multovl  1.3
Multiple overlaps of genomic regions
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bamio.hh
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35 #ifndef MULTOVL_BAMIO_HEADER
36 #define MULTOVL_BAMIO_HEADER
37 
38 // == HEADER bamio.hh ==
39 
47 // -- Standard headers --
48 
49 #include <string>
50 #include <vector>
51 
52 // -- Library headers --
53 
54 #include "trackio.hh"
55 #include "fileformat.hh"
56 
57 // -- BAM tools --
58 
59 #include "api/BamReader.h"
60 #include "api/BamAux.h"
61 
62 namespace multovl {
63 namespace io {
64 
70 class BamReader: public TrackReader
71 {
72 public:
73 
76  explicit BamReader(const std::string& infname);
77 
85  virtual
86  std::string read_into(std::string& chrom, Region& reg);
87 
88  ~BamReader();
89 
90 private:
91 
92  BamTools::BamReader _bamreader;
93  BamTools::RefVector _refs;
94  BamTools::BamAlignment _albuf; // BAM aligned region input buffer
95 
96 }; // END OF CLASS BamReader
97 
98 // -- Output --
99 
100 // Add code here if you want to do BAM-formatted output. Not implemented yet.
101 
102 } // namespace io
103 } // namespace multovl
104 
105 #endif // MULTOVL_BAMIO_HEADER
virtual std::string read_into(std::string &chrom, Region &reg)
Definition: trackio.hh:69
Module to handle file format recognition.
Definition: bamio.hh:70
Instances of the Region class represent regions on a sequence. They have first and last coordinates...
Definition: region.hh:65
BamReader(const std::string &infname)
Base classes to read/write input/output tracks (collections of regions).