// Author: Mark Chaisson
#pragma once

#include <pbdata/utils/SMRTTitle.hpp>

template <typename T_Sequence>
bool GetNextReadThroughSemaphore(ReaderAgglomerate &reader, MappingParameters &params,
                                 T_Sequence &read, std::string &readGroupId, int &associatedRandInt,
                                 MappingSemaphores &semaphores)
{
    // Wait on a semaphore
    if (params.nProc > 1) {
#ifdef __APPLE__
        sem_wait(semaphores.reader);
#else
        sem_wait(&semaphores.reader);
#endif
    }

    bool returnValue = true;
    //
    // CCS Reads are read differently from other reads.  Do static casting here
    // of this.
    //
    if (reader.GetNext(read, associatedRandInt) == 0) {
        returnValue = false;
    }

    //
    // Set the read group id before releasing the semaphore, since other
    // threads may change the reader object to a new read group before
    // sending this alignment out to printing.
    readGroupId = reader.readGroupId;

    if (params.nProc > 1) {
#ifdef __APPLE__
        sem_post(semaphores.reader);
#else
        sem_post(&semaphores.reader);
#endif
    }
    return returnValue;
}

bool ReadHasMeaningfulQualityValues(FASTQSequence &sequence)
{
    if (sequence.qual.Empty() == true) {
        return 0;
    } else {
        int numZero = 0, numNonZero = 0;
        if (sequence.qual.data == NULL) {
            return false;
        }
        numZero = CountZero(sequence.qual.data, sequence.length);
        numNonZero = sequence.length - numZero;
        int subNumZero = 0, subNonZero = 0;

        if (sequence.substitutionQV.data == NULL) {
            return false;
        }
        subNumZero = CountZero(sequence.substitutionQV.data, sequence.length);
        subNonZero = sequence.length - subNumZero;

        if (numZero < 0.5 * numNonZero and subNumZero < 0.5 * subNonZero) {
            return true;
        } else {
            return false;
        }
    }
}

// Given a SMRT sequence and a subread interval, make the subread.
// Input:
//   smrtRead         - a SMRT sequence
//   subreadInterval  - a subread interval
//   params           - mapping parameters
// Output:
//   subreadSequence - the constructed subread
void MakeSubreadOfInterval(SMRTSequence &subreadSequence, SMRTSequence &smrtRead,
                           ReadInterval &subreadInterval, MappingParameters &params)
{
    int start = subreadInterval.start;
    int end = subreadInterval.end;

    assert(smrtRead.length >= subreadSequence.length);
    smrtRead.MakeSubreadAsMasked(subreadSequence, start, end);

    if (!params.preserveReadTitle) {
        smrtRead.SetSubreadTitle(subreadSequence, subreadSequence.SubreadStart(),
                                 subreadSequence.SubreadEnd());
    } else {
        subreadSequence.CopyTitle(smrtRead.title);
    }
    subreadSequence.zmwData = smrtRead.zmwData;
}

// Given a SMRT sequence and one of its subreads, make the
// reverse complement of the subread in the coordinate of the
// reverse complement sequence of the SMRT sequence.
// Input:
//   smrtRead          - a SMRT read
//   subreadSequence   - a subread of smrtRead
// Output:
//   subreadSequenceRC - the reverse complement of the subread
//                       in the coordinate of the reverse
//                       complement of the SMRT read.
void MakeSubreadRC(SMRTSequence &subreadSequenceRC, SMRTSequence &subreadSequence,
                   SMRTSequence &smrtRead)
{
    assert(smrtRead.length >= subreadSequence.length);
    // Reverse complement sequence of the subread.
    subreadSequence.MakeRC(subreadSequenceRC);
    // Update start and end positions of subreadSequenceRC in the
    // coordinate of reverse compelement sequence of the SMRT read.
    subreadSequenceRC.SubreadStart(smrtRead.length - subreadSequence.SubreadEnd());
    subreadSequenceRC.SubreadEnd(smrtRead.length - subreadSequence.SubreadStart());
    subreadSequenceRC.zmwData = smrtRead.zmwData;
}

int CountZero(unsigned char *ptr, int length)
{
    int i;
    int nZero = 0;
    for (i = 0; i < length; i++) {
        if (ptr[i] == 0) {
            ++nZero;
        }
    }
    return nZero;
}

void MakeSubreadIntervals(std::vector<SMRTSequence> &subreads,
                          std::vector<ReadInterval> &subreadIntervals)
{
    subreadIntervals.clear();
    for (auto subread : subreads) {
        subreadIntervals.push_back(ReadInterval(subread.SubreadStart(), subread.SubreadEnd(),
                                                subread.highQualityRegionScore));
    }
}

int GetIndexOfConcordantTemplate(const std::vector<ReadInterval> &subreadIntervals)
{
    assert(subreadIntervals.size() != 0);
    if (subreadIntervals.size() == 1)
        return 0;  // Zmw has exactly one subread.
    else if (subreadIntervals.size() == 2) {
        // Zmw has two subreads, return index of the longer one.
        const ReadInterval &first = subreadIntervals[0];
        const ReadInterval &second = subreadIntervals[1];
        if (first.Length() < second.Length())
            return 1;
        else
            return 0;
    } else {
        // Zmw has more than two subreads, look for the median-length subread
        // in subreadIntervals[1:-1]. The first and last subreads are not
        // considered because they are usually non-full-pass.
        std::vector<ReadInterval> intervals;
        intervals.insert(intervals.begin(), subreadIntervals.begin() + 1,
                         subreadIntervals.end() - 1);
        std::sort(intervals.begin(), intervals.end(),
                  [](const ReadInterval &a, const ReadInterval &b) -> bool {
                      return a.Length() < b.Length();
                  });
        const ReadInterval &template_interval = intervals[int(intervals.size() / 2)];
        for (int pos = 1; pos < int(subreadIntervals.size()) - 1; pos++) {
            if (subreadIntervals[pos] == template_interval) {
                return pos;
            }
        }
    }
    return 0;
}