Add AssignedDepth Measure

Author: Daniel Cooke

src/CMakeLists.txt

@@ -383,6 +383,8 @@ set(CORE_SOURCES
     core/csr/measures/base_mismatch_count.cpp
     core/csr/measures/base_mismatch_fraction.hpp
     core/csr/measures/base_mismatch_fraction.cpp
+    core/csr/measures/assigned_depth.hpp
+    core/csr/measures/assigned_depth.cpp
 
     core/models/haplotype_likelihood_array.hpp
     core/models/haplotype_likelihood_array.cpp

src/core/csr/measures/assigned_depth.cpp

@@ -0,0 +1,73 @@
+// Copyright (c) 2015-2019 Daniel Cooke
+// Use of this source code is governed by the MIT license that can be found in the LICENSE file.
+
+#include "assigned_depth.hpp"
+
+#include <numeric>
+#include <algorithm>
+#include <iterator>
+
+#include <boost/variant.hpp>
+
+#include "core/types/allele.hpp"
+#include "io/variant/vcf_record.hpp"
+#include "utils/genotype_reader.hpp"
+#include "../facets/samples.hpp"
+#include "../facets/read_assignments.hpp"
+
+namespace octopus { namespace csr {
+
+const std::string AssignedDepth::name_ = "ADP";
+
+std::unique_ptr<Measure> AssignedDepth::do_clone() const
+{
+    return std::make_unique<AssignedDepth>(*this);
+}
+
+namespace {
+
+template <typename Map>
+std::size_t sum_value_sizes(const Map& map) noexcept
+{
+    return std::accumulate(std::cbegin(map), std::cend(map), std::size_t {0},
+                           [] (auto curr, const auto& p) noexcept { return curr + p.second.size(); });
+}
+    
+} // namespace
+
+Measure::ResultType AssignedDepth::do_evaluate(const VcfRecord& call, const FacetMap& facets) const
+{
+    const auto& samples = get_value<Samples>(facets.at("Samples"));
+    const auto& assignments = get_value<ReadAssignments>(facets.at("ReadAssignments"));
+    std::vector<std::size_t> result {};
+    result.reserve(samples.size());
+    for (const auto& sample : samples) {
+        const auto alleles = get_called_alleles(call, sample).first;
+        const auto allele_support = compute_allele_support(alleles, assignments, sample);
+        result.push_back(sum_value_sizes(allele_support));
+    }
+    return result;
+}
+
+Measure::ResultCardinality AssignedDepth::do_cardinality() const noexcept
+{
+    return ResultCardinality::num_samples;
+}
+
+const std::string& AssignedDepth::do_name() const
+{
+    return name_;
+}
+
+std::string AssignedDepth::do_describe() const
+{
+    return "Number of reads overlapping the position that could be assigned to an allele";
+}
+
+std::vector<std::string> AssignedDepth::do_requirements() const
+{
+    return {"Samples", "ReadAssignments"};
+}
+    
+} // namespace csr
+} // namespace octopus

src/core/csr/measures/assigned_depth.hpp

@@ -0,0 +1,32 @@
+// Copyright (c) 2015-2019 Daniel Cooke
+// Use of this source code is governed by the MIT license that can be found in the LICENSE file.
+
+#ifndef assigned_depth_hpp
+#define assigned_depth_hpp
+
+#include <string>
+#include <vector>
+
+#include "measure.hpp"
+
+namespace octopus {
+
+class VcfRecord;
+
+namespace csr {
+
+class AssignedDepth : public Measure
+{
+    const static std::string name_;
+    std::unique_ptr<Measure> do_clone() const override;
+    ResultType do_evaluate(const VcfRecord& call, const FacetMap& facets) const override;
+    ResultCardinality do_cardinality() const noexcept override;
+    const std::string& do_name() const override;
+    std::string do_describe() const override;
+    std::vector<std::string> do_requirements() const override;
+};
+
+} // namespace csr
+} // namespace octopus
+
+#endif

src/core/csr/measures/measure_factory.cpp

@@ -60,6 +60,7 @@ void init(MeasureMakerMap& measure_makers)
     measure_makers[name<VariantLength>()]               = [] () { return make_wrapped_measure<VariantLength>(); };
     measure_makers[name<BaseMismatchCount>()]           = [] () { return make_wrapped_measure<BaseMismatchCount>(); };
     measure_makers[name<BaseMismatchFraction>()]        = [] () { return make_wrapped_measure<BaseMismatchFraction>(); };
+    measure_makers[name<AssignedDepth>()]               = [] () { return make_wrapped_measure<AssignedDepth>(); };
 }
 
 class BadParameterList : public UserError

src/core/csr/measures/measures_fwd.hpp

@@ -47,5 +47,6 @@
 #include "core/csr/measures/variant_length.hpp"
 #include "core/csr/measures/base_mismatch_count.hpp"
 #include "core/csr/measures/base_mismatch_fraction.hpp"
+#include "core/csr/measures/assigned_depth.hpp"
 
 #endif