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#include "deepvariant/channels/avg_base_quality_channel.h"

#include <cstdint>
#include <string>
#include <vector>

#include "deepvariant/protos/deepvariant.pb.h"
#include "absl/log/log.h"

namespace learning {
namespace genomics {
namespace deepvariant {

void AvgBaseQualityChannel::FillReadLevelData(
    const Read& read, const DeepVariantCall& dv_call,
    const std::vector<std::string>& alt_alleles,
    std::vector<unsigned char>& read_level_data) {
  read_level_data = std::vector<unsigned char>(
      1, ScaleColor(AvgBaseQuality(read), kMaxAvgBaseQuality));
}
void AvgBaseQualityChannel::FillRefData(const std::string& ref_bases,
                                        std::vector<unsigned char>& ref_data) {
  ref_data = std::vector<unsigned char>(
      width_, static_cast<std::uint8_t>(kMaxPixelValueAsFloat));
}

// Scales an input value to pixel range 0-254.
std::uint8_t AvgBaseQualityChannel::ScaleColor(int value, float max_val) const {
  if (static_cast<float>(value) > max_val) {
    value = max_val;
  }
  return static_cast<int>(kMaxPixelValueAsFloat *
                          (static_cast<float>(value) / max_val));
}

// Average Base Quality: Averages base quality over length of read.
int AvgBaseQualityChannel::AvgBaseQuality(const Read& read) {
  int base_qual_sum = 0;
  for (const auto& base_qual : read.aligned_quality()) {
    base_qual_sum += base_qual;
    // Base qualities range between 0 and 93
    if (base_qual < 0 || base_qual > 93) {
      LOG(FATAL) << "Encountered base quality outside of bounds (0,93):"
                 << base_qual << ", read=" << read.fragment_name();
    }
  }
  float avg_base_qual = (static_cast<float>(base_qual_sum) /
                         static_cast<float>(read.aligned_quality().size()));
  return static_cast<int>(avg_base_qual);
}
}  // namespace deepvariant
}  // namespace genomics
}  // namespace learning