Merge branch 'master' of gitlab.rlp.net:muellan/metacache

muellan · May 9, 2019 · 78b48a8 · 78b48a8
2 parents e213634 + 11ab3b9
commit 78b48a8
Show file tree

Hide file tree

Showing 5 changed files with 35 additions and 14 deletions.
diff --git a/src/classification.cpp b/src/classification.cpp
@@ -672,14 +672,14 @@ void map_queries_to_targets_default(
 
     if(opt.output.showTaxAbundances) {
         show_abundances(results.perTaxonOut, allTaxCounts,
-                        results.statistics.total(), opt.output);
+                        results.statistics, opt.output);
     }
 
     if(opt.output.showAbundanceEstimatesOnRank != taxonomy::rank::none) {
         estimate_abundance(db, allTaxCounts, opt.output.showAbundanceEstimatesOnRank);
 
         show_abundance_estimates(results.perTaxonOut, allTaxCounts,
-                                 results.statistics.total(), opt.output);
+                                 results.statistics, opt.output);
     }
 }
 
@@ -715,6 +715,10 @@ void map_candidates_to_targets(const vector<string>& queryHeaders,
                                const database& db, const query_options& opt,
                                classification_results& results)
 {
+    if(opt.output.mapViewMode != map_view_mode::none) {
+        show_query_mapping_header(results.perReadOut, opt.output);
+    }
+
     //taxon -> read count
     taxon_count_map allTaxCounts;
 
@@ -737,14 +741,14 @@ void map_candidates_to_targets(const vector<string>& queryHeaders,
 
     if(opt.output.showTaxAbundances) {
         show_abundances(results.perTaxonOut, allTaxCounts,
-                        results.statistics.total(), opt.output);
+                        results.statistics, opt.output);
     }
 
     if(opt.output.showAbundanceEstimatesOnRank != taxonomy::rank::none) {
         estimate_abundance(db, allTaxCounts, opt.output.showAbundanceEstimatesOnRank);
 
         show_abundance_estimates(results.perTaxonOut, allTaxCounts,
-                                 results.statistics.total(), opt.output);
+                                 results.statistics, opt.output);
     }
 }
 

diff --git a/src/printing.cpp b/src/printing.cpp
@@ -473,47 +473,62 @@ void show_matches_per_targets(std::ostream& os,
 //-------------------------------------------------------------------
 void show_abundance_table(std::ostream& os,
                           const taxon_count_map& allTaxCounts,
-                          const classification_statistics::count_t totalCount,
+                          const classification_statistics& statistics,
                           const classification_output_options&  opt)
 {
+    os << opt.format.comment
+       << "rank" << opt.format.rankSuffix
+       << "name" << opt.format.column
+       << "taxid" << opt.format.column
+       << "number of reads" << opt.format.column
+       << "abundance\n"; 
+
     for(const auto& tc : allTaxCounts) {
         if(tc.first) {
             os << tc.first->rank_name() << opt.format.rankSuffix
-               << tc.first->name();
+               << tc.first->name() << opt.format.column;
+            if(tc.first->rank() == taxon_rank::Sequence)
+               os << tc.first->parent_id();
+            else
+               os << tc.first->id();
         } else {
             os << "none";
         }
         os << opt.format.column << tc.second << opt.format.column
-           << (tc.second / double(totalCount) * 100) << "%\n";
+           << (tc.second / double(statistics.total()) * 100) << "%\n";
     }
+    os << "unclassified" << opt.format.column
+       << '0' << opt.format.column
+       << statistics.unassigned() << opt.format.column
+       << statistics.unclassified_rate() * 100 << "%\n";
 }
 
 
 
 //-------------------------------------------------------------------
 void show_abundances(std::ostream& os,
                      const taxon_count_map& allTaxCounts,
-                     const classification_statistics::count_t totalCount,
+                     const classification_statistics& statistics,
                      const classification_output_options& opt)
 {
     os << opt.format.comment
-        << "query summary: number of queries mapped per taxon\n";
-    show_abundance_table(os, allTaxCounts, totalCount, opt);
+       << "query summary: number of queries mapped per taxon\n";
+    show_abundance_table(os, allTaxCounts, statistics, opt);
 }
 
 
 
 //-------------------------------------------------------------------
 void show_abundance_estimates(std::ostream& os,
                               const taxon_count_map& allTaxCounts,
-                              const classification_statistics::count_t totalCount,
+                              const classification_statistics& statistics,
                               const classification_output_options& opt)
 {
     os << opt.format.comment
        << "estimated abundance (number of queries) per "
        << taxonomy::rank_name(opt.showAbundanceEstimatesOnRank) << "\n";
 
-    show_abundance_table(os, allTaxCounts, totalCount, opt);
+    show_abundance_table(os, allTaxCounts, statistics, opt);
 }
 
 

diff --git a/src/printing.h b/src/printing.h
@@ -115,7 +115,7 @@ void show_matches_per_targets(std::ostream&,
  *****************************************************************************/
 void show_abundances(std::ostream&,
                      const taxon_count_map&,
-                     const classification_statistics::count_t,
+                     const classification_statistics&,
                      const classification_output_options&);
 
 
@@ -127,7 +127,7 @@ void show_abundances(std::ostream&,
  *****************************************************************************/
 void show_abundance_estimates(std::ostream&,
                               const taxon_count_map&,
-                              const classification_statistics::count_t,
+                              const classification_statistics&,
                               const classification_output_options&);
 
 

diff --git a/src/taxonomy.h b/src/taxonomy.h
@@ -305,6 +305,8 @@ class taxonomy
             return taxonomy::rank_name(rank_);
         }
 
+        taxon_id parent_id() const noexcept { return parent_; }
+
         bool has_parent() const noexcept {
             return parent_ != taxonomy::none_id();
         }

diff --git a/test/data.tar.gz b/test/data.tar.gz