1 // ***************************************************************************
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2 // BamReader.h (c) 2009 Derek Barnett, Michael Str�mberg
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3 // Marth Lab, Department of Biology, Boston College
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4 // All rights reserved.
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5 // ---------------------------------------------------------------------------
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6 // Last modified: 8 June 2010 (DB)
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7 // ---------------------------------------------------------------------------
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8 // Uses BGZF routines were adapted from the bgzf.c code developed at the Broad
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10 // ---------------------------------------------------------------------------
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11 // Provides the basic functionality for reading BAM files
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12 // ***************************************************************************
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20 // BamTools includes
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23 namespace BamTools {
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27 // constructor / destructor
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35 // ----------------------
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36 // BAM file operations
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37 // ----------------------
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41 // performs random-access jump to reference, position
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42 bool Jump(int refID, int position = 0);
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43 // opens BAM file (and optional BAM index file, if provided)
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44 void Open(const std::string& filename, const std::string& indexFilename = "");
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45 // returns file pointer to beginning of alignments
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48 // ----------------------
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49 // access alignment data
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50 // ----------------------
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52 // retrieves next available alignment (returns success/fail)
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53 bool GetNextAlignment(BamAlignment& bAlignment);
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54 // retrieves next available alignment core data (returns success/fail)
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55 // ** DOES NOT parse any character data (bases, qualities, tag data)
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56 // these can be accessed, if necessary, from the supportData
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57 // useful for operations requiring ONLY positional or other alignment-related information
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58 bool GetNextAlignmentCore(BamAlignment& bAlignment, BamAlignmentSupportData& supportData);
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60 // ----------------------
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61 // access auxiliary data
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62 // ----------------------
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64 // returns SAM header text
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65 const std::string GetHeaderText(void) const;
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66 // returns number of reference sequences
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67 int GetReferenceCount(void) const;
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68 // returns vector of reference objects
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69 const BamTools::RefVector GetReferenceData(void) const;
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70 // returns reference id (used for BamReader::Jump()) for the given reference name
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71 int GetReferenceID(const std::string& refName) const;
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72 // returns the name of the file associated with this BamReader
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73 const std::string GetFilename(void) const;
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75 // ----------------------
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76 // BAM index operations
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77 // ----------------------
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79 // creates index for BAM file, saves to file (default = bamFilename + ".bai")
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80 bool CreateIndex(void);
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82 // private implementation
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84 struct BamReaderPrivate;
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85 BamReaderPrivate* d;
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88 } // namespace BamTools
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90 #endif // BAMREADER_H
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