src/utils/bamtools_pileup_engine.h

   1 // ***************************************************************************
   2 // bamtools_pileup_engine.h (c) 2010 Derek Barnett, Erik Garrison
   3 // Marth Lab, Department of Biology, Boston College
   4 // ---------------------------------------------------------------------------
   5 // Last modified: 10 October 2011
   6 // ---------------------------------------------------------------------------
   7 // Provides pileup at position functionality for various tools.
   8 // ***************************************************************************
   9
  10 #ifndef BAMTOOLS_PILEUP_ENGINE_H
  11 #define BAMTOOLS_PILEUP_ENGINE_H
  12
  13 #include "utils/utils_global.h"
  14
  15 #include <api/BamAlignment.h>
  16 #include <vector>
  17
  18 namespace BamTools {
  19
  20 // contains auxiliary data about a single BamAlignment
  21 // at current position considered
  22 struct UTILS_EXPORT PileupAlignment {
  23
  24     // data members
  25     BamAlignment Alignment;
  26     int32_t PositionInAlignment;
  27     bool IsCurrentDeletion;
  28     bool IsNextDeletion;
  29     bool IsNextInsertion;
  30     int DeletionLength;
  31     int InsertionLength;
  32     bool IsSegmentBegin;
  33     bool IsSegmentEnd;
  34
  35     // ctor
  36     PileupAlignment(const BamAlignment& al)
  37         : Alignment(al)
  38         , PositionInAlignment(-1)
  39         , IsCurrentDeletion(false)
  40         , IsNextDeletion(false)
  41         , IsNextInsertion(false)
  42         , DeletionLength(0)
  43         , InsertionLength(0)
  44         , IsSegmentBegin(false)
  45         , IsSegmentEnd(false)
  46     { }
  47 };
  48
  49 // contains all data at a position
  50 struct UTILS_EXPORT PileupPosition {
  51
  52     // data members
  53     int RefId;
  54     int Position;
  55     std::vector<PileupAlignment> PileupAlignments;
  56
  57     // ctor
  58     PileupPosition(const int& refId = 0,
  59                    const int& position = 0,
  60                    const std::vector<PileupAlignment>& alignments = std::vector<PileupAlignment>())
  61         : RefId(refId)
  62         , Position(position)
  63         , PileupAlignments(alignments)
  64     { }
  65 };
  66
  67 class UTILS_EXPORT PileupVisitor {
  68
  69     public:
  70         PileupVisitor(void) { }
  71         virtual ~PileupVisitor(void) { }
  72
  73     public:
  74         virtual void Visit(const PileupPosition& pileupData) =0;
  75 };
  76
  77 class UTILS_EXPORT PileupEngine {
  78
  79     public:
  80         PileupEngine(void);
  81         ~PileupEngine(void);
  82
  83     public:
  84         bool AddAlignment(const BamAlignment& al);
  85         void AddVisitor(PileupVisitor* visitor);
  86         void Flush(void);
  87
  88     private:
  89         struct PileupEnginePrivate;
  90         PileupEnginePrivate* d;
  91 };
  92
  93 } // namespace BamTools
  94
  95 #endif // BAMTOOLS_PILEUP_ENGINE_H