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