vashFunctions.hpp

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/*
 * Copyright (c) 2023 Anthony J. Greenberg
 *
 * 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 CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
 * THE POSSIBILITY OF SUCH DAMAGE.
 */
 
 
#pragma once
 
#include <cstdint>
#include <cstddef>
#include <vector>
#include <array>
#include <unordered_map>
 
#include "gvarHash.hpp"
#include "similarityMatrix.hpp"
 
namespace BayesicSpace {
    constexpr size_t SIZE_OF_SIZET{sizeof(size_t) / sizeof(uint32_t)};
    constexpr size_t N_BED_TEST_BYTES{3};
    [[gnu::warn_unused_result]] uint16_t countSetBits(uint16_t inVal);
    [[gnu::warn_unused_result]] uint64_t countSetBits(const std::vector<uint8_t> &inVec);
    [[gnu::warn_unused_result]] uint64_t countSetBits(const std::vector<uint8_t> &inVec, const LocationWithLength &window);
    [[gnu::warn_unused_result]] size_t getAvailableRAM();
    [[gnu::warn_unused_result]] uint32_t murMurHashMixer(const std::array<uint32_t, SIZE_OF_SIZET> &key, const uint32_t &seed);
    [[gnu::warn_unused_result]] uint32_t murMurHashFinalizer(const uint32_t &inputHash);
    [[gnu::warn_unused_result]] uint32_t murMurHash(const std::array<uint32_t, SIZE_OF_SIZET> &key, const uint32_t &seed);
    [[gnu::warn_unused_result]] uint32_t murMurHash(const std::vector<size_t> &key, const uint32_t &seed);
    [[gnu::warn_unused_result]] uint32_t murMurHash(const std::vector<uint32_t> &key, const uint32_t &seed);
    [[gnu::warn_unused_result]] uint32_t murMurHash(const std::vector<uint16_t> &key, const LocationWithLength &keyWindow, const uint32_t &seed);
    void testBedMagicBytes(const std::array<char, N_BED_TEST_BYTES> &bytesToTest);
    [[gnu::warn_unused_result]] std::vector< std::pair<size_t, size_t> > makeThreadRanges(const CountAndSize &threadPoolSizes);
    [[gnu::warn_unused_result]] std::vector<size_t> makeChunkSizes(const size_t &nElements, const size_t &nChunks);
    [[gnu::warn_unused_result]] std::vector< std::pair<RowColIdx, RowColIdx> > makeChunkRanges(const LocationWithLength &startAndChunkSize, const size_t nChunks);
    [[gnu::warn_unused_result]] std::pair<HashGroupItPairCount, HashGroupItPairCount>
        makeGroupRanges(const std::vector<HashGroup> &groupVector, const HashGroupItPairCount &startHGPC, const size_t &chunkSize);
    void binarizeBedLocus(const LocationWithLength &bedLocusWindow, const std::vector<char> &bedLocus, const size_t &nIndividuals,
                                                    const LocationWithLength &binLocusWindow, std::vector<uint8_t> &binLocus);
    void binarizeMacLocus(const std::vector<int> &macLocus, const LocationWithLength &binLocusWindow, std::vector<uint8_t> &binLocus);
    [[gnu::warn_unused_result]] std::vector<std::string> getLocusNames(const std::string &bimFileName);
    void parseCL(int &argc, char **argv, std::unordered_map<std::string, std::string> &cli);
    void extractCLinfo(const std::unordered_map<std::string, std::string> &parsedCLI, std::unordered_map<std::string, int> &intVariables,
            std::unordered_map<std::string, float> &floatVariables, std::unordered_map<std::string, std::string> &stringVariables);
}