src/api/SamReadGroup.cpp

   1 // ***************************************************************************
   2 // SamReadGroup.cpp (c) 2010 Derek Barnett
   3 // Marth Lab, Department of Biology, Boston College
   4 // All rights reserved.
   5 // ---------------------------------------------------------------------------
   6 // Last modified: 4 March 2011 (DB)
   7 // ---------------------------------------------------------------------------
   8 // Provides direct read/write access to the SAM read group data fields.
   9 // ***************************************************************************
  10
  11 #include <api/SamReadGroup.h>
  12 using namespace BamTools;
  13 using namespace std;
  14
  15 /*! \struct BamTools::SamReadGroup
  16     \brief Represents a SAM read group entry.
  17
  18     Provides direct read/write access to the SAM read group data fields.
  19
  20     \sa http://samtools.sourceforge.net/SAM-1.3.pdf
  21 */
  22 /*! \var SamReadGroup::ID
  23     \brief corresponds to \@RG ID:\<ID\>
  24 */
  25 /*! \var SamReadGroup::Sample
  26     \brief corresponds to \@RG SM:\<Sample\>
  27 */
  28 /*! \var SamReadGroup::Library
  29     \brief corresponds to \@RG LB:\<Library\>
  30 */
  31 /*! \var SamReadGroup::Description
  32     \brief corresponds to \@RG DS:\<Description\>
  33 */
  34 /*! \var SamReadGroup::PlatformUnit
  35     \brief corresponds to \@RG PU:\<PlatformUnit\>
  36 */
  37 /*! \var SamReadGroup::PredictedInsertSize
  38     \brief corresponds to \@RG PI:\<PredictedInsertSize\>
  39 */
  40 /*! \var SamReadGroup::SequencingCenter
  41     \brief corresponds to \@RG CN:\<SequencingCenter\>
  42 */
  43 /*! \var SamReadGroup::ProductionDate
  44     \brief corresponds to \@RG DT:\<ProductionDate\>
  45 */
  46 /*! \var SamReadGroup::SequencingTechnology
  47     \brief corresponds to \@RG PL:\<SequencingTechnology\>
  48 */
  49
  50 /*! \fn SamReadGroup::SamReadGroup(void)
  51     \brief default constructor
  52 */
  53 SamReadGroup::SamReadGroup(void)
  54     : ID("")
  55     , Sample("")
  56     , Library("")
  57     , Description("")
  58     , PlatformUnit("")
  59     , PredictedInsertSize("")
  60     , SequencingCenter("")
  61     , ProductionDate("")
  62     , SequencingTechnology("")
  63 { }
  64
  65 /*! \fn SamReadGroup::SamReadGroup(const std::string& id)
  66     \brief constructs read group with \a id
  67
  68     \param id desired read group ID
  69 */
  70 SamReadGroup::SamReadGroup(const std::string& id)
  71     : ID(id)
  72     , Sample("")
  73     , Library("")
  74     , Description("")
  75     , PlatformUnit("")
  76     , PredictedInsertSize("")
  77     , SequencingCenter("")
  78     , ProductionDate("")
  79     , SequencingTechnology("")
  80 { }
  81
  82 /*! \fn SamReadGroup::SamReadGroup(const SamReadGroup& other)
  83     \brief copy constructor
  84 */
  85 SamReadGroup::SamReadGroup(const SamReadGroup& other)
  86     : ID(other.ID)
  87     , Sample(other.Sample)
  88     , Library(other.Library)
  89     , Description(other.Description)
  90     , PlatformUnit(other.PlatformUnit)
  91     , PredictedInsertSize(other.PredictedInsertSize)
  92     , SequencingCenter(other.SequencingCenter)
  93     , ProductionDate(other.ProductionDate)
  94     , SequencingTechnology(other.SequencingTechnology)
  95 { }
  96
  97 /*! \fn SamReadGroup::~SamReadGroup(void)
  98     \brief destructor
  99 */
 100 SamReadGroup::~SamReadGroup(void) { }
 101
 102 /*! \fn void SamReadGroup::Clear(void)
 103     \brief Clears all data fields.
 104 */
 105 void SamReadGroup::Clear(void) {
 106     ID.clear();
 107     Sample.clear();
 108     Library.clear();
 109     Description.clear();
 110     PlatformUnit.clear();
 111     PredictedInsertSize.clear();
 112     SequencingCenter.clear();
 113     ProductionDate.clear();
 114     SequencingTechnology.clear();
 115 }
 116
 117 /*! \fn bool SamReadGroup::HasID(void) const
 118     \brief Returns \c true if read group contains \@RG: ID:\<ID\>
 119 */
 120 bool SamReadGroup::HasID(void) const {
 121     return (!ID.empty());
 122 }
 123
 124 /*! \fn bool SamReadGroup::HasSample(void) const
 125     \brief Returns \c true if read group contains \@RG SM:\<Sample\>
 126 */
 127 bool SamReadGroup::HasSample(void) const {
 128     return (!Sample.empty());
 129 }
 130
 131 /*! \fn bool SamReadGroup::HasLibrary(void) const
 132     \brief Returns \c true if read group contains \@RG LB:\<Library\>
 133 */
 134 bool SamReadGroup::HasLibrary(void) const {
 135     return (!Library.empty());
 136 }
 137
 138 /*! \fn bool SamReadGroup::HasDescription(void) const
 139     \brief Returns \c true if read group contains \@RG DS:\<Description\>
 140 */
 141 bool SamReadGroup::HasDescription(void) const {
 142     return (!Description.empty());
 143 }
 144
 145 /*! \fn bool SamReadGroup::HasPlatformUnit(void) const
 146     \brief Returns \c true if read group contains \@RG PU:\<PlatformUnit\>
 147 */
 148 bool SamReadGroup::HasPlatformUnit(void) const {
 149     return (!PlatformUnit.empty());
 150 }
 151
 152 /*! \fn bool SamReadGroup::HasPredictedInsertSize(void) const
 153     \brief Returns \c true if read group contains \@RG PI:\<PredictedInsertSize\>
 154 */
 155 bool SamReadGroup::HasPredictedInsertSize(void) const {
 156     return (!PredictedInsertSize.empty());
 157 }
 158
 159 /*! \fn bool SamReadGroup::HasSequencingCenter(void) const
 160     \brief Returns \c true if read group contains \@RG CN:\<SequencingCenter\>
 161 */
 162 bool SamReadGroup::HasSequencingCenter(void) const {
 163     return (!SequencingCenter.empty());
 164 }
 165
 166 /*! \fn bool SamReadGroup::HasProductionDate(void) const
 167     \brief Returns \c true if read group contains \@RG DT:\<ProductionDate\>
 168 */
 169 bool SamReadGroup::HasProductionDate(void) const {
 170     return (!ProductionDate.empty());
 171 }
 172
 173 /*! \fn bool SamReadGroup::HasSequencingTechnology(void) const
 174     \brief Returns \c true if read group contains \@RG PL:\<SequencingTechnology\>
 175 */
 176 bool SamReadGroup::HasSequencingTechnology(void) const {
 177     return (!SequencingTechnology.empty());
 178 }