helperFunctions.hpp

Go to the documentation of this file.

/*
 * Copyright (c) 2024-2025 Anthony J. Greenberg and Rebekah Rogers
 *
 * 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 <memory>
#include <array>
#include <string>
#include <utility> // for std::pair
#include <vector>
 
#include "sam.h"
 
#include "isoseqAlgn.hpp"
 
namespace isaSpace {
    constexpr size_t nGFFfields{9UL};
    using bamGFFvector = std::vector< std::pair<BAMrecord, ExonGroup> >;

    [[nodiscard]] std::string extractAttributeName(const TokenAttibuteListPair &tokenAndAttrList);

    [[nodiscard]] std::string extractParentName(const std::string &attributeString);

    [[nodiscard]] bool rangesOverlap(const std::pair<hts_pos_t, hts_pos_t> &range1, const std::pair<hts_pos_t, hts_pos_t> &range2) noexcept;

    [[nodiscard]] std::array<std::string, nGFFfields> parseGFFline(const std::string &gffLine);

    [[nodiscard]] std::unordered_map< std::string, std::vector<ExonGroup> > parseGFF(const std::string &gffFileName);

    [[nodiscard]] std::vector<std::vector<float>::const_iterator> getPeaks(const std::vector<float> &values, const float &threshold);

    [[nodiscard]] std::vector<std::vector<float>::const_iterator> getValleys(const std::vector<float> &values, const float &threshold);

    [[nodiscard]] std::vector<float> getReferenceMatchStatus(const std::vector<uint32_t> &cigar);

    [[nodiscard]] ReadExonCoverage getExonCoverageStats(const std::pair<BAMrecord, ExonGroup> &readAndExons);

    [[nodiscard]] std::string stringifyExonCoverage(const ReadExonCoverage &readRecord, char separator = '\t');

    [[nodiscard]] std::string stringifyAlignmentRange(const bamGFFvector::const_iterator &begin, const bamGFFvector::const_iterator &end);
    [[nodiscard]] std::string stringifyUnmappedRegions(const bamGFFvector::const_iterator &begin, const bamGFFvector::const_iterator &end, const BinomialWindowParameters &windowParameters);
    [[nodiscard]] std::pair<std::string, std::string> getUnmappedRegionsAndFASTQ(const bamGFFvector::const_iterator &begin, const bamGFFvector::const_iterator &end, const BinomialWindowParameters &windowParameters);

    [[nodiscard]] ReadPortion parseRemappedReadName(const std::string &remappedReadName);
    [[nodiscard]] std::unique_ptr<bam1_t, BAMrecordDeleter> modifyCIGAR(const ReadPortion &modRange, const std::unique_ptr<bam1_t, BAMrecordDeleter> &bamRecord);
    void addRemappedSecondaryAlignment(
            const std::unique_ptr<sam_hdr_t, BAMheaderDeleter> &newRecordHeader, const std::unique_ptr<bam1_t, BAMrecordDeleter> &newRecord, const ReadPortion &remapInfo,
            const std::unique_ptr<sam_hdr_t, BAMheaderDeleter> &originalHeader, const float &remapIdentityCutoff, std::vector< std::unique_ptr<bam1_t, BAMrecordDeleter> > &readMapVector);

    std::unique_ptr<BGZF, BGZFhandleDeleter> openBGZFtoAppend(const std::string &bamFileName);

    [[nodiscard]] std::vector< std::pair<bamGFFvector::const_iterator, bamGFFvector::const_iterator> > 
        makeThreadRanges(const bamGFFvector &targetVector, const size_t &threadCount);

    [[nodiscard]] std::unordered_map<std::string, std::string> parseCL(int &argc, char **argv);

    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);
}