-// ***************************************************************************
-// BamReader (c) 2009 Derek Barnett
-// Marth Lab, Deptartment of Biology, Boston College
-// All rights reserved.
-// ---------------------------------------------------------------------------
-// Provides the basic functionality for reading BAM files
-// ***************************************************************************
-
-#pragma once
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <zlib.h>
-
-#include <algorithm>
-#include <string>
-#include <utility>
-#include <vector>
-using namespace std;
-
-#include "BamAlignment.h"
-
-// our zlib constants
-#define GZIP_ID1 31
-#define GZIP_ID2 139
-#define CM_DEFLATE 8
-#define FLG_FEXTRA 4
-#define OS_UNKNOWN 255
-#define BGZF_XLEN 6
-#define BGZF_ID1 66
-#define BGZF_ID2 67
-#define BGZF_LEN 2
-#define GZIP_WINDOW_BITS -15
-#define Z_DEFAULT_MEM_LEVEL 8
-
-// our BZGF constants
-#define BLOCK_HEADER_LENGTH 18
-#define BLOCK_FOOTER_LENGTH 8
-#define MAX_BLOCK_SIZE 65536
-#define DEFAULT_BLOCK_SIZE 65536
-
-// our BAM constants
-#define BAM_CORE_SIZE 32
-#define BAM_CMATCH 0
-#define BAM_CINS 1
-#define BAM_CDEL 2
-#define BAM_CREF_SKIP 3
-#define BAM_CSOFT_CLIP 4
-#define BAM_CHARD_CLIP 5
-#define BAM_CPAD 6
-#define BAM_CIGAR_SHIFT 4
-#define BAM_CIGAR_MASK ((1 << BAM_CIGAR_SHIFT) - 1)
-
-// BAM indexing constants
-#define MAX_BIN 37450 // =(8^6-1)/7+1
-#define BAM_MIN_CHUNK_GAP 32768
-#define BAM_LIDX_SHIFT 14
-
-// our variable sizes
-#define SIZEOF_INT 4
-
-// define our BZGF structure
-#ifndef BGZF_DATA
-#define BGZF_DATA
-struct BgzfData {
- unsigned int UncompressedBlockSize;
- unsigned int CompressedBlockSize;
- unsigned int BlockLength;
- unsigned int BlockOffset;
- uint64_t BlockAddress;
- bool IsOpen;
- FILE* Stream;
- char* UncompressedBlock;
- char* CompressedBlock;
-
- // constructor
- BgzfData(void)
- : UncompressedBlockSize(DEFAULT_BLOCK_SIZE)
- , CompressedBlockSize(MAX_BLOCK_SIZE)
- , BlockLength(0)
- , BlockOffset(0)
- , BlockAddress(0)
- , IsOpen(false)
- , Stream(NULL)
- , UncompressedBlock(NULL)
- , CompressedBlock(NULL)
- {
- try {
- CompressedBlock = new char[CompressedBlockSize];
- UncompressedBlock = new char[UncompressedBlockSize];
- } catch(bad_alloc&) {
- printf("ERROR: Unable to allocate memory for our BGZF object.\n");
- exit(1);
- }
- }
-
- // destructor
- ~BgzfData(void) {
- if(CompressedBlock) delete [] CompressedBlock;
- if(UncompressedBlock) delete [] UncompressedBlock;
- }
-};
-#endif // BGZF_DATA
-
-
-// --------------------------- //
-// BamIndex-related typedefs
-// --------------------------- //
-
-// offset for linear indexing
-typedef vector<uint64_t> LinearOffsetVector;
-
-// alignment 'chunk' boundaries
-typedef pair<uint64_t, uint64_t> ChunkPair;
-typedef vector<ChunkPair> ChunkVector;
-
-// BAM bins.. each contains (binID, alignment 'chunks')
-typedef pair<uint32_t, ChunkVector*> BamBin;
-typedef vector<BamBin> BinVector;
-
-// each reference sequence has a BinVector and LinearOffsetVector
-typedef pair<BinVector*, LinearOffsetVector*> RefIndex;
-
-// full BamIndex defined as:
-typedef vector<RefIndex*> BamIndex;
-
-class BamReader {
-
- // constructor/destructor
- public:
- BamReader(void);
- ~BamReader(void);
-
- // public interface
- public:
- // closes the BAM file
- void Close(void);
- // retrieves header text
- const string GetHeaderText(void) const;
- // saves the alignment to the alignment archive
- bool GetNextAlignment(BamAlignment& bAlignment);
- // return number of reference sequences in BAM file
- const int GetReferenceCount(void) const;
- // return vector of RefData entries
- const RefVector GetReferenceData(void) const;
- // get refID from reference name
- const int GetReferenceID(const string& refName) const;
- // jumps to 'left' position on refID
- bool Jump(int refID, unsigned int left = 0);
- // opens the BAM file
- void Open(const string& filename, const string& indexFilename = "");
- // move file pointer back to first alignment
- bool Rewind(void);
-
- // internal methods
- private:
- // checks BGZF block header
- bool BgzfCheckBlockHeader(char* header);
- // closes the BAM file
- void BgzfClose(void);
- // de-compresses the current block
- int BgzfInflateBlock(int blockLength);
- // opens the BAM file for reading
- void BgzfOpen(const string& filename);
- // reads BGZF data into a byte buffer
- unsigned int BgzfRead(char* data, const unsigned int dataLen);
- // reads BGZF block
- int BgzfReadBlock(void);
- // seek to position in BAM file
- bool BgzfSeek(int64_t position);
- // get file position in BAM file
- int64_t BgzfTell(void);
- // unpacks a buffer into an unsigned int
- static inline unsigned int BgzfUnpackUnsignedInt(char* buffer);
- // unpacks a buffer into an unsigned short
- static inline unsigned short BgzfUnpackUnsignedShort(char* buffer);
- // calculate bins that overlap region ( left to reference end for now )
- int BinsFromRegion(int, unsigned int, uint16_t[MAX_BIN]);
- // calculates alignment end position based on starting position and provided CIGAR operations
- unsigned int CalculateAlignmentEnd(const unsigned int& position, const vector<CigarOp>& cigarData);
- // clear out (delete pointers in) index data structure
- void ClearIndex(void);
- // calculate file offset for first alignment chunk overlapping 'left'
- int64_t GetOffset(int refID, unsigned int left);
- // checks to see if alignment overlaps current region
- bool IsOverlap(BamAlignment& bAlignment);
- // retrieves header text from BAM file
- void LoadHeaderData(void);
- // builds BamIndex data structure from BAM index file
- void LoadIndexData(FILE* indexStream);
- // retrieves BAM alignment under file pointer
- bool LoadNextAlignment(BamAlignment& bAlignment);
- // builds reference data structure from BAM file
- void LoadReferenceData(void);
- // open BAM index file (if successful, loads index)
- void OpenIndex(const string& indexFilename);
-
- // aligment file & index file data
- private:
- BgzfData m_BGZF;
- string m_headerText;
- BamIndex* m_index;
- RefVector m_references;
- bool m_isIndexLoaded;
- int64_t m_alignmentsBeginOffset;
-
- // user-specified region values
- private:
- bool m_isRegionSpecified;
- int m_currentRefID;
- unsigned int m_currentLeft;
-
- // BAM character constants
- private:
- static const char* DNA_LOOKUP;
- static const char* CIGAR_LOOKUP;
-};
-
-// unpacks a buffer into an unsigned int
-inline unsigned int BamReader::BgzfUnpackUnsignedInt(char* buffer) {
- union { unsigned int value; unsigned char valueBuffer[sizeof(unsigned int)]; } un;
- un.valueBuffer[0] = buffer[0];
- un.valueBuffer[1] = buffer[1];
- un.valueBuffer[2] = buffer[2];
- un.valueBuffer[3] = buffer[3];
- return un.value;
-}
-
-// unpacks a buffer into an unsigned short
-inline unsigned short BamReader::BgzfUnpackUnsignedShort(char* buffer) {
- union { unsigned short value; unsigned char valueBuffer[sizeof(unsigned short)];} un;
- un.valueBuffer[0] = buffer[0];
- un.valueBuffer[1] = buffer[1];
- return un.value;
-}
-
-// allows sorting/searching of a vector of pairs (instead of using maps)
-template <typename Key, typename Value>
-class LookupKeyCompare {
-
- typedef pair< Key, Value > LookupData;
- typedef typename LookupData::first_type Key_t;
-
- public:
- bool operator() (const LookupData& lhs, const LookupData& rhs) const { return keyLess(lhs.first, rhs.first); }
- bool operator() (const LookupData& lhs, const Key_t& k) const { return keyLess(lhs.first, k); }
- bool operator() (const Key_t& k, const LookupData& rhs) const { return keyLess(k, rhs.first); }
- private:
- bool keyLess(const Key_t& k1, const Key_t& k2) const { return k1 < k2; }
-};
-
-// return index of item if found, else return container.size()
-template < typename InputIterator, typename EqualityComparable >
-typename iterator_traits<InputIterator>::difference_type
-Index(const InputIterator& begin, const InputIterator& end, const EqualityComparable& item) {
- return distance(begin, find(begin, end, item));
-}
-
+// ***************************************************************************\r
+// BamReader.h (c) 2009 Derek Barnett, Michael Str�mberg\r
+// Marth Lab, Department of Biology, Boston College\r
+// All rights reserved.\r
+// ---------------------------------------------------------------------------\r
+// Last modified: 8 June 2010 (DB)\r
+// ---------------------------------------------------------------------------\r
+// Uses BGZF routines were adapted from the bgzf.c code developed at the Broad\r
+// Institute.\r
+// ---------------------------------------------------------------------------\r
+// Provides the basic functionality for reading BAM files\r
+// ***************************************************************************\r
+\r
+#ifndef BAMREADER_H\r
+#define BAMREADER_H\r
+\r
+// C++ includes\r
+#include <string>\r
+\r
+// BamTools includes\r
+#include "BamAux.h"\r
+\r
+namespace BamTools {\r
+\r
+class BamReader {\r
+\r
+ // constructor / destructor\r
+ public:\r
+ BamReader(void);\r
+ ~BamReader(void);\r
+\r
+ // public interface\r
+ public:\r
+\r
+ // ----------------------\r
+ // BAM file operations\r
+ // ----------------------\r
+\r
+ // close BAM file\r
+ void Close(void);\r
+ // performs random-access jump to reference, position\r
+ bool Jump(int refID, int position = 0);\r
+ // opens BAM file (and optional BAM index file, if provided)\r
+ void Open(const std::string& filename, const std::string& indexFilename = "");\r
+ // returns file pointer to beginning of alignments\r
+ bool Rewind(void);\r
+\r
+ // ----------------------\r
+ // access alignment data\r
+ // ----------------------\r
+\r
+ // retrieves next available alignment (returns success/fail)\r
+ bool GetNextAlignment(BamAlignment& bAlignment);\r
+ // retrieves next available alignment core data (returns success/fail)\r
+ // ** DOES NOT parse any character data (bases, qualities, tag data)\r
+ // these can be accessed, if necessary, from the supportData \r
+ // useful for operations requiring ONLY positional or other alignment-related information\r
+ bool GetNextAlignmentCore(BamAlignment& bAlignment, BamAlignmentSupportData& supportData);\r
+\r
+ // ----------------------\r
+ // access auxiliary data\r
+ // ----------------------\r
+\r
+ // returns SAM header text\r
+ const std::string GetHeaderText(void) const;\r
+ // returns number of reference sequences\r
+ int GetReferenceCount(void) const;\r
+ // returns vector of reference objects\r
+ const BamTools::RefVector GetReferenceData(void) const;\r
+ // returns reference id (used for BamReader::Jump()) for the given reference name\r
+ int GetReferenceID(const std::string& refName) const;\r
+ // returns the name of the file associated with this BamReader\r
+ const std::string GetFilename(void) const;\r
+\r
+ // ----------------------\r
+ // BAM index operations\r
+ // ----------------------\r
+\r
+ // creates index for BAM file, saves to file (default = bamFilename + ".bai")\r
+ bool CreateIndex(void);\r
+\r
+ // private implementation\r
+ private:\r
+ struct BamReaderPrivate;\r
+ BamReaderPrivate* d;\r
+};\r
+\r
+} // namespace BamTools\r
+\r
+#endif // BAMREADER_H\r
projects / bamtools.git / blobdiff