Misc improvements

leoisl · Jun 12, 2023 · 1c53eb7 · 1c53eb7
1 parent 27629b3
commit 1c53eb7
Show file tree

Hide file tree

Showing 5 changed files with 12 additions and 14 deletions.
diff --git a/include/fastaq.h b/include/fastaq.h
@@ -34,7 +34,7 @@ struct Fastaq {
         const uint_least16_t, const std::string header = "");
 
     void add_entry(
-        const std::string&, const std::string&, const std::string header = "");
+        const std::string&, const std::string&, const std::string &header = "");
 
     void clear();
 

diff --git a/include/utils.h b/include/utils.h
@@ -72,7 +72,7 @@ void define_clusters(
     MinimizerHitClusters& clusters_of_hits,
     const std::vector<uint32_t> &prg_min_path_lengths,
     const std::vector<std::string> &prg_names,
-    std::shared_ptr<MinimizerHits> minimizer_hits, const int max_diff,
+    std::shared_ptr<MinimizerHits> &minimizer_hits, const int max_diff,
     const float& fraction_kmers_required_for_cluster, const uint32_t min_cluster_size,
     const uint32_t expected_number_kmers_in_read_sketch,
     ClusterDefFile& cluster_def_file);
@@ -96,8 +96,8 @@ MinimizerHitClusters get_minimizer_hit_clusters(
     const Seq &seq,
     const std::vector<uint32_t> &prg_min_path_lengths,
     const std::vector<std::string> &prg_names,
-    std::shared_ptr<MinimizerHits> minimizer_hits,
-    std::shared_ptr<pangenome::Graph> pangraph, const int max_diff,
+    std::shared_ptr<MinimizerHits> &minimizer_hits,
+    const int max_diff,
     const float& fraction_kmers_required_for_cluster,
     ClusterDefFile &cluster_def_file,
     ClusterFilterFile &cluster_filter_file,
@@ -106,7 +106,7 @@ MinimizerHitClusters get_minimizer_hit_clusters(
     const uint32_t rng_seed);
 
 uint32_t pangraph_from_read_file(const SampleData& sample,
-    std::shared_ptr<pangenome::Graph> pangraph, Index &index,
+    std::shared_ptr<pangenome::Graph> &pangraph, Index &index,
     const int max_diff, const float& e_rate,
     const fs::path& sample_outdir, const uint32_t min_cluster_size = 10,
     const uint32_t genome_size = 5000000, const uint32_t max_covg = 300,

diff --git a/src/fastaq.cpp b/src/fastaq.cpp
@@ -81,7 +81,7 @@ void Fastaq::add_entry(const std::string& name, const std::string& sequence,
 }
 
 void Fastaq::add_entry(
-    const std::string& name, const std::string& sequence, const std::string header)
+    const std::string& name, const std::string& sequence, const std::string &header)
 {
     const bool fasta_entry_has_a_name = name.length() > 0;
     if (!fasta_entry_has_a_name) {

diff --git a/src/pangenome/pangraph.cpp b/src/pangenome/pangraph.cpp
@@ -148,7 +148,7 @@ std::vector<LocalNodePtr> pangenome::Graph::infer_node_vcf_reference_path(
     const auto& prg = *prg_ptr;
     if (vcf_refs.find(prg.name) != vcf_refs.end()) {
         const auto& vcf_reference_sequence = vcf_refs.at(prg.name);
-        const auto reference_path = prg.get_valid_vcf_reference(vcf_reference_sequence);
+        auto reference_path = prg.get_valid_vcf_reference(vcf_reference_sequence);
         if (!reference_path.empty())
             return reference_path;
     }

diff --git a/src/utils.cpp b/src/utils.cpp
@@ -186,8 +186,6 @@ void decide_if_add_cluster_or_not(
     if (!cluster_def_file.is_fake_file) {
 #pragma omp critical(cluster_def_file)
         {
-            // TODO: to create this file, we either need to know the PRG names without loading the PRGs
-            // TODO: or to output the id
             cluster_def_file << seq.name << "\t" << prg_names[(*mh_previous)->get_prg_id()] << "\t";
             if (cluster_should_be_accepted) {
                 cluster_def_file << "accepted\t";
@@ -221,7 +219,7 @@ void define_clusters(
     MinimizerHitClusters& clusters_of_hits, // Note: clusters_of_hits here is in insertion mode
     const std::vector<uint32_t> &prg_min_path_lengths,
     const std::vector<std::string> &prg_names,
-    std::shared_ptr<MinimizerHits> minimizer_hits, const int max_diff,
+    std::shared_ptr<MinimizerHits> &minimizer_hits, const int max_diff,
     const float& fraction_kmers_required_for_cluster, const uint32_t min_cluster_size,
     const uint32_t expected_number_kmers_in_read_sketch,
     ClusterDefFile& cluster_def_file)
@@ -480,8 +478,8 @@ MinimizerHitClusters get_minimizer_hit_clusters(
     const Seq &seq,
     const std::vector<uint32_t> &prg_min_path_lengths,
     const std::vector<std::string> &prg_names,
-    std::shared_ptr<MinimizerHits> minimizer_hits,
-    std::shared_ptr<pangenome::Graph> pangraph, const int max_diff,
+    std::shared_ptr<MinimizerHits> &minimizer_hits,
+    const int max_diff,
     const float& fraction_kmers_required_for_cluster,
     ClusterDefFile &cluster_def_file,
     ClusterFilterFile &cluster_filter_file,
@@ -513,7 +511,7 @@ MinimizerHitClusters get_minimizer_hit_clusters(
 
 // TODO: this should be in a constructor of pangenome::Graph or in a factory class
 uint32_t pangraph_from_read_file(const SampleData& sample,
-    std::shared_ptr<pangenome::Graph> pangraph, Index &index,
+    std::shared_ptr<pangenome::Graph> &pangraph, Index &index,
     const int max_diff, const float& e_rate,
     const fs::path& sample_outdir, const uint32_t min_cluster_size,
     const uint32_t genome_size, const uint32_t max_covg, uint32_t threads,
@@ -636,7 +634,7 @@ uint32_t pangraph_from_read_file(const SampleData& sample,
                 MinimizerHitClusters clusters_of_hits =
                     get_minimizer_hit_clusters(sample_name, sequence,
                         index.get_prg_min_path_lengths(), index.get_prg_names(),
-                        minimizer_hits, pangraph, max_diff,
+                        minimizer_hits, max_diff,
                         fraction_kmers_required_for_cluster, cluster_def_file,
                         cluster_filter_file, min_cluster_size,
                         expected_number_kmers_in_read_sketch, rng_seed);