/*

 * Copyright 2018 Google LLC.

 *

 * Redistribution and use in source and binary forms, with or without

 * modification, are permitted provided that the following conditions

 * are met:

 *

 * 1. Redistributions of source code must retain the above copyright notice,

 *    this list of conditions and the following disclaimer.

 *

 * 2. Redistributions in binary form must reproduce the above copyright

 *    notice, this list of conditions and the following disclaimer in the

 *    documentation and/or other materials provided with the distribution.

 *

 * 3. Neither the name of the copyright holder nor the names of its

 *    contributors may be used to endorse or promote products derived from this

 *    software without specific prior written permission.

 *

 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"

 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE

 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE

 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE

 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR

 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF

 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS

 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN

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 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE

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 */

#include <algorithm>

#include <cmath>

#include "absl/log/check.h"

#include "third_party/nucleus/util/math.h"

namespace nucleus {

double PhredToPError(const int phred) {

  CHECK_GE(phred, 0);

  return std::pow(10.0, -static_cast<double>(phred) / 10.0);

}

double PhredToLog10PError(const int phred) {

  CHECK_GE(phred, 0);

  return -static_cast<double>(phred) / 10;

}

double PErrorToPhred(const double perror) {

  CHECK_GT(perror, 0);

  CHECK_LE(perror, 1);

  return Log10PErrorToPhred(PErrorToLog10PError(perror));

}

int PErrorToRoundedPhred(const double perror) {

  CHECK_GT(perror, 0);

  CHECK_LE(perror, 1);

  return Log10PErrorToRoundedPhred(PErrorToLog10PError(perror));

}

double PErrorToLog10PError(const double perror) {

  CHECK_GT(perror, 0);

  CHECK_LE(perror, 1);

  return std::log10(perror);

}

double Log10PErrorToPhred(const double log10_perror) {

  CHECK_LE(log10_perror, 0);

  return -10 * log10_perror;

}

int Log10PErrorToRoundedPhred(const double log10_perror) {

  return std::abs(std::round(Log10PErrorToPhred(log10_perror)));

}

double Log10PTrueToPhred(const double log10_ptrue,

                         const double value_if_not_finite) {

  const double ptrue = Log10ToReal(log10_ptrue);

  const double perror = std::log10(1 - ptrue);

  return std::isfinite(perror) ? -10 * perror : value_if_not_finite;

}

double Log10ToReal(const double log10_probability) {

  CHECK_LE(log10_probability, 0.0);

  return std::pow(10, log10_probability);

}

std::vector<double> ZeroShiftLikelihoods(

    const std::vector<double>& likelihoods) {

  std::vector<double> normalized(likelihoods.size());

  double max = *std::max_element(likelihoods.cbegin(), likelihoods.cend());

  std::transform(likelihoods.cbegin(), likelihoods.cend(),

                 normalized.begin(),

                 [max](double x) { return x - max; });

  return normalized;

}

}  // namespace nucleus