q_collapsed_metric.h

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#pragma once
#include "interop/constants/enums.h"
#include "interop/model/metric_base/base_cycle_metric.h"
#include "interop/model/metric_base/metric_set.h"
#include "interop/io/layout/base_metric.h"
#include "interop/io/format/generic_layout.h"
#include "interop/model/metrics/q_metric.h"

namespace illumina { namespace interop { namespace model { namespace metrics {

    class q_collapsed_header : public q_score_header
    {
    public:
        q_collapsed_header() : m_record_size(0) {}
        q_collapsed_header(const qscore_bin_vector_type& bins) : q_score_header(bins), m_record_size(0){}
        static q_collapsed_header default_header()
        {
            return q_collapsed_header();
        }
        void clear()
        {
            m_record_size=0;
            q_score_header::clear();
        }
    private:
        ::uint32_t m_record_size; // Hack to support this format
    private:
        template<class MetricType, int Version>
        friend struct io::generic_layout;
    };
    class q_collapsed_metric : public metric_base::base_cycle_metric
    {
    public:
        enum{
            TYPE=constants::QCollapsed,
            LATEST_VERSION=6
        };
        typedef ::uint64_t ulong_t;
        typedef q_collapsed_header header_type;
    public:
        q_collapsed_metric() :
                metric_base::base_cycle_metric(0,0,0),
                m_q20(0),
                m_q30(0),
                m_total(0),
                m_median_qscore(0),
                m_cumulative_q20(0),
                m_cumulative_q30(0),
                m_cumulative_total(0) {}
        q_collapsed_metric(const header_type&) :
                metric_base::base_cycle_metric(0,0,0),
                m_q20(0),
                m_q30(0),
                m_total(0),
                m_median_qscore(0),
                m_cumulative_q20(0),
                m_cumulative_q30(0),
                m_cumulative_total(0) {}
        q_collapsed_metric(const uint_t lane,
                           const uint_t tile,
                           const uint_t cycle,
                           const uint_t q20,
                           const uint_t q30,
                           const uint_t total,
                           const uint_t median_qscore) :
                metric_base::base_cycle_metric(lane, tile, cycle),
                m_q20(q20),
                m_q30(q30),
                m_total(total),
                m_median_qscore(median_qscore),
                m_cumulative_q20(0),
                m_cumulative_q30(0),
                m_cumulative_total(0)

        {
        }

    public:
        uint_t q20()const
        {
            return m_q20;
        }
        uint_t q30()const
        {
            return m_q30;
        }
        uint_t total()const
        {
            return m_total;
        }
        uint_t median_qscore()const
        {
            return m_median_qscore;
        }
        float median_qscore_flt()const
        {
            if (m_median_qscore == std::numeric_limits<uint_t>::max() || m_median_qscore == 0)
                return std::numeric_limits<float>::quiet_NaN();
            return static_cast<float>(m_median_qscore);
        }
        ulong_t cumulative_q20()const
        {
            return m_cumulative_q20;
        }
        ulong_t cumulative_q30()const
        {
            return m_cumulative_q30;
        }
        ulong_t cumulative_total()const
        {
            return m_cumulative_total;
        }
        float percent_over_q20()const
        {
            return 100.0f * m_q20 / m_total;
        }
        float percent_over_q30()const
        {
            return 100.0f * m_q30 / m_total;
        }
        float cumulative_percent_over_q20()const
        {
            return 100.0f * m_cumulative_q20 / m_cumulative_total;
        }
        float cumulative_percent_over_q30()const
        {
            return 100.0f * m_cumulative_q30 / m_cumulative_total;
        }
        void accumulate(const q_collapsed_metric& metric)
        {
            m_cumulative_q20 = m_q20;
            m_cumulative_q30 = m_q30;
            m_cumulative_total = m_total;
            if(&metric != this) {
                m_cumulative_q20 += metric.m_cumulative_q20;
                m_cumulative_q30 += metric.m_cumulative_q30;
                m_cumulative_total += metric.m_cumulative_total;
            }
        }

    public:
        static const char* prefix(){return "Q";}
        static const char* suffix(){return "2030";}

    private:
        uint_t m_q20;
        uint_t m_q30;
        uint_t m_total;
        uint_t m_median_qscore;
        ulong_t m_cumulative_q20;
        ulong_t m_cumulative_q30;
        ulong_t m_cumulative_total;

    private:
        template<class MetricType, int Version>
        friend struct io::generic_layout;
    };


}}}}