fix: solving issues with rebasing on dev

include/localPRG.h

@@ -157,8 +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, float min_gene_coverage_proportion) const;
-        float max_relative_gene_coverage, bool no_gene_coverage_filtering) const;
+        float max_relative_gene_coverage, float min_gene_coverage_proportion, bool no_gene_coverage_filtering) const;
     std::vector<LocalNodePtr> get_valid_vcf_reference(const std::string&) const;
 
     void add_variants_to_vcf(VCF&, pangenome::NodePtr, const std::string&,

src/compare_main.cpp

@@ -150,13 +150,6 @@ void setup_compare_subcommand(CLI::App& app)
         ->type_name("FLOAT")
         ->group("Filtering");
 
-    compare_subcmd
-        ->add_flag(
-            "--no-gene-coverage-filtering", opt->no_gene_coverage_filtering,
-            "Do not filter genes based on their coverage, effectively ignoring the three "
-            "previous params. This is useful if you are not using read datasets.")
-        ->group("Filtering");
-
     compare_subcmd
         ->add_option(
             "--min-gene-coverage-proportion", opt->min_gene_coverage_proportion,
@@ -169,6 +162,14 @@ void setup_compare_subcommand(CLI::App& app)
         ->type_name("FLOAT")
         ->group("Filtering");
 
+    compare_subcmd
+        ->add_flag(
+            "--no-gene-coverage-filtering", opt->no_gene_coverage_filtering,
+            "Do not filter genes based on their coverage, effectively ignoring params "
+            "--min-abs-gene-coverage, --min-rel-gene-coverage, --max-rel-gene-coverage and --min-gene-coverage-proportion. "
+            "This is useful if you are not using read datasets.")
+        ->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");
@@ -354,8 +355,8 @@ 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.min_gene_coverage_proportion);
-                opt.max_relative_gene_coverage, opt.no_gene_coverage_filtering);
+                opt.max_relative_gene_coverage, opt.min_gene_coverage_proportion,
+                opt.no_gene_coverage_filtering);
 
             if (kmp.empty()) {
                 c = pangraph_sample->remove_node(c->second);

src/denovo_discovery/discover_main.cpp

@@ -158,13 +158,6 @@ void setup_discover_subcommand(CLI::App& app)
         ->type_name("FLOAT")
         ->group("Filtering");
 
-    discover_subcmd
-        ->add_flag(
-            "--no-gene-coverage-filtering", opt->no_gene_coverage_filtering,
-            "Do not filter genes based on their coverage, effectively ignoring the three "
-            "previous params. This is useful if you are not using read datasets.")
-        ->group("Filtering");
-
     discover_subcmd
         ->add_option(
             "--min-gene-coverage-proportion", opt->min_gene_coverage_proportion,
@@ -177,6 +170,14 @@ void setup_discover_subcommand(CLI::App& app)
         ->type_name("FLOAT")
         ->group("Filtering");
 
+    discover_subcmd
+        ->add_flag(
+            "--no-gene-coverage-filtering", opt->no_gene_coverage_filtering,
+            "Do not filter genes based on their coverage, effectively ignoring params "
+            "--min-abs-gene-coverage, --min-rel-gene-coverage, --max-rel-gene-coverage and --min-gene-coverage-proportion. "
+            "This is useful if you are not using read datasets.")
+        ->group("Filtering");
+
     description
         = "Minimum size of a cluster of hits between a read and a loci to consider "
           "the loci present";
@@ -312,8 +313,8 @@ 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.min_gene_coverage_proportion);
-             opt.max_relative_gene_coverage, opt.no_gene_coverage_filtering);
+             opt.max_relative_gene_coverage, opt.min_gene_coverage_proportion,
+             opt.no_gene_coverage_filtering);
 
         if (kmp.empty()) {
             // mark the node as to remove

src/localPRG.cpp

@@ -1699,8 +1699,8 @@ 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, float min_gene_coverage_proportion) const
-    float max_relative_gene_coverage, bool no_gene_coverage_filtering) const
+    float max_relative_gene_coverage, float min_gene_coverage_proportion,
+    bool no_gene_coverage_filtering) const
 {
     if (pnode->covg == 0) {
         BOOST_LOG_TRIVIAL(warning) << "Node " << pnode->get_name() << " has no reads";
@@ -1725,62 +1725,59 @@ void LocalPRG::add_consensus_path_to_fastaq(Fastaq& output_fq, pangenome::NodePt
     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 "
     if (!no_gene_coverage_filtering) {
-        if (mean_covg < min_absolute_gene_coverage) {
+        // 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 "
-            << "mean coverage (" << mean_covg << ") "
-            << "being too low, less than the --min-abs-gene-coverage parameter (" << min_absolute_gene_coverage << ")";
-        kmp.clear();
-        return;
-    }
+                << "coverage proportion (" << coverage_proportion << ") "
+                << "being too low, less than the --min-gene-coverage-proportion parameter ("
+                << min_gene_coverage_proportion << ")";
+            kmp.clear();
+            return;
+        }
 
-    if (mean_covg < min_relative_gene_coverage*global_covg) {
-        BOOST_LOG_TRIVIAL(warning)
-            << "Filtering out gene " << name << " due to "
-            << "mean coverage (" << mean_covg << ") "
-            << "being too low, less than the "
-            << "--min-rel-gene-coverage * global coverage ("
-            << min_relative_gene_coverage << " * " << global_covg << " = "
-            << min_relative_gene_coverage * global_covg << "). "
-            << "Is global coverage very different from the expected (too low/high)? "
-            << "Try setting a better genome length (see --genome-size param).";
-        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 "
+                << "mean coverage (" << mean_covg << ") "
+                << "being too low, less than the --min-abs-gene-coverage parameter (" << min_absolute_gene_coverage << ")";
+            kmp.clear();
+            return;
+        }
 
-    if (mean_covg > max_relative_gene_coverage*global_covg) {
-        BOOST_LOG_TRIVIAL(warning)
-            << "Filtering out gene " << name << " due to "
-            << "mean coverage (" << mean_covg << ") "
-            << "being too high, larger than the "
-            << "--max-rel-gene-coverage * global coverage ("
-            << max_relative_gene_coverage << " * " << global_covg << " = "
-            << max_relative_gene_coverage * global_covg << "). "
-            << "Is global coverage very different from the expected (too low/high)? "
-            << "Try setting a better genome length (see --genome-size param).";
+        if (mean_covg < min_relative_gene_coverage*global_covg) {
+            BOOST_LOG_TRIVIAL(warning)
+                << "Filtering out gene " << name << " due to "
+                << "mean coverage (" << mean_covg << ") "
+                << "being too low, less than the "
+                << "--min-rel-gene-coverage * global coverage ("
+                << min_relative_gene_coverage << " * " << global_covg << " = "
+                << min_relative_gene_coverage * global_covg << "). "
+                << "Is global coverage very different from the expected (too low/high)? "
+                << "Try setting a better genome length (see --genome-size param).";
             kmp.clear();
             return;
         }
+
+        if (mean_covg > max_relative_gene_coverage*global_covg) {
+            BOOST_LOG_TRIVIAL(warning)
+                << "Filtering out gene " << name << " due to "
+                << "mean coverage (" << mean_covg << ") "
+                << "being too high, larger than the "
+                << "--max-rel-gene-coverage * global coverage ("
+                << max_relative_gene_coverage << " * " << global_covg << " = "
+                << max_relative_gene_coverage * global_covg << "). "
+                << "Is global coverage very different from the expected (too low/high)? "
+                << "Try setting a better genome length (see --genome-size param).";
+                kmp.clear();
+                return;
+        }
     }
 
     std::string fq_name = pnode->get_name();

src/map_main.cpp

@@ -164,13 +164,6 @@ void setup_map_subcommand(CLI::App& app)
         ->type_name("FLOAT")
         ->group("Filtering");
 
-    map_subcmd
-        ->add_flag(
-            "--no-gene-coverage-filtering", opt->no_gene_coverage_filtering,
-            "Do not filter genes based on their coverage, effectively ignoring the three "
-            "previous params. This is useful if you are not using read datasets.")
-        ->group("Filtering");
-
     map_subcmd
         ->add_option(
             "--min-gene-coverage-proportion", opt->min_gene_coverage_proportion,
@@ -183,6 +176,14 @@ void setup_map_subcommand(CLI::App& app)
         ->type_name("FLOAT")
         ->group("Filtering");
 
+    map_subcmd
+        ->add_flag(
+            "--no-gene-coverage-filtering", opt->no_gene_coverage_filtering,
+            "Do not filter genes based on their coverage, effectively ignoring params "
+            "--min-abs-gene-coverage, --min-rel-gene-coverage, --max-rel-gene-coverage and --min-gene-coverage-proportion. "
+            "This is useful if you are not using read datasets.")
+        ->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");
@@ -396,8 +397,8 @@ 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.no_gene_coverage_filtering);
-            opt.max_relative_gene_coverage, opt.min_gene_coverage_proportion);
+            opt.max_relative_gene_coverage, opt.min_gene_coverage_proportion,
+            opt.no_gene_coverage_filtering);
 
         if (kmp.empty()) {
 #pragma omp critical(nodes_to_remove)