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: 18 April 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 \samSpecURL
  21 */
  22 /*! \var SamReadGroup::Description
  23     \brief corresponds to \@RG DS:\<Description\>
  24 */
  25 /*! \var SamReadGroup::FlowOrder
  26     \brief corresponds to \@RG FO:\<FlowOrder\>
  27 */
  28 /*! \var SamReadGroup::ID
  29     \brief corresponds to \@RG ID:\<ID\>
  30
  31     Required for valid SAM header.
  32 */
  33 /*! \var SamReadGroup::KeySequence
  34     \brief corresponds to \@RG KS:\<KeySequence\>
  35 */
  36 /*! \var SamReadGroup::Library
  37     \brief corresponds to \@RG LB:\<Library\>
  38 */
  39 /*! \var SamReadGroup::PlatformUnit
  40     \brief corresponds to \@RG PU:\<PlatformUnit\>
  41 */
  42 /*! \var SamReadGroup::PredictedInsertSize
  43     \brief corresponds to \@RG PI:\<PredictedInsertSize\>
  44 */
  45 /*! \var SamReadGroup::ProductionDate
  46     \brief corresponds to \@RG DT:\<ProductionDate\>
  47 */
  48 /*! \var SamReadGroup::Program
  49     \brief corresponds to \@RG PG:\<Program\>
  50 */
  51 /*! \var SamReadGroup::Sample
  52     \brief corresponds to \@RG SM:\<Sample\>
  53 */
  54 /*! \var SamReadGroup::SequencingCenter
  55     \brief corresponds to \@RG CN:\<SequencingCenter\>
  56 */
  57 /*! \var SamReadGroup::SequencingTechnology
  58     \brief corresponds to \@RG PL:\<SequencingTechnology\>
  59 */
  60
  61 /*! \fn SamReadGroup::SamReadGroup(void)
  62     \brief default constructor
  63 */
  64 SamReadGroup::SamReadGroup(void)
  65     : Description("")
  66     , FlowOrder("")
  67     , ID("")
  68     , KeySequence("")
  69     , Library("")
  70     , PlatformUnit("")
  71     , PredictedInsertSize("")
  72     , ProductionDate("")
  73     , Program("")
  74     , Sample("")
  75     , SequencingCenter("")
  76     , SequencingTechnology("")
  77 { }
  78
  79 /*! \fn SamReadGroup::SamReadGroup(const std::string& id)
  80     \brief constructs read group with \a id
  81
  82     \param id desired read group ID
  83 */
  84 SamReadGroup::SamReadGroup(const std::string& id)
  85     : Description("")
  86     , FlowOrder("")
  87     , ID(id)
  88     , KeySequence("")
  89     , Library("")
  90     , PlatformUnit("")
  91     , PredictedInsertSize("")
  92     , ProductionDate("")
  93     , Program("")
  94     , Sample("")
  95     , SequencingCenter("")
  96     , SequencingTechnology("")
  97 { }
  98
  99 /*! \fn SamReadGroup::SamReadGroup(const SamReadGroup& other)
 100     \brief copy constructor
 101 */
 102 SamReadGroup::SamReadGroup(const SamReadGroup& other)
 103     : Description(other.Description)
 104     , FlowOrder(other.FlowOrder)
 105     , ID(other.ID)
 106     , KeySequence(other.KeySequence)
 107     , Library(other.Library)
 108     , PlatformUnit(other.PlatformUnit)
 109     , PredictedInsertSize(other.PredictedInsertSize)
 110     , ProductionDate(other.ProductionDate)
 111     , Program(other.Program)
 112     , Sample(other.Sample)
 113     , SequencingCenter(other.SequencingCenter)
 114     , SequencingTechnology(other.SequencingTechnology)
 115 { }
 116
 117 /*! \fn SamReadGroup::~SamReadGroup(void)
 118     \brief destructor
 119 */
 120 SamReadGroup::~SamReadGroup(void) { }
 121
 122 /*! \fn void SamReadGroup::Clear(void)
 123     \brief Clears all data fields.
 124 */
 125 void SamReadGroup::Clear(void) {
 126     Description.clear();
 127     FlowOrder.clear();
 128     ID.clear();
 129     KeySequence.clear();
 130     Library.clear();
 131     PlatformUnit.clear();
 132     PredictedInsertSize.clear();
 133     ProductionDate.clear();
 134     Program.clear();
 135     Sample.clear();
 136     SequencingCenter.clear();
 137     SequencingTechnology.clear();
 138 }
 139
 140 /*! \fn bool SamReadGroup::HasDescription(void) const
 141     \brief Returns \c true if read group contains \@RG DS:\<Description\>
 142 */
 143 bool SamReadGroup::HasDescription(void) const {
 144     return (!Description.empty());
 145 }
 146
 147 /*! \fn bool SamReadGroup::HasFlowOrder(void) const
 148     \brief Returns \c true if read group contains \@RG FO:\<FlowOrder\>
 149 */
 150 bool SamReadGroup::HasFlowOrder(void) const {
 151     return (!FlowOrder.empty());
 152 }
 153
 154 /*! \fn bool SamReadGroup::HasID(void) const
 155     \brief Returns \c true if read group contains \@RG: ID:\<ID\>
 156 */
 157 bool SamReadGroup::HasID(void) const {
 158     return (!ID.empty());
 159 }
 160
 161 /*! \fn bool SamReadGroup::HasKeySequence(void) const
 162     \brief Returns \c true if read group contains \@RG KS:\<KeySequence\>
 163 */
 164 bool SamReadGroup::HasKeySequence(void) const {
 165     return (!KeySequence.empty());
 166 }
 167
 168 /*! \fn bool SamReadGroup::HasLibrary(void) const
 169     \brief Returns \c true if read group contains \@RG LB:\<Library\>
 170 */
 171 bool SamReadGroup::HasLibrary(void) const {
 172     return (!Library.empty());
 173 }
 174
 175 /*! \fn bool SamReadGroup::HasPlatformUnit(void) const
 176     \brief Returns \c true if read group contains \@RG PU:\<PlatformUnit\>
 177 */
 178 bool SamReadGroup::HasPlatformUnit(void) const {
 179     return (!PlatformUnit.empty());
 180 }
 181
 182 /*! \fn bool SamReadGroup::HasPredictedInsertSize(void) const
 183     \brief Returns \c true if read group contains \@RG PI:\<PredictedInsertSize\>
 184 */
 185 bool SamReadGroup::HasPredictedInsertSize(void) const {
 186     return (!PredictedInsertSize.empty());
 187 }
 188
 189 /*! \fn bool SamReadGroup::HasProductionDate(void) const
 190     \brief Returns \c true if read group contains \@RG DT:\<ProductionDate\>
 191 */
 192 bool SamReadGroup::HasProductionDate(void) const {
 193     return (!ProductionDate.empty());
 194 }
 195
 196 /*! \fn bool SamReadGroup::HasProgram(void) const
 197     \brief Returns \c true if read group contains \@RG PG:\<Program\>
 198 */
 199 bool SamReadGroup::HasProgram(void) const {
 200     return (!Program.empty());
 201 }
 202
 203 /*! \fn bool SamReadGroup::HasSample(void) const
 204     \brief Returns \c true if read group contains \@RG SM:\<Sample\>
 205 */
 206 bool SamReadGroup::HasSample(void) const {
 207     return (!Sample.empty());
 208 }
 209
 210 /*! \fn bool SamReadGroup::HasSequencingCenter(void) const
 211     \brief Returns \c true if read group contains \@RG CN:\<SequencingCenter\>
 212 */
 213 bool SamReadGroup::HasSequencingCenter(void) const {
 214     return (!SequencingCenter.empty());
 215 }
 216
 217 /*! \fn bool SamReadGroup::HasSequencingTechnology(void) const
 218     \brief Returns \c true if read group contains \@RG PL:\<SequencingTechnology\>
 219 */
 220 bool SamReadGroup::HasSequencingTechnology(void) const {
 221     return (!SequencingTechnology.empty());
 222 }