetected duplex reads | " << num_undetected_duplex_reads_end_str;
for (int i = 0 ; i < 25-num_undetected_duplex_reads_end_str.size() ; i++){
cout << "| Number of undetected duplex reads | " << num_undetected_duplex_reads_start;
for (int i = 0 ; i < 25-std::to_string(num_undetected_duplex_reads_start).size() ; i++){
cout << " ";
}
cout << " | " << num_undetected_duplex_reads_start;
for (int i = 0 ; i < 25-std::to_string(num_undetected_duplex_reads_start).size() ; i++){
cout << " | " << num_undetected_duplex_reads_end;
for (int i = 0 ; i < 25-std::to_string(num_undetected_duplex_reads_end).size() ; i++){
cout << " ";
}
cout << "|" << endl;

string num_jumpings_reads_end_str = std::to_string(num_jumpings_reads_end);
cout << "| Number of jumping reads | " << num_jumpings_reads_end_str;
for (int i = 0 ; i < 25-num_jumpings_reads_end_str.size() ; i++){
cout << "| Number of jumping reads | " << num_jumpings_reads_start;
for (int i = 0 ; i < 25-std::to_string(num_jumpings_reads_start).size() ; i++){
cout << " ";
}
cout << " | " << num_jumpings_reads_start;
for (int i = 0 ; i < 25-std::to_string(num_jumpings_reads_start).size() ; i++){
cout << " | " << num_jumpings_reads_end;
for (int i = 0 ; i < 25-std::to_string(num_jumpings_reads_end).size() ; i++){
cout << " ";
}
cout << "|" << endl;

string num_partially_aligned_reads_start_str = std::to_string(num_partially_aligned_reads_start);
cout << "| Number of partially aligned reads | " << num_partially_aligned_reads_start_str;
for (int i = 0 ; i < 25-num_partially_aligned_reads_start_str.size() ; i++){
cout << "| Number of partially aligned reads | " << num_partially_aligned_reads_start;
for (int i = 0 ; i < 25-std::to_string(num_partially_aligned_reads_start).size() ; i++){
cout << " ";
}
cout << " | " << num_partially_aligned_reads;
for (int i = 0 ; i < 25-std::to_string(num_partially_aligned_reads).size() ; i++){
cout << " | " << num_partially_aligned_reads_end;
for (int i = 0 ; i < 25-std::to_string(num_partially_aligned_reads_end).size() ; i++){
cout << " ";
}
cout << "|" << endl;

string num_unaligned_reads_start_str = std::to_string(num_unaligned_reads_start);
cout << "| Number of unaligned reads | " << num_unaligned_reads_start_str;
for (int i = 0 ; i < 25-num_unaligned_reads_start_str.size() ; i++){
cout << "| Number of unaligned reads | " << num_unaligned_reads_start;
for (int i = 0 ; i < 25-std::to_string(num_unaligned_reads_start).size() ; i++){
cout << " ";
}
cout << " | " << num_unaligned_reads;
for (int i = 0 ; i < 25-std::to_string(num_unaligned_reads).size() ; i++){
cout << " | " << num_unaligned_reads_end;
for (int i = 0 ; i < 25-std::to_string(num_unaligned_reads_end).size() ; i++){
cout << " ";
}
cout << "|" << endl;
Expand Down

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