Add command line option "--aggregate-annotations"

Author: Daniel Cooke

scripts/train_random_forest.py

@@ -226,6 +226,7 @@ def run_octopus(octopus, reference, reads, regions, threads, output,
                   ['-t', str(regions), \
                    '--ignore-unmapped-contigs', \
                    '--disable-call-filtering', \
+                   '--aggregate-annotations', \
                    '--threads', str(threads), \
                    '-o', str(output)]
     if annotations == "all":

src/config/option_collation.cpp

@@ -2280,6 +2280,11 @@ auto get_caller_type(const OptionMap& options, const std::vector<SampleName>& sa
     return get_caller_type(options, samples, get_pedigree(options, samples));
 }
 
+bool aggregate_annotations(const OptionMap& options)
+{
+    return options.at("aggregate-annotations").as<bool>();
+}
+
 std::unique_ptr<VariantCallFilterFactory>
 make_call_filter_factory(const ReferenceGenome& reference, ReadPipe& read_pipe, const OptionMap& options,
                          boost::optional<fs::path> temp_directory)
@@ -2350,6 +2355,7 @@ make_call_filter_factory(const ReferenceGenome& reference, ReadPipe& read_pipe,
                 auto annotations = get_requested_measure_annotations(options);
                 output_options.annotations.insert(std::begin(annotations), std::end(annotations));
             }
+            output_options.aggregate_allele_annotations = aggregate_annotations(options);
             result->set_output_options(std::move(output_options));
         }
     }

src/config/option_parser.cpp

@@ -748,6 +748,10 @@ OptionMap parse_options(const int argc, const char** argv)
      po::value<std::vector<std::string>>()->multitoken()->implicit_value(std::vector<std::string> {"active"}, "active")->composing(),
      "Annotations to write to final VCF")
 
+     ("aggregate-annotations",
+     po::bool_switch()->default_value(false),
+     "Aggregate all multi-value annotations into a single value")
+    
     ("filter-vcf",
      po::value<fs::path>(),
      "Filter the given Octopus VCF without calling")

src/core/csr/filters/training_filter_factory.cpp

@@ -59,9 +59,7 @@ std::unique_ptr<VariantCallFilter> TrainingFilterFactory::do_make(FacetFactory f
     output_config.annotations.clear();
     output_config.annotations.reserve(measures_.size());
     for (const auto& measure : measures_) output_config.annotations.insert(measure.name());
-    output_config.clear_info = true;
     output_config.clear_existing_filters = true;
-    output_config.aggregate_allele_annotations = true;
     return std::make_unique<PassingVariantCallFilter>(std::move(facet_factory), std::move(measures_),
                                                       output_config, threading, progress);
 }