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#ifndef _BLASR_FASTQ_SEQUENCE_HPP_
#define _BLASR_FASTQ_SEQUENCE_HPP_
#include <pbdata/DNASequence.hpp>
#include <pbdata/FASTASequence.hpp>
#include <pbdata/matrix/Matrix.hpp>
#include <pbdata/qvs/QualityValue.hpp>
#include <pbdata/qvs/QualityValueVector.hpp>
#include <pbdata/reads/ZMWGroupEntry.hpp>
enum QVList
{
InsertionQV = 0x1,
DeletionQV = 0x2,
SubstitutionQV = 0x4,
MergeQV = 0x8,
SubstitutionTag = 0x10,
DeletionTag = 0x20
};
enum QVIndex
{
I_QualityValue = 0,
I_InsertionQV = 1,
I_DeletionQV = 2,
I_SubstitutionQV = 3,
I_MergeQV = 4,
I_SubstitutionTag = 5,
I_DeletionTag = 6
};
class FASTQSequence : public FASTASequence
{
public:
static int charToQuality;
QualityValueVector<QualityValue> qual;
QualityValueVector<QualityValue> deletionQV;
QualityValueVector<QualityValue> preBaseDeletionQV;
QualityValueVector<QualityValue> insertionQV;
QualityValueVector<QualityValue> substitutionQV;
QualityValueVector<QualityValue> mergeQV;
Nucleotide *deletionTag;
Nucleotide *substitutionTag;
QualityValue deletionQVPrior, insertionQVPrior, substitutionQVPrior, preBaseDeletionQVPrior;
QVScale qvScale;
QVScale GetQVScale() const;
void SetQVScale(QVScale qvScaleP);
QualityValueVector<QualityValue> *GetQVPointerByIndex(int index);
int GetStorageSize() const;
FASTQSequence();
inline ~FASTQSequence();
QualityValue GetDeletionQV(DNALength pos) const;
QualityValue GetMergeQV(DNALength pos) const;
Nucleotide GetSubstitutionTag(DNALength pos) const;
Nucleotide GetDeletionTag(DNALength pos) const;
QualityValue GetInsertionQV(DNALength pos) const;
QualityValue GetSubstitutionQV(DNALength pos) const;
QualityValue GetPreBaseDeletionQV(DNALength pos, Nucleotide nuc) const;
void ShallowCopy(const FASTQSequence &rhs);
void ReferenceSubstring(const FASTQSequence &rhs);
void ReferenceSubstring(const FASTQSequence &rhs, DNALength pos);
void ReferenceSubstring(const FASTQSequence &rhs, DNALength pos, DNALength substrLength);
void ClearAndNull(QualityValue *value);
void CopyQualityValues(const FASTQSequence &rhs);
void AllocateQualitySpace(DNALength qualLength);
void AllocateDeletionQVSpace(DNALength qualLength);
void AllocateMergeQVSpace(DNALength len);
void AllocateDeletionTagSpace(DNALength qualLength);
void AllocatePreBaseDeletionQVSpace(DNALength qualLength);
void AllocateInsertionQVSpace(DNALength qualLength);
void AllocateSubstitutionQVSpace(DNALength qualLength);
void AllocateSubstitutionTagSpace(DNALength qualLength);
void AllocateRichQualityValues(DNALength qualLength);
void Copy(const FASTQSequence &rhs);
// Reverse complement its sequence, reverse quality values.
FASTQSequence &ReverseComplementSelf(void);
FASTQSequence &operator=(const FASTQSequence &rhs);
FASTQSequence(const FASTQSequence &rhs);
void Assign(FASTQSequence &rhs);
void PrintFastq(std::ostream &out, int lineLength = 50) const;
void PrintFastqQuality(std::ostream &out, int lineLength = 50) const;
QVIndex GetQVIndex(const std::string &qvName) const;
/// Get QVs in std::vector<uint8_t> associated with the given QVIndex.
/// \returns true if qvs are available, false otherwise
/// \param [in] qvIndex - enum QVIndex
/// \param [out] qvs - obtained QVs.
/// \param [in] reverse - reverse orders of QVs or not
bool GetQVs(const QVIndex &qvIndex, std::vector<uint8_t> &qvs, bool reverse = false) const;
/// Get QVs in std::vector<uint8_t>, given with QV Name.
/// \returns true if qvs are available, false, otherwise
/// \param [in] qvName - InsertionQV, DeletionQV, SubstitionQV, MergeQV, SubstitutionTag, DeletionTag
/// \param [out] qvs - obtians QVs.
/// \param [in] reverse - reverse orders of QVs or not.
bool GetQVs(const std::string &qvName, std::vector<uint8_t> &qvs, bool reverse = false) const;
/// Get QVs in string, given with QV Name.
/// \returns true if qvs are available, false, otherwise
/// \param [in] qvName - InsertionQV, DeletionQV, SubstitionQV, MergeQV, SubstitutionTag, DeletionTag
/// \param [out] qvs - obtians QVs.
/// \param [in] reverse - reverse order of QVs or not
bool GetQVs(const std::string &qvName, std::string &qvs, bool reverse = false) const;
void PrintAsciiRichQuality(std::ostream &out, int whichQuality, int lineLength = 50) const;
void PrintAsciiQual(std::ostream &out, int lineLength = 50) const;
void PrintQual(std::ostream &out, int lineLength = 50) const;
void PrintQualSeq(std::ostream &out, int lineLength = 50) const;
void MakeRC(FASTQSequence &rc);
void Free();
void LowerCaseMask(int qThreshold);
float GetAverageQuality() const;
#ifdef USE_PBBAM
/// Copy name, sequence, and QVs from BamRecord.
void Copy(const PacBio::BAM::BamRecord &record);
#endif
};
inline FASTQSequence::~FASTQSequence() { FASTQSequence::Free(); }
#endif // _BLASR_FASTQ_SEQUENCE_HPP_
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