File: CompressedSequence.hpp

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#ifndef _BLASR_COMPRESSED_SEQUENCE_HPP_
#define _BLASR_COMPRESSED_SEQUENCE_HPP_

#include <cassert>
#include <cstdint>
#include <cstring>
#include <fstream>
#include <iostream>
#include <ostream>

#include <pbdata/Enumerations.h>
#include <pbdata/Types.h>
#include <pbdata/DNASequence.hpp>
#include <pbdata/FASTASequence.hpp>
#include <pbdata/NucConversion.hpp>
#include <pbdata/ReverseCompressIndex.hpp>
#include <pbdata/qvs/QualityValue.hpp>
#include <pbdata/reads/ZMWGroupEntry.hpp>
#include <pbdata/utils.hpp>

typedef unsigned char CompressedNucleotide;

template <typename T_Sequence>
class CompressedSequence : public FASTASequence
{
private:
    int hasIndex;
    int hasTitle;
    ReverseCompressIndex index;

    static const unsigned char MaskCount = 0xf;
    static const unsigned char MaskNuc = 0xf0;
    static const unsigned char ShiftCount = 4;

public:
    //
    // This is just a placeholder for now.
    // No extra data here, just the ability to decompress.  Right now
    // the utilities for the compressed dna sequences
    // are in CompressedSeqUtils.h, which could move here later.
    //
    QualityValue *qual;

    void CopyConfiguration(CompressedSequence<T_Sequence> &rhs);

    void ShallowCopy(CompressedSequence<T_Sequence> &rhs);

    void MakeRC(CompressedSequence &rc);

    Nucleotide operator[](DNALength i);

    Nucleotide GetNuc(DNALength i);

    unsigned char GetCount(DNALength i);

    char *GetName();

    void Copy(FASTASequence &rhs);

    float GetAverageQuality();

    void SortHomopolymerQualities();

    CompressedSequence();
    ~CompressedSequence();

    void Free();

    void SetHasTitle();

    void SetHasIndex();

    void Write(std::string outFileName);

    void Read(std::string inFileName);

    int BuildFourBitReverseIndex(int binSize);

    int BuildReverseIndex(int maxRun, int binSize);

    GenomeLength Lookup4BitCompressedSequencePos(int cpPos);

    int LookupSequencePos(int cpPos);

    char GetCount(unsigned char ch);

    DNALength FourBitCompressHomopolymers();

    static int Only4BitACTG(CompressedNucleotide *seq, int seqLength);

    int Only4BitACTG();

    void RemoveCompressionCounts();

    DNALength FourBitDecompressHomopolymers(int start, int end, T_Sequence &decompSeq);

    DNALength CondenseHomopolymers();
};

#include "CompressedSequenceImpl.hpp"

#endif  // _BLASR_COMPRESSED_SEQUENCE_HPP_