SamSequence.h

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// ***************************************************************************
// SamSequence.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides direct read/write access to the SAM sequence data fields.
// ***************************************************************************
 
#ifndef SAM_SEQUENCE_H
#define SAM_SEQUENCE_H
 
#include <string>
#include <vector>
#include "api/BamAux.h"
#include "api/api_global.h"
 
namespace BamTools {
 
struct API_EXPORT SamSequence
{
 
    // ctor & dtor
    SamSequence();
    SamSequence(const std::string& name, const int& length);
    SamSequence(const std::string& name, const std::string& length);
 
    // query/modify entire sequence
    void Clear();  // clears all contents
 
    // convenience query methods
    bool HasAssemblyID() const;  // returns true if sequence has an assembly ID
    bool HasChecksum() const;    // returns true if sequence has an MD5 checksum
    bool HasLength() const;      // returns true if sequence has a length
    bool HasName() const;        // returns true if sequence has a name
    bool HasSpecies() const;     // returns true if sequence has a species ID
    bool HasURI() const;         // returns true if sequence has a URI
 
    // data members
    std::string AssemblyID;                   // AS:<AssemblyID>
    std::string Checksum;                     // M5:<Checksum>
    std::string Length;                       // LN:<Length>      *Required for valid SAM header*
    std::string Name;                         // SN:<Name>        *Required for valid SAM header*
    std::string Species;                      // SP:<Species>
    std::string URI;                          // UR:<URI>
    std::vector<CustomHeaderTag> CustomTags;  // optional custom tags
};

inline bool operator==(const SamSequence& lhs, const SamSequence& rhs)
{
    if (lhs.Name != rhs.Name) {
        return false;
    }
    if (lhs.Length != rhs.Length) {
        return false;
    }
    if (lhs.HasChecksum() && rhs.HasChecksum()) {
        return (lhs.Checksum == rhs.Checksum);
    } else {
        return true;
    }
}
 
}  // namespace BamTools
 
#endif  // SAM_SEQUENCE_H