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Solves compiler errors
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Samuel Horsfield committed Jan 17, 2025
1 parent cc5fd43 commit 9980a8c
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Showing 3 changed files with 37 additions and 20 deletions.
5 changes: 3 additions & 2 deletions src/ORF_clustering.h
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Original file line number Diff line number Diff line change
Expand Up @@ -13,12 +13,13 @@ void assign_centroids(const ColoredCDBG<MyUnitigMap>& ccdbg,
const std::vector<Kmer>& head_kmer_arr,
const size_t& overlap,
const ORFNodeVector& ORF_info,
std::vector<std::tuple<int, int, size_t, size_t, std::shared_ptr<std::string>>>& centroid_vector)
std::vector<std::tuple<int, int, size_t, size_t, std::shared_ptr<std::string>>>& centroid_vector);

ORFGroupPair group_ORFs(const std::map<size_t, std::string>& ORF_file_paths,
const ColoredCDBG<MyUnitigMap>& ccdbg,
const std::vector<Kmer>& head_kmer_arr,
const size_t& overlap);
const size_t& overlap,
tbb::concurrent_unordered_map<std::string, ORFNodeVector> centroid_map);

std::pair<ORFClusterMap, robin_hood::unordered_map<std::string, std::string>> produce_clusters(const std::map<size_t, std::string>& ORF_file_paths,
const ColoredCDBG<MyUnitigMap>& ccdbg,
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32 changes: 16 additions & 16 deletions src/graph.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -167,9 +167,9 @@ GraphTuple Graph::update (const std::string& graphfile,
const std::vector<std::string>& start_codons_for,
const std::vector<std::string>& start_codons_rev,
size_t num_threads,
const bool is_ref,
bool is_ref,
const std::unordered_set<std::string>& ref_set,
const std::string& path_dir
const std::string& path_dir,
const bool write_graph) {

// Set number of threads
Expand Down Expand Up @@ -204,7 +204,7 @@ GraphTuple Graph::update (const std::string& graphfile,
// generate graph, writing if write_graph == true
size_t lastindex = infile1.find_last_of(".");
std::string outgraph = infile1.substr(0, lastindex);
_ccdbg_b = buildGraph(infile1, infile2, is_ref, kmer, num_threads, false, false, outgraph);
ColoredCDBG<MyUnitigMap> _ccdbg_b = buildGraph(infile1, infile2, is_ref, kmer, num_threads, false, false, outgraph);

// get colour names for new graph
std::vector<std::string> input_colours_b = _ccdbg_b.getColorNames();
Expand Down Expand Up @@ -246,7 +246,7 @@ GraphTuple Graph::update (const std::string& graphfile,
_NewSet.set();
for (int i = 0; i < input_colours.size(); i++)
{
if (input_colours_a.find(input_colours[i]) != input_colours_a.end())
if (std::find(input_colours_a.begin(), input_colours_a.end(), input_colours[i]) != input_colours_a.end())
{
_NewSet[i] = 0;
_RefSet[i] = 1;
Expand Down Expand Up @@ -355,10 +355,10 @@ std::pair<std::map<size_t, std::string>, std::map<size_t, std::string>> Graph::f
// initilise all colour keys, determining which colours to analyse
for (size_t colour_ID = 0; colour_ID < input_colours_all.size(); colour_ID++)
{
if ((bool)_NewSet[i])
if ((bool)_NewSet[colour_ID])
{
input_colours.push_back(input_colours_all.at(colour_ID));
input_colours_ID.push_back(colour_ID)
input_colours_ID.push_back(colour_ID);
ORF_file_paths[colour_ID] = "";
Edge_file_paths[colour_ID] = "";
}
Expand Down Expand Up @@ -424,8 +424,6 @@ std::pair<std::map<size_t, std::string>, std::map<size_t, std::string>> Graph::f
const int aa_kmer = std::round((float) (overlap + 1) / (float) 6) - 1;

// determine which input colours should be traversed
std::vector<

#pragma omp parallel for
for (size_t colour_index = 0; colour_index < input_colours.size(); colour_index++)
{
Expand Down Expand Up @@ -601,7 +599,7 @@ std::pair<std::map<size_t, std::string>, std::map<size_t, std::string>> Graph::f
//robin_hood::unordered_map<size_t, robin_hood::unordered_map<size_t, float>> ORFToScoreMap;

#pragma omp parallel for
for (int colour_index = 0; colour_index < ORF_file_paths.size(); colour_ID++)
for (int colour_index = 0; colour_index < ORF_file_paths.size(); colour_index++)
{
// pull out colour_ID
size_t colour_ID = input_colours_ID.at(colour_index);
Expand Down Expand Up @@ -639,8 +637,8 @@ std::pair<std::map<size_t, std::string>, std::map<size_t, std::string>> Graph::f

// get score
std::string old_centroid_seq = generate_sequence_nm(std::get<0>(old_centroid_info), std::get<1>(old_centroid_info), overlap, _ccdbg, _KmerArray);
const auto ORF_aa = translate(old_centroid_seq).substr(1,(ORF_DNA.size() / 3) - 2);
ORF_hash = hasher{}(ORF_aa);
const auto ORF_aa = translate(old_centroid_seq).substr(1,(old_centroid_seq.size() / 3) - 2);
const auto ORF_hash = hasher{}(ORF_aa);
gene_prob = all_ORF_scores.at(ORF_hash);

// update centroid score in place
Expand Down Expand Up @@ -728,7 +726,8 @@ std::pair<std::map<size_t, std::string>, std::map<size_t, std::string>> Graph::f
int centroid_ID = 0;
for (const auto& entry : centroid_map) {
const std::string& header = "-1_" + std::to_string(centroid_ID);
const std::string& sequence = entry.second;
const auto& ORF_info = entry.second;
const std::string sequence = generate_sequence_nm(std::get<0>(ORF_info), std::get<1>(ORF_info), overlap, _ccdbg, _KmerArray);

// Write the header
outfile << ">" << header << "\n";
Expand Down Expand Up @@ -1207,14 +1206,14 @@ void Graph::_read_centroids (const std::string& fasta_file,
while ((l = kseq_read(seq)) >= 0)
{
// read sequence
std::string& sequence = seq->seq.s;
std::string& header = seq->name.s;
std::string sequence = seq->seq.s;
std::string header = seq->name.s;

// convert string to uppercase to avoid indexing issues
//std::transform(sequence.begin(), sequence.end(), sequence.begin(), ::ascii_toupper_char);

// map sequence to DBG
centroid_map[header] = map_seq_to_graph(sequence, _ccdbg);
centroid_map[header] = map_seq_to_graph(sequence, _ccdbg, kmer);
}

// destroy seq and fp objects
Expand Down Expand Up @@ -1279,7 +1278,8 @@ void clear_graph(Graph& g)
}

ORFNodeVector map_seq_to_graph(const std::string& sequence,
const ColoredCDBG<MyUnitigMap>& ccdbg)
const ColoredCDBG<MyUnitigMap>& ccdbg,
const int kmer)
{
// TODO map sequence to DBG and get full coordinates
std::vector<int> node_vector;
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20 changes: 18 additions & 2 deletions src/graph.h
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Original file line number Diff line number Diff line change
Expand Up @@ -110,6 +110,20 @@ class Graph {
const bool is_ref,
const std::unordered_set<std::string>& ref_set,
const std::string& path_dir);

GraphTuple update (const std::string& graphfile,
const std::string& coloursfile,
const std::string& infile1,
const std::string& infile2,
const std::vector<std::string>& stop_codons_for,
const std::vector<std::string>& stop_codons_rev,
const std::vector<std::string>& start_codons_for,
const std::vector<std::string>& start_codons_rev,
size_t num_threads,
bool is_ref,
const std::unordered_set<std::string>& ref_set,
const std::string& path_dir,
const bool write_graph);

// get graph object from serialised file
void in(const std::string& infile,
Expand Down Expand Up @@ -142,7 +156,8 @@ std::pair<std::map<size_t, std::string>, std::map<size_t, std::string>> findGene
const std::string& cluster_file,
const float& score_tolerance,
const std::string& tmp_dir,
const std::string& path_dir);
const std::string& path_dir,
const bool update);


std::pair<RefindMap, bool> refind_gene(const size_t& colour_ID,
Expand Down Expand Up @@ -236,7 +251,8 @@ std::unordered_map<size_t, std::unordered_set<size_t>> read_edge_file(const std:
void clear_graph(Graph& g);

ORFNodeVector map_seq_to_graph(const std::string& sequence,
const ColoredCDBG<MyUnitigMap>& ccdbg);
const ColoredCDBG<MyUnitigMap>& ccdbg,
const int kmer);

//void use_count(std::shared_ptr<Graph> sp);

Expand Down

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