src/api/SamReadGroup.cpp

   1 // ***************************************************************************
   2 // SamReadGroup.cpp (c) 2010 Derek Barnett
   3 // Marth Lab, Department of Biology, Boston College
   4 // ---------------------------------------------------------------------------
   5 // Last modified: 18 April 2011 (DB)
   6 // ---------------------------------------------------------------------------
   7 // Provides direct read/write access to the SAM read group data fields.
   8 // ***************************************************************************
   9
  10 #include <api/SamReadGroup.h>
  11 using namespace BamTools;
  12 using namespace std;
  13
  14 /*! \struct BamTools::SamReadGroup
  15     \brief Represents a SAM read group entry.
  16
  17     Provides direct read/write access to the SAM read group data fields.
  18
  19     \sa \samSpecURL
  20 */
  21 /*! \var SamReadGroup::Description
  22     \brief corresponds to \@RG DS:\<Description\>
  23 */
  24 /*! \var SamReadGroup::FlowOrder
  25     \brief corresponds to \@RG FO:\<FlowOrder\>
  26 */
  27 /*! \var SamReadGroup::ID
  28     \brief corresponds to \@RG ID:\<ID\>
  29
  30     Required for valid SAM header.
  31 */
  32 /*! \var SamReadGroup::KeySequence
  33     \brief corresponds to \@RG KS:\<KeySequence\>
  34 */
  35 /*! \var SamReadGroup::Library
  36     \brief corresponds to \@RG LB:\<Library\>
  37 */
  38 /*! \var SamReadGroup::PlatformUnit
  39     \brief corresponds to \@RG PU:\<PlatformUnit\>
  40 */
  41 /*! \var SamReadGroup::PredictedInsertSize
  42     \brief corresponds to \@RG PI:\<PredictedInsertSize\>
  43 */
  44 /*! \var SamReadGroup::ProductionDate
  45     \brief corresponds to \@RG DT:\<ProductionDate\>
  46 */
  47 /*! \var SamReadGroup::Program
  48     \brief corresponds to \@RG PG:\<Program\>
  49 */
  50 /*! \var SamReadGroup::Sample
  51     \brief corresponds to \@RG SM:\<Sample\>
  52 */
  53 /*! \var SamReadGroup::SequencingCenter
  54     \brief corresponds to \@RG CN:\<SequencingCenter\>
  55 */
  56 /*! \var SamReadGroup::SequencingTechnology
  57     \brief corresponds to \@RG PL:\<SequencingTechnology\>
  58 */
  59
  60 /*! \fn SamReadGroup::SamReadGroup(void)
  61     \brief default constructor
  62 */
  63 SamReadGroup::SamReadGroup(void)
  64     : Description("")
  65     , FlowOrder("")
  66     , ID("")
  67     , KeySequence("")
  68     , Library("")
  69     , PlatformUnit("")
  70     , PredictedInsertSize("")
  71     , ProductionDate("")
  72     , Program("")
  73     , Sample("")
  74     , SequencingCenter("")
  75     , SequencingTechnology("")
  76 { }
  77
  78 /*! \fn SamReadGroup::SamReadGroup(const std::string& id)
  79     \brief constructs read group with \a id
  80
  81     \param id desired read group ID
  82 */
  83 SamReadGroup::SamReadGroup(const std::string& id)
  84     : Description("")
  85     , FlowOrder("")
  86     , ID(id)
  87     , KeySequence("")
  88     , Library("")
  89     , PlatformUnit("")
  90     , PredictedInsertSize("")
  91     , ProductionDate("")
  92     , Program("")
  93     , Sample("")
  94     , SequencingCenter("")
  95     , SequencingTechnology("")
  96 { }
  97
  98 /*! \fn SamReadGroup::SamReadGroup(const SamReadGroup& other)
  99     \brief copy constructor
 100 */
 101 SamReadGroup::SamReadGroup(const SamReadGroup& other)
 102     : Description(other.Description)
 103     , FlowOrder(other.FlowOrder)
 104     , ID(other.ID)
 105     , KeySequence(other.KeySequence)
 106     , Library(other.Library)
 107     , PlatformUnit(other.PlatformUnit)
 108     , PredictedInsertSize(other.PredictedInsertSize)
 109     , ProductionDate(other.ProductionDate)
 110     , Program(other.Program)
 111     , Sample(other.Sample)
 112     , SequencingCenter(other.SequencingCenter)
 113     , SequencingTechnology(other.SequencingTechnology)
 114 { }
 115
 116 /*! \fn SamReadGroup::~SamReadGroup(void)
 117     \brief destructor
 118 */
 119 SamReadGroup::~SamReadGroup(void) { }
 120
 121 /*! \fn void SamReadGroup::Clear(void)
 122     \brief Clears all data fields.
 123 */
 124 void SamReadGroup::Clear(void) {
 125     Description.clear();
 126     FlowOrder.clear();
 127     ID.clear();
 128     KeySequence.clear();
 129     Library.clear();
 130     PlatformUnit.clear();
 131     PredictedInsertSize.clear();
 132     ProductionDate.clear();
 133     Program.clear();
 134     Sample.clear();
 135     SequencingCenter.clear();
 136     SequencingTechnology.clear();
 137 }
 138
 139 /*! \fn bool SamReadGroup::HasDescription(void) const
 140     \brief Returns \c true if read group contains \@RG DS:\<Description\>
 141 */
 142 bool SamReadGroup::HasDescription(void) const {
 143     return (!Description.empty());
 144 }
 145
 146 /*! \fn bool SamReadGroup::HasFlowOrder(void) const
 147     \brief Returns \c true if read group contains \@RG FO:\<FlowOrder\>
 148 */
 149 bool SamReadGroup::HasFlowOrder(void) const {
 150     return (!FlowOrder.empty());
 151 }
 152
 153 /*! \fn bool SamReadGroup::HasID(void) const
 154     \brief Returns \c true if read group contains \@RG: ID:\<ID\>
 155 */
 156 bool SamReadGroup::HasID(void) const {
 157     return (!ID.empty());
 158 }
 159
 160 /*! \fn bool SamReadGroup::HasKeySequence(void) const
 161     \brief Returns \c true if read group contains \@RG KS:\<KeySequence\>
 162 */
 163 bool SamReadGroup::HasKeySequence(void) const {
 164     return (!KeySequence.empty());
 165 }
 166
 167 /*! \fn bool SamReadGroup::HasLibrary(void) const
 168     \brief Returns \c true if read group contains \@RG LB:\<Library\>
 169 */
 170 bool SamReadGroup::HasLibrary(void) const {
 171     return (!Library.empty());
 172 }
 173
 174 /*! \fn bool SamReadGroup::HasPlatformUnit(void) const
 175     \brief Returns \c true if read group contains \@RG PU:\<PlatformUnit\>
 176 */
 177 bool SamReadGroup::HasPlatformUnit(void) const {
 178     return (!PlatformUnit.empty());
 179 }
 180
 181 /*! \fn bool SamReadGroup::HasPredictedInsertSize(void) const
 182     \brief Returns \c true if read group contains \@RG PI:\<PredictedInsertSize\>
 183 */
 184 bool SamReadGroup::HasPredictedInsertSize(void) const {
 185     return (!PredictedInsertSize.empty());
 186 }
 187
 188 /*! \fn bool SamReadGroup::HasProductionDate(void) const
 189     \brief Returns \c true if read group contains \@RG DT:\<ProductionDate\>
 190 */
 191 bool SamReadGroup::HasProductionDate(void) const {
 192     return (!ProductionDate.empty());
 193 }
 194
 195 /*! \fn bool SamReadGroup::HasProgram(void) const
 196     \brief Returns \c true if read group contains \@RG PG:\<Program\>
 197 */
 198 bool SamReadGroup::HasProgram(void) const {
 199     return (!Program.empty());
 200 }
 201
 202 /*! \fn bool SamReadGroup::HasSample(void) const
 203     \brief Returns \c true if read group contains \@RG SM:\<Sample\>
 204 */
 205 bool SamReadGroup::HasSample(void) const {
 206     return (!Sample.empty());
 207 }
 208
 209 /*! \fn bool SamReadGroup::HasSequencingCenter(void) const
 210     \brief Returns \c true if read group contains \@RG CN:\<SequencingCenter\>
 211 */
 212 bool SamReadGroup::HasSequencingCenter(void) const {
 213     return (!SequencingCenter.empty());
 214 }
 215
 216 /*! \fn bool SamReadGroup::HasSequencingTechnology(void) const
 217     \brief Returns \c true if read group contains \@RG PL:\<SequencingTechnology\>
 218 */
 219 bool SamReadGroup::HasSequencingTechnology(void) const {
 220     return (!SequencingTechnology.empty());
 221 }