-// BamAlignment.h\r
-\r
-// Derek Barnett\r
-// Marth Lab, Boston College\r
-// Last modified: 20 March 2009\r
-\r
-#ifndef BAMALIGNMENT_H\r
-#define BAMALIGNMENT_H\r
-\r
-#ifdef WIN32\r
-typedef char int8_t;\r
-typedef unsigned char uint8_t;\r
-typedef short int16_t;\r
-typedef unsigned short uint16_t;\r
-typedef int int32_t;\r
-typedef unsigned int uint32_t;\r
-typedef long long int64_t;\r
-typedef unsigned long long uint64_t;\r
-#else\r
-#include <stdint.h>\r
-#endif\r
-\r
-// C++ includes\r
-#include <string>\r
-using std::string;\r
-\r
-#include <vector>\r
-using std::vector;\r
-\r
-struct CigarOp {\r
- uint32_t Length;\r
- char Type;\r
-};\r
-\r
-struct RefData {\r
- string RefName;\r
- unsigned int RefLength;\r
- bool RefHasAlignments;\r
-\r
- // constructor\r
- RefData(void)\r
- : RefLength(0)\r
- , RefHasAlignments(false)\r
- { }\r
-};\r
-\r
-typedef vector<RefData> RefVector;\r
-\r
-struct BamAlignment {\r
-\r
- // queries against alignment flag - see below for further detail\r
- public:\r
- bool IsPaired(void) const { return ( (AlignmentFlag & PAIRED) != 0 ); }\r
- bool IsProperPair(void) const { return ( (AlignmentFlag & PROPER_PAIR) != 0 ); }\r
- bool IsMapped(void) const { return ( (AlignmentFlag & UNMAPPED) == 0 ); }\r
- bool IsMateMapped(void) const { return ( (AlignmentFlag & MATE_UNMAPPED) == 0 ); }\r
- bool IsReverseStrand(void) const { return ( (AlignmentFlag & REVERSE) != 0 ); }\r
- bool IsMateReverseStrand(void) const { return ( (AlignmentFlag & MATE_REVERSE) != 0 ); }\r
- bool IsFirstMate(void) const { return ( (AlignmentFlag & READ_1) != 0 ); }\r
- bool IsSecondMate(void) const { return ( (AlignmentFlag & READ_2) != 0 ); }\r
- bool IsPrimaryAlignment(void) const { return ( (AlignmentFlag & SECONDARY) == 0 ); }\r
- bool IsFailedQC(void) const { return ( (AlignmentFlag & QC_FAILED) != 0 ); }\r
- bool IsDuplicate(void) const { return ( (AlignmentFlag & DUPLICATE) != 0 ); }\r
-\r
- // data members\r
- public:\r
- string Name; // read name\r
- unsigned int Length; // query length\r
- string QueryBases; // original sequence ( produced from machine )\r
- string AlignedBases; // aligned sequence ( with indels ) \r
- string Qualities; // FASTQ qualities ( still in ASCII characters )\r
- vector<string> Tags;\r
- unsigned int RefID; // ID for reference sequence\r
- unsigned int Position; // position on reference sequence where alignment starts\r
- unsigned int Bin; // bin in BAM file where this alignment resides\r
- unsigned int MapQuality; // mapping quality \r
- unsigned int AlignmentFlag; // see above for available queries\r
- vector<CigarOp> CigarData; // vector of CIGAR operations (length & type) )\r
- unsigned int MateRefID; // ID for reference sequence that mate was aligned to\r
- unsigned int MatePosition; // position that mate was aligned to\r
- unsigned int InsertSize; // mate pair insert size\r
- \r
-\r
- // alignment flag query constants\r
- private:\r
- enum { PAIRED = 1, // Alignment comes from paired-end data\r
- PROPER_PAIR = 2, // Alignment passed paired-end resolution\r
- UNMAPPED = 4, // Read is unmapped\r
- MATE_UNMAPPED = 8, // Mate is unmapped\r
- REVERSE = 16, // Read is on reverse strand\r
- MATE_REVERSE = 32, // Mate is on reverse strand\r
- READ_1 = 64, // This alignment is mate 1 of pair\r
- READ_2 = 128, // This alignment is mate 2 of pair\r
- SECONDARY = 256, // This alignment is not the primary (best) alignment for read\r
- QC_FAILED = 512, // Read did not pass prior quality control steps\r
- DUPLICATE = 1024 // Read is PCR duplicate\r
- };\r
-};\r
-\r
-// commonly used vector in this library\r
-typedef vector< BamAlignment > BamAlignmentVector;\r
-\r
-#endif /* BAMALIGNMENT_H */\r
+// BamAlignment.h
+
+// Derek Barnett
+// Marth Lab, Boston College
+// Last modified: 20 March 2009
+
+#ifndef BAMALIGNMENT_H
+#define BAMALIGNMENT_H
+
+#ifdef WIN32
+typedef char int8_t;
+typedef unsigned char uint8_t;
+typedef short int16_t;
+typedef unsigned short uint16_t;
+typedef int int32_t;
+typedef unsigned int uint32_t;
+typedef long long int64_t;
+typedef unsigned long long uint64_t;
+#else
+#include <stdint.h>
+#endif
+
+// C++ includes
+#include <string>
+using std::string;
+
+#include <vector>
+using std::vector;
+
+struct CigarOp {
+ uint32_t Length;
+ char Type;
+};
+
+struct RefData {
+ string RefName;
+ unsigned int RefLength;
+ bool RefHasAlignments;
+
+ // constructor
+ RefData(void)
+ : RefLength(0)
+ , RefHasAlignments(false)
+ { }
+};
+
+typedef vector<RefData> RefVector;
+
+struct BamAlignment {
+
+ // queries against alignment flag - see below for further detail
+public:
+ bool IsPaired(void) const { return ( (AlignmentFlag & PAIRED) != 0 ); }
+ bool IsProperPair(void) const { return ( (AlignmentFlag & PROPER_PAIR) != 0 ); }
+ bool IsMapped(void) const { return ( (AlignmentFlag & UNMAPPED) == 0 ); }
+ bool IsMateMapped(void) const { return ( (AlignmentFlag & MATE_UNMAPPED) == 0 ); }
+ bool IsReverseStrand(void) const { return ( (AlignmentFlag & REVERSE) != 0 ); }
+ bool IsMateReverseStrand(void) const { return ( (AlignmentFlag & MATE_REVERSE) != 0 ); }
+ bool IsFirstMate(void) const { return ( (AlignmentFlag & READ_1) != 0 ); }
+ bool IsSecondMate(void) const { return ( (AlignmentFlag & READ_2) != 0 ); }
+ bool IsPrimaryAlignment(void) const { return ( (AlignmentFlag & SECONDARY) == 0 ); }
+ bool IsFailedQC(void) const { return ( (AlignmentFlag & QC_FAILED) != 0 ); }
+ bool IsDuplicate(void) const { return ( (AlignmentFlag & DUPLICATE) != 0 ); }
+
+ // returns true and assigns the read group if present in the tag data
+ bool GetReadGroup(string& readGroup) const {
+
+ if(TagData.empty()) return false;
+
+ // localize the tag data
+ char* pTagData = (char*)TagData.data();
+ const unsigned int tagDataLen = TagData.size();
+ unsigned int numBytesParsed = 0;
+
+ bool foundReadGroupTag = false;
+ while(numBytesParsed < tagDataLen) {
+
+ const char* pTagType = pTagData;
+ const char* pTagStorageType = pTagData + 2;
+ pTagData += 3;
+ numBytesParsed += 3;
+
+ // check the current tag
+ if(strncmp(pTagType, "RG", 2) == 0) {
+ foundReadGroupTag = true;
+ break;
+ }
+
+ // get the storage class and find the next tag
+ SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed);
+ }
+
+ // return if the read group tag was not present
+ if(!foundReadGroupTag) return false;
+
+ // assign the read group
+ const unsigned int readGroupLen = strlen(pTagData);
+ readGroup.resize(readGroupLen);
+ memcpy((char*)readGroup.data(), pTagData, readGroupLen);
+ return true;
+ }
+
+ // skips to the next tag
+ static void SkipToNextTag(const char storageType, char* &pTagData, unsigned int& numBytesParsed) {
+ switch(storageType) {
+ case 'A':
+ case 'c':
+ case 'C':
+ numBytesParsed++;
+ pTagData++;
+ break;
+ case 's':
+ case 'S':
+ case 'f':
+ numBytesParsed += 2;
+ pTagData += 2;
+ break;
+ case 'i':
+ case 'I':
+ numBytesParsed += 4;
+ pTagData += 4;
+ break;
+ case 'Z':
+ case 'H':
+ while(*pTagData) {
+ numBytesParsed++;
+ pTagData++;
+ }
+ break;
+ default:
+ printf("ERROR: Unknown tag storage class encountered: [%c]\n", *pTagData);
+ exit(1);
+ }
+ }
+
+ // data members
+public:
+ string Name; // read name
+ unsigned int Length; // query length
+ string QueryBases; // original sequence ( produced from machine )
+ string AlignedBases; // aligned sequence ( with indels )
+ string Qualities; // FASTQ qualities ( still in ASCII characters )
+ string TagData; // contains the tag data (accessor methods will pull the requested information out)
+ unsigned int RefID; // ID for reference sequence
+ unsigned int Position; // position on reference sequence where alignment starts
+ unsigned int Bin; // bin in BAM file where this alignment resides
+ unsigned int MapQuality; // mapping quality
+ unsigned int AlignmentFlag; // see above for available queries
+ vector<CigarOp> CigarData; // vector of CIGAR operations (length & type) )
+ unsigned int MateRefID; // ID for reference sequence that mate was aligned to
+ unsigned int MatePosition; // position that mate was aligned to
+ unsigned int InsertSize; // mate pair insert size
+
+ // alignment flag query constants
+private:
+ enum { PAIRED = 1, // Alignment comes from paired-end data
+ PROPER_PAIR = 2, // Alignment passed paired-end resolution
+ UNMAPPED = 4, // Read is unmapped
+ MATE_UNMAPPED = 8, // Mate is unmapped
+ REVERSE = 16, // Read is on reverse strand
+ MATE_REVERSE = 32, // Mate is on reverse strand
+ READ_1 = 64, // This alignment is mate 1 of pair
+ READ_2 = 128, // This alignment is mate 2 of pair
+ SECONDARY = 256, // This alignment is not the primary (best) alignment for read
+ QC_FAILED = 512, // Read did not pass prior quality control steps
+ DUPLICATE = 1024 // Read is PCR duplicate
+ };
+};
+
+// commonly used vector in this library
+typedef vector< BamAlignment > BamAlignmentVector;
+
+#endif /* BAMALIGNMENT_H */
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