// *************************************************************************** // BamAlignment.h (c) 2009 Derek Barnett // Marth Lab, Department of Biology, Boston College // All rights reserved. // --------------------------------------------------------------------------- // Last modified: 22 April 2011 (DB) // --------------------------------------------------------------------------- // Provides the BamAlignment data structure // *************************************************************************** #ifndef BAMALIGNMENT_H #define BAMALIGNMENT_H #include #include #include #include namespace BamTools { // forward declaration of BamAlignment's friend classes namespace Internal { class BamReaderPrivate; class BamWriterPrivate; } // namespace Internal // BamAlignment data structure struct API_EXPORT BamAlignment { // constructors & destructor public: BamAlignment(void); BamAlignment(const BamAlignment& other); ~BamAlignment(void); // queries against alignment flags public: bool IsDuplicate(void) const; // returns true if this read is a PCR duplicate bool IsFailedQC(void) const; // returns true if this read failed quality control bool IsFirstMate(void) const; // returns true if alignment is first mate on read bool IsMapped(void) const; // returns true if alignment is mapped bool IsMateMapped(void) const; // returns true if alignment's mate is mapped bool IsMateReverseStrand(void) const; // returns true if alignment's mate mapped to reverse strand bool IsPaired(void) const; // returns true if alignment part of paired-end read bool IsPrimaryAlignment(void) const; // returns true if reported position is primary alignment bool IsProperPair(void) const; // returns true if alignment is part of read that satisfied paired-end resolution bool IsReverseStrand(void) const; // returns true if alignment mapped to reverse strand bool IsSecondMate(void) const; // returns true if alignment is second mate on read // manipulate alignment flags public: void SetIsDuplicate(bool ok); // sets value of "PCR duplicate" flag void SetIsFailedQC(bool ok); // sets value of "failed quality control" flag void SetIsFirstMate(bool ok); // sets value of "alignment is first mate" flag void SetIsMapped(bool ok); // sets value of "alignment is mapped" flag void SetIsMateMapped(bool ok); // sets value of "alignment's mate is mapped" flag void SetIsMateReverseStrand(bool ok); // sets value of "alignment's mate mapped to reverse strand" flag void SetIsPaired(bool ok); // sets value of "alignment part of paired-end read" flag void SetIsPrimaryAlignment(bool ok); // sets value of "position is primary alignment" flag void SetIsProperPair(bool ok); // sets value of "alignment is part of read that satisfied paired-end resolution" flag void SetIsReverseStrand(bool ok); // sets value of "alignment mapped to reverse strand" flag void SetIsSecondMate(bool ok); // sets value of "alignment is second mate on read" flag // legacy methods (consider deprecated, but still available) void SetIsMateUnmapped(bool ok); // complement of using SetIsMateMapped() void SetIsSecondaryAlignment(bool ok); // complement of using SetIsPrimaryAlignment() void SetIsUnmapped(bool ok); // complement of using SetIsMapped() // tag data access methods public: // ------------------------------------------------------------------------------------- // N.B. - The following tag access methods may not be used on BamAlignments fetched // using BamReader::GetNextAlignmentCore(). Attempting to use them will not result in // error message (to keep output clean) but will ALWAYS return false. Only user-created // BamAlignments or those retrieved using BamReader::GetNextAlignment() are valid here. // // You can call BuildCharData() on such an alignment retrieved by GetNextAlignmentCore(). // This populates all the character data, and will enable subsequent queries on tag data. // ------------------------------------------------------------------------------------- // adds a tag bool AddTag(const std::string& tag, const std::string& type, const std::string& value); bool AddTag(const std::string& tag, const std::string& type, const uint32_t& value); bool AddTag(const std::string& tag, const std::string& type, const int32_t& value); bool AddTag(const std::string& tag, const std::string& type, const float& value); // adds a "binary array" tag bool AddTag(const std::string& tag, const std::vector& values); bool AddTag(const std::string& tag, const std::vector& values); bool AddTag(const std::string& tag, const std::vector& values); bool AddTag(const std::string& tag, const std::vector& values); bool AddTag(const std::string& tag, const std::vector& values); bool AddTag(const std::string& tag, const std::vector& values); bool AddTag(const std::string& tag, const std::vector& values); // edits a tag bool EditTag(const std::string& tag, const std::string& type, const std::string& value); bool EditTag(const std::string& tag, const std::string& type, const uint32_t& value); bool EditTag(const std::string& tag, const std::string& type, const int32_t& value); bool EditTag(const std::string& tag, const std::string& type, const float& value); // edits a "binary array" tag bool EditTag(const std::string& tag, const std::vector& values); bool EditTag(const std::string& tag, const std::vector& values); bool EditTag(const std::string& tag, const std::vector& values); bool EditTag(const std::string& tag, const std::vector& values); bool EditTag(const std::string& tag, const std::vector& values); bool EditTag(const std::string& tag, const std::vector& values); bool EditTag(const std::string& tag, const std::vector& values); // retrieves data for a tag bool GetTag(const std::string& tag, std::string& destination) const; bool GetTag(const std::string& tag, uint32_t& destination) const; bool GetTag(const std::string& tag, int32_t& destination) const; bool GetTag(const std::string& tag, float& destination) const; // retrieves data for a "binary array" tag bool GetTag(const std::string& tag, std::vector& destination) const; bool GetTag(const std::string& tag, std::vector& destination) const; bool GetTag(const std::string& tag, std::vector& destination) const; // retrieves the BAM tag-type character for a tag bool GetTagType(const std::string& tag, char& type) const; // legacy methods (consider deprecated, but still available) bool GetEditDistance(uint32_t& editDistance) const; // retrieves value of "NM" tag bool GetReadGroup(std::string& readGroup) const; // retrieves value of "RG" tag // returns true if alignment has a record for this tag name bool HasTag(const std::string& tag) const; // removes a tag bool RemoveTag(const std::string& tag); // additional methods public: // populates alignment string fields bool BuildCharData(void); // calculates alignment end position int GetEndPosition(bool usePadded = false, bool zeroBased = true) const; // public data fields public: std::string Name; // read name int32_t Length; // length of query sequence std::string QueryBases; // 'original' sequence (as reported from sequencing machine) std::string AlignedBases; // 'aligned' sequence (includes any indels, padding, clipping) std::string Qualities; // FASTQ qualities (ASCII characters, not numeric values) std::string TagData; // tag data (use provided methods to query/modify) int32_t RefID; // ID number for reference sequence int32_t Position; // position (0-based) where alignment starts uint16_t Bin; // BAM (standard) index bin number for this alignment uint16_t MapQuality; // mapping quality score uint32_t AlignmentFlag; // alignment bit-flag (use provided methods to query/modify) std::vector CigarData; // CIGAR operations for this alignment int32_t MateRefID; // ID number for reference sequence where alignment's mate was aligned int32_t MatePosition; // position (0-based) where alignment's mate starts int32_t InsertSize; // mate-pair insert size std::string Filename; // name of BAM file which this alignment comes from //! \cond // internal utility methods private: bool FindTag(const std::string& tag, char*& pTagData, const unsigned int& tagDataLength, unsigned int& numBytesParsed) const; bool IsValidSize(const std::string& tag, const std::string& type) const; bool SkipToNextTag(const char storageType, char*& pTagData, unsigned int& numBytesParsed) const; // internal data private: struct BamAlignmentSupportData { // data members std::string AllCharData; uint32_t BlockLength; uint32_t NumCigarOperations; uint32_t QueryNameLength; uint32_t QuerySequenceLength; bool HasCoreOnly; // constructor BamAlignmentSupportData(void) : BlockLength(0) , NumCigarOperations(0) , QueryNameLength(0) , QuerySequenceLength(0) , HasCoreOnly(false) { } }; BamAlignmentSupportData SupportData; friend class Internal::BamReaderPrivate; friend class Internal::BamWriterPrivate; //! \endcond }; typedef std::vector BamAlignmentVector; } // namespace BamTools #endif // BAMALIGNMENT_H