Merge pull request #351 from leoisl/min_gene_coverage_proportion

feat: adds parameter --min-gene-coverage-proportion to pandora map, compare and discover

include/compare_main.h

@@ -45,6 +45,7 @@ struct CompareOptions {
     float min_absolute_gene_coverage { 3.0 };
     float min_relative_gene_coverage { 0.05 };
     float max_relative_gene_coverage { 100 };
+    float min_gene_coverage_proportion { 0.8 };
     bool binomial { false };
     bool do_not_auto_update_params { false };
     uint32_t max_covg { 300 };

include/denovo_discovery/discover_main.h

@@ -34,7 +34,8 @@ struct DiscoverOptions {
     uint32_t max_covg { 600 };
     float min_absolute_gene_coverage { 3.0 };
     float min_relative_gene_coverage { 0.05 };
-    float max_relative_gene_coverage { 10 };
+    float max_relative_gene_coverage { 100 };
+    float min_gene_coverage_proportion { 0.8 };
     uint32_t min_cluster_size { 10 };
     uint32_t max_num_kmers_to_avg { 100 };
     bool keep_extra_debugging_files { false };

include/localPRG.h

@@ -157,7 +157,7 @@ class LocalPRG {
         std::vector<LocalNodePtr>&, const uint32_t, const bool, const uint32_t,
         const uint32_t& max_num_kmers_to_average, const uint32_t& sample_id,
         float min_absolute_gene_coverage, float min_relative_gene_coverage,
-        float max_relative_gene_coverage) const;
+        float max_relative_gene_coverage, float min_gene_coverage_proportion) const;
     std::vector<LocalNodePtr> get_valid_vcf_reference(const std::string&) const;
 
     void add_variants_to_vcf(VCF&, pangenome::NodePtr, const std::string&,

include/map_main.h

@@ -49,6 +49,7 @@ struct MapOptions {
     float min_absolute_gene_coverage { 3.0 };
     float min_relative_gene_coverage { 0.05 };
     float max_relative_gene_coverage { 100 };
+    float min_gene_coverage_proportion { 0.8 };
     bool genotype { false };
     bool local_genotype { false };
     bool snps_only { false };

src/compare_main.cpp

@@ -150,6 +150,18 @@ void setup_compare_subcommand(CLI::App& app)
         ->type_name("FLOAT")
         ->group("Filtering");
 
+    compare_subcmd
+        ->add_option(
+            "--min-gene-coverage-proportion", opt->min_gene_coverage_proportion,
+            "Minimum gene coverage proportion to keep a gene. "
+            "Given the coverage on the kmers of the maximum likelihood path of a gene, we compute "
+            "the number of bases that have at least one read covering it. "
+            "If the proportion of such bases is larger than the value in this "
+            "parameter, the gene is kept. Otherwise, the gene is filtered out.")
+        ->capture_default_str()
+        ->type_name("FLOAT")
+        ->group("Filtering");
+
     description = "Add extra step to carefully genotype sites.";
     auto* gt_opt = compare_subcmd->add_flag("--genotype", opt->genotype, description)
                        ->group("Consensus/Variant Calling");
@@ -335,7 +347,7 @@ int pandora_compare(CompareOptions& opt)
             local_prg->add_consensus_path_to_fastaq(consensus_fq, c->second, kmp, lmp,
                 index.get_window_size(), opt.binomial, covg, opt.max_num_kmers_to_avg, 0,
                 opt.min_absolute_gene_coverage, opt.min_relative_gene_coverage,
-                opt.max_relative_gene_coverage);
+                opt.max_relative_gene_coverage, opt.min_gene_coverage_proportion);
 
             if (kmp.empty()) {
                 c = pangraph_sample->remove_node(c->second);

src/denovo_discovery/discover_main.cpp

@@ -158,6 +158,18 @@ void setup_discover_subcommand(CLI::App& app)
         ->type_name("FLOAT")
         ->group("Filtering");
 
+    discover_subcmd
+        ->add_option(
+            "--min-gene-coverage-proportion", opt->min_gene_coverage_proportion,
+            "Minimum gene coverage proportion to keep a gene. "
+            "Given the coverage on the kmers of the maximum likelihood path of a gene, we compute "
+            "the number of bases that have at least one read covering it. "
+            "If the proportion of such bases is larger than the value in this "
+            "parameter, the gene is kept. Otherwise, the gene is filtered out.")
+        ->capture_default_str()
+        ->type_name("FLOAT")
+        ->group("Filtering");
+
     description
         = "Minimum size of a cluster of hits between a read and a loci to consider "
           "the loci present";
@@ -293,7 +305,7 @@ void pandora_discover_core(const SampleData& sample, Index &index, DiscoverOptio
              pangraph_node, kmp, lmp, index.get_window_size(), opt.binomial, covg,
              opt.max_num_kmers_to_avg, 0,
              opt.min_absolute_gene_coverage, opt.min_relative_gene_coverage,
-             opt.max_relative_gene_coverage);
+             opt.max_relative_gene_coverage, opt.min_gene_coverage_proportion);
 
         if (kmp.empty()) {
             // mark the node as to remove

src/localPRG.cpp

@@ -1699,7 +1699,7 @@ void LocalPRG::add_consensus_path_to_fastaq(Fastaq& output_fq, pangenome::NodePt
     const bool bin, const uint32_t global_covg,
     const uint32_t& max_num_kmers_to_average, const uint32_t& sample_id,
     float min_absolute_gene_coverage, float min_relative_gene_coverage,
-    float max_relative_gene_coverage) const
+    float max_relative_gene_coverage, float min_gene_coverage_proportion) const
 {
     if (pnode->covg == 0) {
         BOOST_LOG_TRIVIAL(warning) << "Node " << pnode->get_name() << " has no reads";
@@ -1719,10 +1719,27 @@ void LocalPRG::add_consensus_path_to_fastaq(Fastaq& output_fq, pangenome::NodePt
 
     std::vector<uint32_t> covgs
         = get_covgs_along_localnode_path(pnode, lmp, kmp, sample_id);
+
     auto mean_covg = Maths::mean(covgs.begin(), covgs.end());
     BOOST_LOG_TRIVIAL(debug) << "Found global coverage " << global_covg
                              << " and path  mean " << mean_covg;
 
+    // apply the coverage proportion filter
+    uint32_t amount_of_bases_with_coverage = std::count_if(covgs.begin(), covgs.end(),
+                                                    [](uint32_t covg){return covg > 0;});
+    float coverage_proportion = ((float)amount_of_bases_with_coverage) / covgs.size();
+    const bool coverage_proportion_is_too_low = coverage_proportion < min_gene_coverage_proportion;
+    if (coverage_proportion_is_too_low) {
+        BOOST_LOG_TRIVIAL(warning)
+            << "Filtering out gene " << name << " due to "
+            << "coverage proportion (" << coverage_proportion << ") "
+            << "being too low, less than the --min-gene-coverage-proportion parameter ("
+            << min_gene_coverage_proportion << ")";
+        kmp.clear();
+        return;
+    }
+
+    // apply the min/max coverage filters
     if (mean_covg < min_absolute_gene_coverage) {
         BOOST_LOG_TRIVIAL(warning)
             << "Filtering out gene " << name << " due to "

src/map_main.cpp

@@ -164,6 +164,18 @@ void setup_map_subcommand(CLI::App& app)
         ->type_name("FLOAT")
         ->group("Filtering");
 
+    map_subcmd
+        ->add_option(
+            "--min-gene-coverage-proportion", opt->min_gene_coverage_proportion,
+            "Minimum gene coverage proportion to keep a gene. "
+            "Given the coverage on the kmers of the maximum likelihood path of a gene, we compute "
+            "the number of bases that have at least one read covering it. "
+            "If the proportion of such bases is larger than the value in this "
+            "parameter, the gene is kept. Otherwise, the gene is filtered out.")
+        ->capture_default_str()
+        ->type_name("FLOAT")
+        ->group("Filtering");
+
     description = "Add extra step to carefully genotype sites.";
     auto* gt_opt = map_subcmd->add_flag("--genotype", opt->genotype, description)
                        ->group("Consensus/Variant Calling");
@@ -377,7 +389,7 @@ int pandora_map(MapOptions& opt)
         prg->add_consensus_path_to_fastaq(consensus_fq, pangraph_node, kmp, lmp,
             index.get_window_size(), opt.binomial, covg, opt.max_num_kmers_to_avg, 0,
             opt.min_absolute_gene_coverage, opt.min_relative_gene_coverage,
-            opt.max_relative_gene_coverage);
+            opt.max_relative_gene_coverage, opt.min_gene_coverage_proportion);
 
         if (kmp.empty()) {
 #pragma omp critical(nodes_to_remove)