// Marth Lab, Department of Biology, Boston College\r
// All rights reserved.\r
// ---------------------------------------------------------------------------\r
-// Last modified: 31 March 2010 (DB)\r
+// Last modified: 14 April 2010 (DB)\r
// ---------------------------------------------------------------------------\r
// Provides the basic constants, data structures, etc. for using BAM files\r
// ***************************************************************************\r
struct CigarOp;\r
\r
struct BamAlignment {\r
-\r
- // Queries against alignment flag\r
- public:\r
- // Returns true if this read is a PCR duplicate (determined by external app)\r
- bool IsDuplicate(void) const { return ( (AlignmentFlag & DUPLICATE) != 0 ); }\r
- // Returns true if this read failed quality control (determined by external app)\r
- bool IsFailedQC(void) const { return ( (AlignmentFlag & QC_FAILED) != 0 ); }\r
- // Returns true if alignment is first mate on read\r
- bool IsFirstMate(void) const { return ( (AlignmentFlag & READ_1) != 0 ); }\r
- // Returns true if alignment is mapped\r
- bool IsMapped(void) const { return ( (AlignmentFlag & UNMAPPED) == 0 ); }\r
- // Returns true if alignment's mate is mapped\r
- bool IsMateMapped(void) const { return ( (AlignmentFlag & MATE_UNMAPPED) == 0 ); }\r
- // Returns true if alignment's mate mapped to reverse strand\r
- bool IsMateReverseStrand(void) const { return ( (AlignmentFlag & MATE_REVERSE) != 0 ); }\r
- // Returns true if alignment part of paired-end read\r
- bool IsPaired(void) const { return ( (AlignmentFlag & PAIRED) != 0 ); }\r
- // Returns true if this position is primary alignment (determined by external app)\r
- bool IsPrimaryAlignment(void) const { return ( (AlignmentFlag & SECONDARY) == 0 ); }\r
- // Returns true if alignment is part of read that satisfied paired-end resolution (determined by external app)\r
- bool IsProperPair(void) const { return ( (AlignmentFlag & PROPER_PAIR) != 0 ); }\r
- // Returns true if alignment mapped to reverse strand\r
- bool IsReverseStrand(void) const { return ( (AlignmentFlag & REVERSE) != 0 ); }\r
- // Returns true if alignment is second mate on read\r
- bool IsSecondMate(void) const { return ( (AlignmentFlag & READ_2) != 0 ); }\r
-\r
- // Manipulate alignment flag\r
+
+ // constructors & destructor
+ public:
+ BamAlignment(void);
+ BamAlignment(const BamAlignment& other);
+ ~BamAlignment(void);
+\r
+ // Queries against alignment flags\r
+ public: \r
+ bool IsDuplicate(void) const; // Returns true if this read is a PCR duplicate \r
+ bool IsFailedQC(void) const; // Returns true if this read failed quality control \r
+ bool IsFirstMate(void) const; // Returns true if alignment is first mate on read \r
+ bool IsMapped(void) const; // Returns true if alignment is mapped \r
+ bool IsMateMapped(void) const; // Returns true if alignment's mate is mapped \r
+ bool IsMateReverseStrand(void) const; // Returns true if alignment's mate mapped to reverse strand \r
+ bool IsPaired(void) const; // Returns true if alignment part of paired-end read \r
+ bool IsPrimaryAlignment(void) const; // Returns true if reported position is primary alignment \r
+ bool IsProperPair(void) const; // Returns true if alignment is part of read that satisfied paired-end resolution \r
+ bool IsReverseStrand(void) const; // Returns true if alignment mapped to reverse strand\r
+ bool IsSecondMate(void) const; // Returns true if alignment is second mate on read\r
+\r
+ // Manipulate alignment flags\r
+ public: \r
+ void SetIsDuplicate(bool ok); // Sets "PCR duplicate" flag \r
+ void SetIsFailedQC(bool ok); // Sets "failed quality control" flag \r
+ void SetIsFirstMate(bool ok); // Sets "alignment is first mate" flag \r
+ void SetIsMateUnmapped(bool ok); // Sets "alignment's mate is mapped" flag \r
+ void SetIsMateReverseStrand(bool ok); // Sets "alignment's mate mapped to reverse strand" flag \r
+ void SetIsPaired(bool ok); // Sets "alignment part of paired-end read" flag \r
+ void SetIsProperPair(bool ok); // Sets "alignment is part of read that satisfied paired-end resolution" flag \r
+ void SetIsReverseStrand(bool ok); // Sets "alignment mapped to reverse strand" flag \r
+ void SetIsSecondaryAlignment(bool ok); // Sets "position is primary alignment" flag \r
+ void SetIsSecondMate(bool ok); // Sets "alignment is second mate on read" flag \r
+ void SetIsUnmapped(bool ok); // Sets "alignment is mapped" flag\r
+
+ // Tag data access methods
public:\r
- // Sets "PCR duplicate" bit \r
- void SetIsDuplicate(bool ok) { if (ok) AlignmentFlag |= DUPLICATE; else AlignmentFlag &= ~DUPLICATE; }\r
- // Sets "failed quality control" bit\r
- void SetIsFailedQC(bool ok) { if (ok) AlignmentFlag |= QC_FAILED; else AlignmentFlag &= ~QC_FAILED; }\r
- // Sets "alignment is first mate" bit\r
- void SetIsFirstMate(bool ok) { if (ok) AlignmentFlag |= READ_1; else AlignmentFlag &= ~READ_1; }\r
- // Sets "alignment's mate is mapped" bit\r
- void SetIsMateUnmapped(bool ok) { if (ok) AlignmentFlag |= MATE_UNMAPPED; else AlignmentFlag &= ~MATE_UNMAPPED; }\r
- // Sets "alignment's mate mapped to reverse strand" bit\r
- void SetIsMateReverseStrand(bool ok) { if (ok) AlignmentFlag |= MATE_REVERSE; else AlignmentFlag &= ~MATE_REVERSE; }\r
- // Sets "alignment part of paired-end read" bit\r
- void SetIsPaired(bool ok) { if (ok) AlignmentFlag |= PAIRED; else AlignmentFlag &= ~PAIRED; }\r
- // Sets "alignment is part of read that satisfied paired-end resolution" bit\r
- void SetIsProperPair(bool ok) { if (ok) AlignmentFlag |= PROPER_PAIR; else AlignmentFlag &= ~PROPER_PAIR; }\r
- // Sets "alignment mapped to reverse strand" bit\r
- void SetIsReverseStrand(bool ok) { if (ok) AlignmentFlag |= REVERSE; else AlignmentFlag &= ~REVERSE; }\r
- // Sets "position is primary alignment (determined by external app)"\r
- void SetIsSecondaryAlignment(bool ok) { if (ok) AlignmentFlag |= SECONDARY; else AlignmentFlag &= ~SECONDARY; }\r
- // Sets "alignment is second mate on read" bit\r
- void SetIsSecondMate(bool ok) { if (ok) AlignmentFlag |= READ_2; else AlignmentFlag &= ~READ_2; }\r
- // Sets "alignment is mapped" bit\r
- void SetIsUnmapped(bool ok) { if (ok) AlignmentFlag |= UNMAPPED; else AlignmentFlag &= ~UNMAPPED; }\r
-\r
+ bool GetEditDistance(uint8_t& editDistance) const; // get "NM" tag data - contributed by Aaron Quinlan\r
+ bool GetReadGroup(std::string& readGroup) const; // get "RG" tag data\r
+
+ // Additional data access methods\r
public:\r
-\r
- // get "RG" tag data\r
- bool GetReadGroup(std::string& readGroup) const {\r
-\r
- if ( TagData.empty() ) { return false; }\r
-\r
- // localize the tag data\r
- char* pTagData = (char*)TagData.data();\r
- const unsigned int tagDataLen = TagData.size();\r
- unsigned int numBytesParsed = 0;\r
-\r
- bool foundReadGroupTag = false;\r
- while( numBytesParsed < tagDataLen ) {\r
-\r
- const char* pTagType = pTagData;\r
- const char* pTagStorageType = pTagData + 2;\r
- pTagData += 3;\r
- numBytesParsed += 3;\r
-\r
- // check the current tag\r
- if ( std::strncmp(pTagType, "RG", 2) == 0 ) {\r
- foundReadGroupTag = true;\r
- break;\r
- }\r
-\r
- // get the storage class and find the next tag\r
- if (*pTagStorageType == '\0') { return false; }\r
- SkipToNextTag( *pTagStorageType, pTagData, numBytesParsed );\r
- if (*pTagData == '\0') { return false; }\r
- }\r
-\r
- // return if the read group tag was not present\r
- if ( !foundReadGroupTag ) { return false; }\r
-\r
- // assign the read group\r
- const unsigned int readGroupLen = std::strlen(pTagData);\r
- readGroup.resize(readGroupLen);\r
- std::memcpy( (char*)readGroup.data(), pTagData, readGroupLen );\r
- return true;\r
- }\r
-\r
- // get "NM" tag data - contributed by Aaron Quinlan\r
- bool GetEditDistance(uint8_t& editDistance) const {\r
-\r
- if ( TagData.empty() ) { return false; }\r
-\r
- // localize the tag data\r
- char* pTagData = (char*)TagData.data();\r
- const unsigned int tagDataLen = TagData.size();\r
- unsigned int numBytesParsed = 0;\r
-\r
- bool foundEditDistanceTag = false;\r
- while( numBytesParsed < tagDataLen ) {\r
-\r
- const char* pTagType = pTagData;\r
- const char* pTagStorageType = pTagData + 2;\r
- pTagData += 3;\r
- numBytesParsed += 3;\r
-\r
- // check the current tag\r
- if ( strncmp(pTagType, "NM", 2) == 0 ) {\r
- foundEditDistanceTag = true;\r
- break;\r
- }\r
-\r
- // get the storage class and find the next tag\r
- if (*pTagStorageType == '\0') { return false; }\r
- SkipToNextTag( *pTagStorageType, pTagData, numBytesParsed );\r
- if (*pTagData == '\0') { return false; }\r
- }\r
- // return if the edit distance tag was not present\r
- if ( !foundEditDistanceTag ) { return false; }\r
-\r
- // assign the editDistance value\r
- std::memcpy(&editDistance, pTagData, 1);\r
- return true;\r
- }\r
-\r
+ int GetEndPosition(bool usePadded = false) const; // calculates alignment end position, based on starting position and CIGAR operations
+
+ // 'internal' utility methods \r
private:\r
- static void SkipToNextTag(const char storageType, char* &pTagData, unsigned int& numBytesParsed) {\r
- switch(storageType) {\r
-\r
- case 'A':\r
- case 'c':\r
- case 'C':\r
- ++numBytesParsed;\r
- ++pTagData;\r
- break;\r
-\r
- case 's':\r
- case 'S':\r
- numBytesParsed += 2;\r
- pTagData += 2;\r
- break;\r
-\r
- case 'f':\r
- case 'i':\r
- case 'I':\r
- numBytesParsed += 4;\r
- pTagData += 4;\r
- break;\r
-\r
- case 'Z':\r
- case 'H':\r
- while(*pTagData) {\r
- ++numBytesParsed;\r
- ++pTagData;\r
- }\r
- // ---------------------------\r
- // Added: 3-25-2010 DWB\r
- // Contributed: ARQ\r
- // Fixed: error parsing variable length tag data\r
- ++pTagData;\r
- // ---------------------------\r
- break;\r
-\r
- default:\r
- printf("ERROR: Unknown tag storage class encountered: [%c]\n", *pTagData);\r
- exit(1);\r
- }\r
- }\r
+ static void SkipToNextTag(const char storageType, char* &pTagData, unsigned int& numBytesParsed);\r
\r
// Data members\r
public:\r
int32_t MatePosition; // Position (0-based) where alignment's mate starts\r
int32_t InsertSize; // Mate-pair insert size\r
\r
- // Alignment flag query constants\r
+ // Alignment flag query constants
+ // Use the get/set methods above instead\r
private:\r
- enum { PAIRED = 1,\r
- PROPER_PAIR = 2,\r
- UNMAPPED = 4,\r
- MATE_UNMAPPED = 8,\r
- REVERSE = 16,\r
- MATE_REVERSE = 32,\r
- READ_1 = 64,\r
- READ_2 = 128,\r
- SECONDARY = 256,\r
- QC_FAILED = 512,\r
- DUPLICATE = 1024\r
+ enum { PAIRED = 1\r
+ , PROPER_PAIR = 2\r
+ , UNMAPPED = 4\r
+ , MATE_UNMAPPED = 8\r
+ , REVERSE = 16\r
+ , MATE_REVERSE = 32\r
+ , READ_1 = 64\r
+ , READ_2 = 128\r
+ , SECONDARY = 256\r
+ , QC_FAILED = 512\r
+ , DUPLICATE = 1024 \r
};\r
};\r
\r
};\r
\r
struct RefData {\r
+
// data members\r
std::string RefName; // Name of reference sequence\r
int32_t RefLength; // Length of reference sequence\r
bool RefHasAlignments; // True if BAM file contains alignments mapped to reference sequence\r
+
// constructor\r
- RefData(void)\r
- : RefLength(0)\r
- , RefHasAlignments(false)\r
+ RefData(const int32_t& length = 0,
+ bool ok = false)\r
+ : RefLength(length)\r
+ , RefHasAlignments(ok)\r
{ }\r
};\r
\r
// ----------------------------------------------------------------\r
// Indexing structs & typedefs\r
\r
-struct Chunk {\r
+struct Chunk {
+\r
// data members\r
uint64_t Start;\r
uint64_t Stop;\r
+
// constructor\r
- Chunk(const uint64_t& start = 0, const uint64_t& stop = 0)\r
+ Chunk(const uint64_t& start = 0,
+ const uint64_t& stop = 0)\r
: Start(start)\r
, Stop(stop)\r
{ }\r
};\r
\r
typedef std::vector<ReferenceIndex> BamIndex;\r
+
+// ----------------------------------------------------------------
+// BamAlignment member methods
+
+// constructors & destructor
+inline
+BamAlignment::BamAlignment(void) { }
+
+inline
+BamAlignment::BamAlignment(const BamAlignment& other)
+ : Name(other.Name)
+ , Length(other.Length)
+ , QueryBases(other.QueryBases)
+ , AlignedBases(other.AlignedBases)
+ , Qualities(other.Qualities)
+ , TagData(other.TagData)
+ , RefID(other.RefID)
+ , Position(other.Position)
+ , Bin(other.Bin)
+ , MapQuality(other.MapQuality)
+ , AlignmentFlag(other.AlignmentFlag)
+ , CigarData(other.CigarData)
+ , MateRefID(other.MateRefID)
+ , MatePosition(other.MatePosition)
+ , InsertSize(other.InsertSize)
+{ }
+
+inline
+BamAlignment::~BamAlignment(void) { }
+
+// Queries against alignment flags\r
+inline bool BamAlignment::IsDuplicate(void) const { return ( (AlignmentFlag & DUPLICATE) != 0 ); }\r
+inline bool BamAlignment::IsFailedQC(void) const { return ( (AlignmentFlag & QC_FAILED) != 0 ); }\r
+inline bool BamAlignment::IsFirstMate(void) const { return ( (AlignmentFlag & READ_1) != 0 ); }\r
+inline bool BamAlignment::IsMapped(void) const { return ( (AlignmentFlag & UNMAPPED) == 0 ); }\r
+inline bool BamAlignment::IsMateMapped(void) const { return ( (AlignmentFlag & MATE_UNMAPPED) == 0 ); }\r
+inline bool BamAlignment::IsMateReverseStrand(void) const { return ( (AlignmentFlag & MATE_REVERSE) != 0 ); }\r
+inline bool BamAlignment::IsPaired(void) const { return ( (AlignmentFlag & PAIRED) != 0 ); }\r
+inline bool BamAlignment::IsPrimaryAlignment(void) const { return ( (AlignmentFlag & SECONDARY) == 0 ); }\r
+inline bool BamAlignment::IsProperPair(void) const { return ( (AlignmentFlag & PROPER_PAIR) != 0 ); }\r
+inline bool BamAlignment::IsReverseStrand(void) const { return ( (AlignmentFlag & REVERSE) != 0 ); }\r
+inline bool BamAlignment::IsSecondMate(void) const { return ( (AlignmentFlag & READ_2) != 0 ); }
+
+// Manipulate alignment flags \r
+inline void BamAlignment::SetIsDuplicate(bool ok) { if (ok) AlignmentFlag |= DUPLICATE; else AlignmentFlag &= ~DUPLICATE; }\r
+inline void BamAlignment::SetIsFailedQC(bool ok) { if (ok) AlignmentFlag |= QC_FAILED; else AlignmentFlag &= ~QC_FAILED; }\r
+inline void BamAlignment::SetIsFirstMate(bool ok) { if (ok) AlignmentFlag |= READ_1; else AlignmentFlag &= ~READ_1; }\r
+inline void BamAlignment::SetIsMateUnmapped(bool ok) { if (ok) AlignmentFlag |= MATE_UNMAPPED; else AlignmentFlag &= ~MATE_UNMAPPED; }\r
+inline void BamAlignment::SetIsMateReverseStrand(bool ok) { if (ok) AlignmentFlag |= MATE_REVERSE; else AlignmentFlag &= ~MATE_REVERSE; }\r
+inline void BamAlignment::SetIsPaired(bool ok) { if (ok) AlignmentFlag |= PAIRED; else AlignmentFlag &= ~PAIRED; }\r
+inline void BamAlignment::SetIsProperPair(bool ok) { if (ok) AlignmentFlag |= PROPER_PAIR; else AlignmentFlag &= ~PROPER_PAIR; }\r
+inline void BamAlignment::SetIsReverseStrand(bool ok) { if (ok) AlignmentFlag |= REVERSE; else AlignmentFlag &= ~REVERSE; }\r
+inline void BamAlignment::SetIsSecondaryAlignment(bool ok) { if (ok) AlignmentFlag |= SECONDARY; else AlignmentFlag &= ~SECONDARY; }\r
+inline void BamAlignment::SetIsSecondMate(bool ok) { if (ok) AlignmentFlag |= READ_2; else AlignmentFlag &= ~READ_2; }\r
+inline void BamAlignment::SetIsUnmapped(bool ok) { if (ok) AlignmentFlag |= UNMAPPED; else AlignmentFlag &= ~UNMAPPED; }
+
+// calculates alignment end position, based on starting position and CIGAR operations
+inline \r
+int BamAlignment::GetEndPosition(bool usePadded) const {\r
+\r
+ // initialize alignment end to starting position\r
+ int alignEnd = Position;\r
+\r
+ // iterate over cigar operations\r
+ std::vector<CigarOp>::const_iterator cigarIter = CigarData.begin();\r
+ std::vector<CigarOp>::const_iterator cigarEnd = CigarData.end();\r
+ for ( ; cigarIter != cigarEnd; ++cigarIter) {\r
+ const char cigarType = (*cigarIter).Type;\r
+ if ( cigarType == 'M' || cigarType == 'D' || cigarType == 'N' ) {\r
+ alignEnd += (*cigarIter).Length;\r
+ }
+ else if ( usePadded && cigarType == 'I' ) {
+ alignEnd += (*cigarIter).Length;
+ }\r
+ }\r
+ return alignEnd;\r
+}\r
+\r
+// get "NM" tag data - contributed by Aaron Quinlan
+// stores data in 'editDistance', returns success/fail
+inline \r
+bool BamAlignment::GetEditDistance(uint8_t& editDistance) const {\r
+\r
+ if ( TagData.empty() ) { return false; }\r
+\r
+ // localize the tag data\r
+ char* pTagData = (char*)TagData.data();\r
+ const unsigned int tagDataLen = TagData.size();\r
+ unsigned int numBytesParsed = 0;\r
+\r
+ bool foundEditDistanceTag = false;\r
+ while( numBytesParsed < tagDataLen ) {\r
+\r
+ const char* pTagType = pTagData;\r
+ const char* pTagStorageType = pTagData + 2;\r
+ pTagData += 3;\r
+ numBytesParsed += 3;\r
+\r
+ // check the current tag\r
+ if ( strncmp(pTagType, "NM", 2) == 0 ) {\r
+ foundEditDistanceTag = true;\r
+ break;\r
+ }\r
+\r
+ // get the storage class and find the next tag\r
+ if (*pTagStorageType == '\0') { return false; }\r
+ SkipToNextTag( *pTagStorageType, pTagData, numBytesParsed );\r
+ if (*pTagData == '\0') { return false; }\r
+ }\r
+ // return if the edit distance tag was not present\r
+ if ( !foundEditDistanceTag ) { return false; }\r
+\r
+ // assign the editDistance value\r
+ std::memcpy(&editDistance, pTagData, 1);\r
+ return true;\r
+}
+
+// get "RG" tag data
+// stores data in 'readGroup', returns success/fail
+inline \r
+bool BamAlignment::GetReadGroup(std::string& readGroup) const {\r
+\r
+ if ( TagData.empty() ) { return false; }\r
+\r
+ // localize the tag data\r
+ char* pTagData = (char*)TagData.data();\r
+ const unsigned int tagDataLen = TagData.size();\r
+ unsigned int numBytesParsed = 0;\r
+\r
+ bool foundReadGroupTag = false;\r
+ while( numBytesParsed < tagDataLen ) {\r
+\r
+ const char* pTagType = pTagData;\r
+ const char* pTagStorageType = pTagData + 2;\r
+ pTagData += 3;\r
+ numBytesParsed += 3;\r
+\r
+ // check the current tag\r
+ if ( std::strncmp(pTagType, "RG", 2) == 0 ) {\r
+ foundReadGroupTag = true;\r
+ break;\r
+ }\r
+\r
+ // get the storage class and find the next tag\r
+ if (*pTagStorageType == '\0') { return false; }\r
+ SkipToNextTag( *pTagStorageType, pTagData, numBytesParsed );\r
+ if (*pTagData == '\0') { return false; }\r
+ }\r
+\r
+ // return if the read group tag was not present\r
+ if ( !foundReadGroupTag ) { return false; }\r
+\r
+ // assign the read group\r
+ const unsigned int readGroupLen = std::strlen(pTagData);\r
+ readGroup.resize(readGroupLen);\r
+ std::memcpy( (char*)readGroup.data(), pTagData, readGroupLen );\r
+ return true;\r
+}
+
+inline
+void BamAlignment::SkipToNextTag(const char storageType, char* &pTagData, unsigned int& numBytesParsed) {\r
+
+ switch(storageType) {\r
+\r
+ case 'A':\r
+ case 'c':\r
+ case 'C':\r
+ ++numBytesParsed;\r
+ ++pTagData;\r
+ break;\r
+\r
+ case 's':\r
+ case 'S':\r
+ numBytesParsed += 2;\r
+ pTagData += 2;\r
+ break;\r
+\r
+ case 'f':\r
+ case 'i':\r
+ case 'I':\r
+ numBytesParsed += 4;\r
+ pTagData += 4;\r
+ break;\r
+\r
+ case 'Z':\r
+ case 'H':\r
+ while(*pTagData) {\r
+ ++numBytesParsed;\r
+ ++pTagData;\r
+ }\r
+ // ---------------------------\r
+ // Added: 3-25-2010 DWB\r
+ // Contributed: ARQ\r
+ // Fixed: error parsing variable length tag data\r
+ ++pTagData;\r
+ // ---------------------------\r
+ break;\r
+\r
+ default:\r
+ printf("ERROR: Unknown tag storage class encountered: [%c]\n", *pTagData);\r
+ exit(1);\r
+ }\r
+}
\r
// ----------------------------------------------------------------\r
// Added: 3-35-2010 DWB\r
// swaps endianness of 16-bit value 'in place'\r
inline void SwapEndian_16(int16_t& x) {\r
x = ((x >> 8) | (x << 8));\r
-}\r
+}
\r
inline void SwapEndian_16(uint16_t& x) {\r
x = ((x >> 8) | (x << 8));\r
((x >> 8) & 0x0000FF00) | \r
(x << 24)\r
);\r
-}\r
+}
\r
inline void SwapEndian_32(uint32_t& x) {\r
x = ( (x >> 24) | \r
(x << 56)\r
);\r
}\r
-\r
+
+// swaps endianness of 'next 2 bytes' in a char buffer (in-place)\r
inline void SwapEndian_16p(char* data) {\r
uint16_t& value = (uint16_t&)*data; \r
SwapEndian_16(value);\r
}\r
-\r
+
+// swaps endianness of 'next 4 bytes' in a char buffer (in-place)\r
inline void SwapEndian_32p(char* data) {\r
uint32_t& value = (uint32_t&)*data; \r
SwapEndian_32(value);\r
}\r
-\r
+
+// swaps endianness of 'next 8 bytes' in a char buffer (in-place)\r
inline void SwapEndian_64p(char* data) {\r
uint64_t& value = (uint64_t&)*data; \r
SwapEndian_64(value);\r
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