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: 18 April 2011 (DB)
   7 // ---------------------------------------------------------------------------
   8 // Provides direct read/write access to the SAM read group data fields.
   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 struct API_EXPORT SamReadGroup {
  20
  21     // ctor & dtor
  22     SamReadGroup(void);
  23     SamReadGroup(const std::string& id);
  24     SamReadGroup(const SamReadGroup& other);
  25     ~SamReadGroup(void);
  26
  27     // query/modify entire read group
  28     void Clear(void);                           // clears all data fields
  29
  30     // convenience query methods
  31     bool HasDescription(void) const;            // returns true if read group has a description
  32     bool HasFlowOrder(void) const;              // returns true if read group has a flow order entry
  33     bool HasID(void) const;                     // returns true if read group has a group ID
  34     bool HasKeySequence(void) const;            // returns true if read group has a key sequence
  35     bool HasLibrary(void) const;                // returns true if read group has a library name
  36     bool HasPlatformUnit(void) const;           // returns true if read group has a platform unit ID
  37     bool HasPredictedInsertSize(void) const;    // returns true if read group has a predicted insert size
  38     bool HasProductionDate(void) const;         // returns true if read group has a production date
  39     bool HasProgram(void) const;                // returns true if read group has a program entry
  40     bool HasSample(void) const;                 // returns true if read group has a sample name
  41     bool HasSequencingCenter(void) const;       // returns true if read group has a sequencing center ID
  42     bool HasSequencingTechnology(void) const;   // returns true if read group has a sequencing technology ID
  43
  44
  45     // data fields
  46     std::string Description;                    // DS:<Description>
  47     std::string FlowOrder;                      // FO:<FlowOrder>
  48     std::string ID;                             // ID:<ID>              *Required for valid SAM header*
  49     std::string KeySequence;                    // KS:<KeySequence>
  50     std::string Library;                        // LB:<Library>
  51     std::string PlatformUnit;                   // PU:<PlatformUnit>
  52     std::string PredictedInsertSize;            // PI:<PredictedInsertSize>
  53     std::string ProductionDate;                 // DT:<ProductionDate>
  54     std::string Program;                        // PG:<Program>
  55     std::string Sample;                         // SM:<Sample>
  56     std::string SequencingCenter;               // CN:<SequencingCenter>
  57     std::string SequencingTechnology;           // PL:<SequencingTechnology>
  58 };
  59
  60 /*! \fn bool operator==(const SamReadGroup& lhs, const SamReadGroup& rhs)
  61     \brief tests equality by comparing read group IDs
  62 */
  63 API_EXPORT inline bool operator==(const SamReadGroup& lhs, const SamReadGroup& rhs) {
  64     return lhs.ID == rhs.ID;
  65 }
  66
  67 } // namespace BamTools
  68
  69 #endif // SAM_READGROUP_H