// Author: Mark Chaisson
#pragma once

#include "BlasrHeaders.h"
#include "BlasrMiscs.hpp"

//------------------MAP READS---------------------------------//
template <typename T_Sequence, typename T_RefSequence, typename T_SuffixArray,
          typename T_TupleCountTable>
void MapRead(T_Sequence &read, T_Sequence &readRC, T_RefSequence &genome, T_SuffixArray &sarray,
             BWT &bwt, SeqBoundaryFtr<FASTQSequence> &seqBoundary, T_TupleCountTable &ct,
             SequenceIndexDatabase<FASTQSequence> &seqdb, MappingParameters &params,
             MappingMetrics &metrics, std::vector<T_AlignmentCandidate *> &alignmentPtrs,
             MappingBuffers &mappingBuffers, MappingIPC *mapData, MappingSemaphores &semaphores);

template <typename T_Sequence>
void MapRead(T_Sequence &read, T_Sequence &readRC,
             std::vector<T_AlignmentCandidate *> &alignmentPtrs, MappingBuffers &mappingBuffers,
             MappingIPC *mapData, MappingSemaphores &semaphores);

/*
void MapReads(MappingData<T_SuffixArray, T_GenomeSequence, T_Tuple> *mapData);
*/

//------------------MAKE ALIGNMENTS---------------------------//
template <typename T_TargetSequence, typename T_QuerySequence, typename TDBSequence>
void AlignIntervals(T_TargetSequence &genome, T_QuerySequence &read, T_QuerySequence &rcRead,
                    WeightedIntervalSet &weightedIntervals, int mutationCostMatrix[][5], int ins,
                    int del, int sdpTupleSize, int useSeqDB,
                    SequenceIndexDatabase<TDBSequence> &seqDB,
                    std::vector<T_AlignmentCandidate *> &alignments, MappingParameters &params,
                    MappingBuffers &mappingBuffers, int procId = 0);

template <typename T_RefSequence, typename T_Sequence>
void PairwiseLocalAlign(T_Sequence &qSeq, T_RefSequence &tSeq, int k, MappingParameters &params,
                        T_AlignmentCandidate &alignment, MappingBuffers &mappingBuffers,
                        AlignmentType alignType = Global);

// Extend target aligned sequence of the input alignement to both ends
// by flankSize bases. Update alignment->tAlignedSeqPos,
// alignment->tAlignedSeqLength and alignment->tAlignedSeq.
void FlankTAlignedSeq(T_AlignmentCandidate *alignment, SequenceIndexDatabase<FASTQSequence> &seqdb,
                      DNASequence &genome, int flankSize);

// Align a subread of a SMRT sequence to target sequence of an alignment.
// Input:
//   subread         - a subread of a SMRT sequence.
//   unrolledRead    - the full SMRT sequence.
//   alignment       - an alignment.
//   passDirection   - whether or not the subread has the
//                     same direction as query of the alignment.
//                     0 = true, 1 = false.
//   subreadInterval - [start, end) interval of the subread in the
//                     SMRT read.
//   subreadIndex    - index of the subread in allReadAlignments.
//   params          - mapping paramters.
// Output:
//   allReadAlignments - where the sequence and alignments of the
//                       subread are saved.
//   threadOut         - an out stream for debugging the current thread.
void AlignSubreadToAlignmentTarget(ReadAlignments &allReadAlignments, SMRTSequence &subread,
                                   SMRTSequence &unrolledRead, T_AlignmentCandidate *alignment,
                                   int passDirection, ReadInterval &subreadInterval,
                                   int subreadIndex, MappingParameters &params,
                                   MappingBuffers &mappingBuffers, std::ostream &threadOut);

#include "BlasrAlignImpl.hpp"