src/api/SamReadGroup.h

   1 // ***************************************************************************
   2 // SamReadGroup.h (c) 2010 Derek Barnett
   3 // Marth Lab, Department of Biology, Boston College
   4 // All rights reserved.
   5 // ---------------------------------------------------------------------------
   6 // Last modified: 23 December 2010 (DB)
   7 // ---------------------------------------------------------------------------
   8 // Provides functionality for querying/manipulating read group data
   9 // **************************************************************************
  10
  11 #ifndef SAM_READGROUP_H
  12 #define SAM_READGROUP_H
  13
  14 #include "api/api_global.h"
  15 #include <string>
  16
  17 namespace BamTools {
  18
  19 class API_EXPORT SamReadGroup {
  20
  21     // ctor & dtor
  22     public:
  23         SamReadGroup(void);
  24         SamReadGroup(const std::string& id);
  25         explicit SamReadGroup(const SamReadGroup& other);
  26         ~SamReadGroup(void);
  27
  28     // public methods
  29     public:
  30
  31         // clear all contents
  32         void Clear(void);
  33
  34         // convenience methods to check if SamReadGroup contains these values:
  35         bool HasID(void) const;
  36         bool HasSample(void) const;
  37         bool HasLibrary(void) const;
  38         bool HasDescription(void) const;
  39         bool HasPlatformUnit(void) const;
  40         bool HasPredictedInsertSize(void) const;
  41         bool HasSequencingCenter(void) const;
  42         bool HasProductionDate(void) const;
  43         bool HasSequencingTechnology(void) const;
  44
  45     // data members
  46     public:
  47         std::string ID;                   // ID:<ID>
  48         std::string Sample;               // SM:<Sample>
  49         std::string Library;              // LB:<Library>
  50         std::string Description;          // DS:<Description>
  51         std::string PlatformUnit;         // PU:<PlatformUnit>
  52         std::string PredictedInsertSize;  // PI:<PredictedInsertSize>
  53         std::string SequencingCenter;     // CN:<SequencingCenter>
  54         std::string ProductionDate;       // DT:<ProductionDate>
  55         std::string SequencingTechnology; // PL:<SequencingTechnology>
  56 };
  57
  58 // ---------------------------------------------------
  59 // comparison operators
  60
  61 // for equality: compare IDs
  62 inline bool operator==(const SamReadGroup& lhs, const SamReadGroup& rhs) {
  63     return lhs.ID == rhs.ID;
  64 }
  65
  66 } // namespace BamTools
  67
  68 #endif // SAM_READGROUP_H