Relax restriction on active Measures for annotations

Author: Daniel Cooke

src/core/csr/filters/conditional_threshold_filter.cpp

@@ -43,6 +43,7 @@ ConditionalThresholdVariantCallFilter::ConditionalThresholdVariantCallFilter(Fac
 , soft_ranges_ {}
 , chooser_ {std::move(chooser)}
 , unique_filter_keys_ {}
+, first_chooser_measure_index_ {}
 , num_chooser_measures_ {chooser_measures.size()}
 {
     measures_.shrink_to_fit();
@@ -60,6 +61,7 @@ ConditionalThresholdVariantCallFilter::ConditionalThresholdVariantCallFilter(Fac
         unique_filter_keys_.push_back(are_all_unique(filter_keys));
         k += p.soft.size();
     }
+    first_chooser_measure_index_ = i;
 }
 
 bool ConditionalThresholdVariantCallFilter::passes_all_hard_filters(const MeasureVector& measures) const
@@ -85,7 +87,9 @@ std::vector<std::string> ConditionalThresholdVariantCallFilter::get_failing_vcf_
 
 std::size_t ConditionalThresholdVariantCallFilter::choose_filter(const MeasureVector& measures) const
 {
-    const MeasureVector chooser_measures(std::prev(std::cend(measures), num_chooser_measures_), std::cend(measures));
+    const auto first_chooser_measure_itr = std::next(std::cbegin(measures), first_chooser_measure_index_);
+    const auto last_chooser_measure_itr = std::next(first_chooser_measure_itr, num_chooser_measures_);
+    const MeasureVector chooser_measures {first_chooser_measure_itr, last_chooser_measure_itr};
     return chooser_(chooser_measures);
 }
 

src/core/csr/filters/conditional_threshold_filter.hpp

@@ -47,7 +47,7 @@ class ConditionalThresholdVariantCallFilter : public ThresholdVariantCallFilter
     std::vector<MeasureIndexRange> hard_ranges_, soft_ranges_;
     std::function<std::size_t(std::vector<Measure::ResultType>)> chooser_;
     std::vector<bool> unique_filter_keys_;
-    std::size_t num_chooser_measures_;
+    std::size_t first_chooser_measure_index_, num_chooser_measures_;
 
     virtual bool passes_all_hard_filters(const MeasureVector& measures) const override;
     virtual bool passes_all_soft_filters(const MeasureVector& measures) const override;

src/core/csr/filters/random_forest_filter.cpp

@@ -129,17 +129,17 @@ RandomForestFilter::RandomForestFilter(FacetFactory facet_factory,
 , forest_paths_ {std::move(ranger_forests)}
 , chooser_ {std::move(chooser)}
 , forest_measure_info_ {}
+, first_chooser_measure_index_ {0}
 , num_chooser_measures_ {chooser_measures.size()}
 , options_ {std::move(options)}
 , threading_ {threading}
 , num_records_ {0}
 , data_buffer_ {}
 {
     forest_measure_info_.reserve(ranger_forests.size());
-    std::size_t index {0};
     for (const auto& measures : forest_measures) {
-        forest_measure_info_.push_back({index, measures.size()});
-        index += measures.size();
+        forest_measure_info_.push_back({first_chooser_measure_index_, measures.size()});
+        first_chooser_measure_index_ += measures.size();
     }
 }
 
@@ -185,7 +185,9 @@ Phred<double> RandomForestFilter::min_soft_call_quality() const noexcept
 
 std::int8_t RandomForestFilter::choose_forest(const MeasureVector& measures) const
 {
-    const MeasureVector chooser_measures(std::prev(std::cend(measures), num_chooser_measures_), std::cend(measures));
+    const auto first_chooser_measure_itr = std::next(std::cbegin(measures), first_chooser_measure_index_);
+    const auto last_chooser_measure_itr = std::next(first_chooser_measure_itr, num_chooser_measures_);
+    const MeasureVector chooser_measures {first_chooser_measure_itr, last_chooser_measure_itr};
     return chooser_(chooser_measures);
 }
 

src/core/csr/filters/random_forest_filter.hpp

@@ -81,7 +81,7 @@ class RandomForestFilter : public DoublePassVariantCallFilter
     std::vector<std::unique_ptr<ranger::Forest>> forests_;
     std::function<std::int8_t(std::vector<Measure::ResultType>)> chooser_;
     std::vector<ForestMeasureInfo> forest_measure_info_;
-    std::size_t num_chooser_measures_;
+    std::size_t first_chooser_measure_index_, num_chooser_measures_;
     Options options_;
     ConcurrencyPolicy threading_;
 

src/core/csr/filters/variant_call_filter.cpp

@@ -30,6 +30,7 @@
 #include "utils/parallel_transform.hpp"
 #include "io/variant/vcf_writer.hpp"
 #include "io/variant/vcf_spec.hpp"
+#include "core/csr/measures/measure_factory.hpp"
 
 namespace octopus { namespace csr {
 
@@ -66,7 +67,7 @@ VariantCallFilter::VariantCallFilter(FacetFactory facet_factory,
 : measures_ {std::move(measures)}
 , debug_log_ {logging::get_debug_log()}
 , facet_factory_ {std::move(facet_factory)}
-, facet_names_ {get_all_requirements(measures_)}
+, facet_names_ {}
 , output_config_ {output_config}
 , duplicate_measures_ {}
 , workers_ {get_pool_size(threading)}
@@ -83,9 +84,11 @@ VariantCallFilter::VariantCallFilter(FacetFactory facet_factory,
     logging::WarningLogger warn_log {};
     for (const auto& annotation : output_config_.annotations) {
         if (!contains(measures_, annotation)) {
-            stream(warn_log) << "The measure " << annotation << " is not active and will not be reported";
+            measures_.push_back(make_measure(annotation));
         }
     }
+    measures_.shrink_to_fit();
+    facet_names_ = get_all_requirements(measures_);
 }
 
 inline VcfHeader read_header(const VcfWriter& writer)