1 // ***************************************************************************
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2 // BamAux.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: 15 July 2010 (DB)
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7 // ---------------------------------------------------------------------------
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8 // Provides the basic constants, data structures, etc. for using BAM files
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9 // ***************************************************************************
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20 #include <exception>
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26 // Platform-specific type definitions
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27 #ifndef BAMTOOLS_TYPES
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28 #define BAMTOOLS_TYPES
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30 typedef char int8_t;
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31 typedef unsigned char uint8_t;
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32 typedef short int16_t;
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33 typedef unsigned short uint16_t;
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34 typedef int int32_t;
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35 typedef unsigned int uint32_t;
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36 typedef long long int64_t;
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37 typedef unsigned long long uint64_t;
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41 #endif // BAMTOOLS_TYPES
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43 namespace BamTools {
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46 const int BAM_CORE_SIZE = 32;
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47 const int BAM_CMATCH = 0;
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48 const int BAM_CINS = 1;
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49 const int BAM_CDEL = 2;
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50 const int BAM_CREF_SKIP = 3;
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51 const int BAM_CSOFT_CLIP = 4;
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52 const int BAM_CHARD_CLIP = 5;
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53 const int BAM_CPAD = 6;
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54 const int BAM_CIGAR_SHIFT = 4;
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55 const int BAM_CIGAR_MASK = ((1 << BAM_CIGAR_SHIFT) - 1);
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57 // BAM index constants
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58 const int MAX_BIN = 37450; // =(8^6-1)/7+1
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59 const int BAM_MIN_CHUNK_GAP = 32768;
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60 const int BAM_LIDX_SHIFT = 14;
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62 // Explicit variable sizes
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63 const int BT_SIZEOF_INT = 4;
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67 struct BamAlignment {
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69 // constructors & destructor
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72 BamAlignment(const BamAlignment& other);
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73 ~BamAlignment(void);
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75 // Queries against alignment flags
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77 bool IsDuplicate(void) const; // Returns true if this read is a PCR duplicate
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78 bool IsFailedQC(void) const; // Returns true if this read failed quality control
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79 bool IsFirstMate(void) const; // Returns true if alignment is first mate on read
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80 bool IsMapped(void) const; // Returns true if alignment is mapped
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81 bool IsMateMapped(void) const; // Returns true if alignment's mate is mapped
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82 bool IsMateReverseStrand(void) const; // Returns true if alignment's mate mapped to reverse strand
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83 bool IsPaired(void) const; // Returns true if alignment part of paired-end read
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84 bool IsPrimaryAlignment(void) const; // Returns true if reported position is primary alignment
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85 bool IsProperPair(void) const; // Returns true if alignment is part of read that satisfied paired-end resolution
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86 bool IsReverseStrand(void) const; // Returns true if alignment mapped to reverse strand
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87 bool IsSecondMate(void) const; // Returns true if alignment is second mate on read
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89 // Manipulate alignment flags
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91 void SetIsDuplicate(bool ok); // Sets "PCR duplicate" flag
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92 void SetIsFailedQC(bool ok); // Sets "failed quality control" flag
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93 void SetIsFirstMate(bool ok); // Sets "alignment is first mate" flag
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94 void SetIsMateUnmapped(bool ok); // Sets "alignment's mate is mapped" flag
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95 void SetIsMateReverseStrand(bool ok); // Sets "alignment's mate mapped to reverse strand" flag
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96 void SetIsPaired(bool ok); // Sets "alignment part of paired-end read" flag
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97 void SetIsProperPair(bool ok); // Sets "alignment is part of read that satisfied paired-end resolution" flag
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98 void SetIsReverseStrand(bool ok); // Sets "alignment mapped to reverse strand" flag
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99 void SetIsSecondaryAlignment(bool ok); // Sets "position is primary alignment" flag
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100 void SetIsSecondMate(bool ok); // Sets "alignment is second mate on read" flag
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101 void SetIsUnmapped(bool ok); // Sets "alignment is mapped" flag
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103 // Tag data access methods
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105 bool GetEditDistance(uint8_t& editDistance) const; // get "NM" tag data - contributed by Aaron Quinlan
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106 bool GetReadGroup(std::string& readGroup) const; // get "RG" tag data
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108 bool GetTag(const std::string& tag, std::string& destination);
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109 template<typename T> bool GetTag(const std::string& tag, T& destination);
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111 // Additional data access methods
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113 int GetEndPosition(bool usePadded = false) const; // calculates alignment end position, based on starting position and CIGAR operations
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115 // 'internal' utility methods
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117 static void SkipToNextTag(const char storageType, char* &pTagData, unsigned int& numBytesParsed);
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121 std::string Name; // Read name
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122 int32_t Length; // Query length
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123 std::string QueryBases; // 'Original' sequence (as reported from sequencing machine)
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124 std::string AlignedBases; // 'Aligned' sequence (includes any indels, padding, clipping)
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125 std::string Qualities; // FASTQ qualities (ASCII characters, not numeric values)
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126 std::string TagData; // Tag data (accessor methods will pull the requested information out)
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127 int32_t RefID; // ID number for reference sequence
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128 int32_t Position; // Position (0-based) where alignment starts
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129 uint16_t Bin; // Bin in BAM file where this alignment resides
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130 uint16_t MapQuality; // Mapping quality score
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131 uint32_t AlignmentFlag; // Alignment bit-flag - see Is<something>() methods to query this value, SetIs<something>() methods to manipulate
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132 std::vector<CigarOp> CigarData; // CIGAR operations for this alignment
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133 int32_t MateRefID; // ID number for reference sequence where alignment's mate was aligned
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134 int32_t MatePosition; // Position (0-based) where alignment's mate starts
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135 int32_t InsertSize; // Mate-pair insert size
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138 struct BamAlignmentSupportData {
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141 std::string AllCharData;
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142 uint32_t BlockLength;
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143 uint32_t NumCigarOperations;
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144 uint32_t QueryNameLength;
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145 uint32_t QuerySequenceLength;
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149 BamAlignmentSupportData(void)
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151 , NumCigarOperations(0)
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152 , QueryNameLength(0)
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153 , QuerySequenceLength(0)
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154 , HasCoreOnly(false)
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158 BamAlignmentSupportData SupportData; // Contains raw character data & lengths
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160 // Alignment flag query constants
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161 // Use the get/set methods above instead
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166 , MATE_UNMAPPED = 8
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168 , MATE_REVERSE = 32
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173 , DUPLICATE = 1024
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177 // ----------------------------------------------------------------
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178 // Auxiliary data structs & typedefs
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183 char Type; // Operation type (MIDNSHP)
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184 uint32_t Length; // Operation length (number of bases)
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187 CigarOp(const char type = '\0',
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188 const uint32_t length = 0)
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197 std::string RefName; // Name of reference sequence
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198 int32_t RefLength; // Length of reference sequence
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199 bool RefHasAlignments; // True if BAM file contains alignments mapped to reference sequence
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202 RefData(const int32_t& length = 0,
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204 : RefLength(length)
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205 , RefHasAlignments(ok)
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209 typedef std::vector<RefData> RefVector;
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210 typedef std::vector<BamAlignment> BamAlignmentVector;
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221 BamRegion(const int& leftID = -1,
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222 const int& leftPos = -1,
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223 const int& rightID = -1,
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224 const int& rightPos = -1)
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225 : LeftRefID(leftID)
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226 , LeftPosition(leftPos)
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227 , RightRefID(rightID)
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228 , RightPosition(rightPos)
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232 // ----------------------------------------------------------------
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233 // BamAlignment member methods
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235 // constructors & destructor
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237 BamAlignment::BamAlignment(void) { }
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240 BamAlignment::BamAlignment(const BamAlignment& other)
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242 , Length(other.Length)
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243 , QueryBases(other.QueryBases)
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244 , AlignedBases(other.AlignedBases)
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245 , Qualities(other.Qualities)
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246 , TagData(other.TagData)
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247 , RefID(other.RefID)
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248 , Position(other.Position)
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250 , MapQuality(other.MapQuality)
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251 , AlignmentFlag(other.AlignmentFlag)
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252 , CigarData(other.CigarData)
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253 , MateRefID(other.MateRefID)
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254 , MatePosition(other.MatePosition)
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255 , InsertSize(other.InsertSize)
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256 , SupportData(other.SupportData)
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260 BamAlignment::~BamAlignment(void) { }
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262 // Queries against alignment flags
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263 inline bool BamAlignment::IsDuplicate(void) const { return ( (AlignmentFlag & DUPLICATE) != 0 ); }
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264 inline bool BamAlignment::IsFailedQC(void) const { return ( (AlignmentFlag & QC_FAILED) != 0 ); }
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265 inline bool BamAlignment::IsFirstMate(void) const { return ( (AlignmentFlag & READ_1) != 0 ); }
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266 inline bool BamAlignment::IsMapped(void) const { return ( (AlignmentFlag & UNMAPPED) == 0 ); }
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267 inline bool BamAlignment::IsMateMapped(void) const { return ( (AlignmentFlag & MATE_UNMAPPED) == 0 ); }
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268 inline bool BamAlignment::IsMateReverseStrand(void) const { return ( (AlignmentFlag & MATE_REVERSE) != 0 ); }
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269 inline bool BamAlignment::IsPaired(void) const { return ( (AlignmentFlag & PAIRED) != 0 ); }
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270 inline bool BamAlignment::IsPrimaryAlignment(void) const { return ( (AlignmentFlag & SECONDARY) == 0 ); }
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271 inline bool BamAlignment::IsProperPair(void) const { return ( (AlignmentFlag & PROPER_PAIR) != 0 ); }
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272 inline bool BamAlignment::IsReverseStrand(void) const { return ( (AlignmentFlag & REVERSE) != 0 ); }
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273 inline bool BamAlignment::IsSecondMate(void) const { return ( (AlignmentFlag & READ_2) != 0 ); }
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275 // Manipulate alignment flags
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276 inline void BamAlignment::SetIsDuplicate(bool ok) { if (ok) AlignmentFlag |= DUPLICATE; else AlignmentFlag &= ~DUPLICATE; }
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277 inline void BamAlignment::SetIsFailedQC(bool ok) { if (ok) AlignmentFlag |= QC_FAILED; else AlignmentFlag &= ~QC_FAILED; }
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278 inline void BamAlignment::SetIsFirstMate(bool ok) { if (ok) AlignmentFlag |= READ_1; else AlignmentFlag &= ~READ_1; }
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279 inline void BamAlignment::SetIsMateUnmapped(bool ok) { if (ok) AlignmentFlag |= MATE_UNMAPPED; else AlignmentFlag &= ~MATE_UNMAPPED; }
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280 inline void BamAlignment::SetIsMateReverseStrand(bool ok) { if (ok) AlignmentFlag |= MATE_REVERSE; else AlignmentFlag &= ~MATE_REVERSE; }
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281 inline void BamAlignment::SetIsPaired(bool ok) { if (ok) AlignmentFlag |= PAIRED; else AlignmentFlag &= ~PAIRED; }
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282 inline void BamAlignment::SetIsProperPair(bool ok) { if (ok) AlignmentFlag |= PROPER_PAIR; else AlignmentFlag &= ~PROPER_PAIR; }
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283 inline void BamAlignment::SetIsReverseStrand(bool ok) { if (ok) AlignmentFlag |= REVERSE; else AlignmentFlag &= ~REVERSE; }
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284 inline void BamAlignment::SetIsSecondaryAlignment(bool ok) { if (ok) AlignmentFlag |= SECONDARY; else AlignmentFlag &= ~SECONDARY; }
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285 inline void BamAlignment::SetIsSecondMate(bool ok) { if (ok) AlignmentFlag |= READ_2; else AlignmentFlag &= ~READ_2; }
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286 inline void BamAlignment::SetIsUnmapped(bool ok) { if (ok) AlignmentFlag |= UNMAPPED; else AlignmentFlag &= ~UNMAPPED; }
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288 // calculates alignment end position, based on starting position and CIGAR operations
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290 int BamAlignment::GetEndPosition(bool usePadded) const {
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292 // initialize alignment end to starting position
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293 int alignEnd = Position;
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295 // iterate over cigar operations
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296 std::vector<CigarOp>::const_iterator cigarIter = CigarData.begin();
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297 std::vector<CigarOp>::const_iterator cigarEnd = CigarData.end();
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298 for ( ; cigarIter != cigarEnd; ++cigarIter) {
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299 const char cigarType = (*cigarIter).Type;
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300 if ( cigarType == 'M' || cigarType == 'D' || cigarType == 'N' ) {
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301 alignEnd += (*cigarIter).Length;
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303 else if ( usePadded && cigarType == 'I' ) {
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304 alignEnd += (*cigarIter).Length;
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310 // get "NM" tag data - contributed by Aaron Quinlan
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311 // stores data in 'editDistance', returns success/fail
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313 bool BamAlignment::GetEditDistance(uint8_t& editDistance) const {
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315 if ( TagData.empty() ) { return false; }
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317 // localize the tag data
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318 char* pTagData = (char*)TagData.data();
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319 const unsigned int tagDataLen = TagData.size();
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320 unsigned int numBytesParsed = 0;
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322 bool foundEditDistanceTag = false;
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323 while( numBytesParsed < tagDataLen ) {
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325 const char* pTagType = pTagData;
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326 const char* pTagStorageType = pTagData + 2;
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328 numBytesParsed += 3;
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330 // check the current tag
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331 if ( strncmp(pTagType, "NM", 2) == 0 ) {
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332 foundEditDistanceTag = true;
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336 // get the storage class and find the next tag
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337 if (*pTagStorageType == '\0') { return false; }
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338 SkipToNextTag( *pTagStorageType, pTagData, numBytesParsed );
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339 if (*pTagData == '\0') { return false; }
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341 // return if the edit distance tag was not present
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342 if ( !foundEditDistanceTag ) { return false; }
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344 // assign the editDistance value
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345 std::memcpy(&editDistance, pTagData, 1);
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349 // get "RG" tag data
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350 // stores data in 'readGroup', returns success/fail
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352 bool BamAlignment::GetReadGroup(std::string& readGroup) const {
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354 if ( TagData.empty() ) { return false; }
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356 // localize the tag data
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357 char* pTagData = (char*)TagData.data();
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358 const unsigned int tagDataLen = TagData.size();
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359 unsigned int numBytesParsed = 0;
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361 bool foundReadGroupTag = false;
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362 while( numBytesParsed < tagDataLen ) {
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364 const char* pTagType = pTagData;
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365 const char* pTagStorageType = pTagData + 2;
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367 numBytesParsed += 3;
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369 // check the current tag
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370 if ( std::strncmp(pTagType, "RG", 2) == 0 ) {
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371 foundReadGroupTag = true;
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375 // get the storage class and find the next tag
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376 if (*pTagStorageType == '\0') { return false; }
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377 SkipToNextTag( *pTagStorageType, pTagData, numBytesParsed );
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378 if (*pTagData == '\0') { return false; }
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381 // return if the read group tag was not present
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382 if ( !foundReadGroupTag ) { return false; }
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384 // assign the read group
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385 const unsigned int readGroupLen = std::strlen(pTagData);
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386 readGroup.resize(readGroupLen);
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387 std::memcpy( (char*)readGroup.data(), pTagData, readGroupLen );
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392 bool BamAlignment::GetTag(const std::string& tag, std::string& destination) {
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394 if ( TagData.empty() ) { return false; }
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396 // localize the tag data
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397 char* pTagData = (char*)TagData.data();
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398 const unsigned int tagDataLen = TagData.size();
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399 unsigned int numBytesParsed = 0;
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401 bool foundReadGroupTag = false;
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402 while( numBytesParsed < tagDataLen ) {
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404 const char* pTagType = pTagData;
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405 const char* pTagStorageType = pTagData + 2;
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407 numBytesParsed += 3;
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409 // check the current tag
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410 if ( std::strncmp(pTagType, tag.c_str(), 2) == 0 ) {
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411 foundReadGroupTag = true;
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415 // get the storage class and find the next tag
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416 if (*pTagStorageType == '\0') { return false; }
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417 SkipToNextTag( *pTagStorageType, pTagData, numBytesParsed );
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418 if (*pTagData == '\0') { return false; }
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421 // return if the read group tag was not present
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422 if ( !foundReadGroupTag ) { return false; }
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424 // assign the read group
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425 const unsigned int dataLen = std::strlen(pTagData);
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426 destination.resize(dataLen);
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427 std::memcpy( (char*)destination.data(), pTagData, dataLen );
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431 template<typename T>
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432 bool BamAlignment::GetTag(const std::string& tag, T& destination) {
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434 if ( TagData.empty() ) { return false; }
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436 // localize the tag data
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437 char* pTagData = (char*)TagData.data();
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438 const unsigned int tagDataLen = TagData.size();
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439 unsigned int numBytesParsed = 0;
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441 bool foundDesiredTag = false;
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442 while( numBytesParsed < tagDataLen ) {
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444 const char* pTagType = pTagData;
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445 const char* pTagStorageType = pTagData + 2;
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447 numBytesParsed += 3;
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449 // check the current tag
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450 if ( strncmp(pTagType, tag.c_str(), 2) == 0 ) {
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451 foundDesiredTag = true;
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455 // get the storage class and find the next tag
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456 if (*pTagStorageType == '\0') { return false; }
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457 SkipToNextTag( *pTagStorageType, pTagData, numBytesParsed );
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458 if (*pTagData == '\0') { return false; }
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460 // return if the edit distance tag was not present
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461 if ( !foundDesiredTag ) { return false; }
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463 // assign the editDistance value
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464 std::memcpy(&destination, pTagData, sizeof(T));
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469 void BamAlignment::SkipToNextTag(const char storageType, char* &pTagData, unsigned int& numBytesParsed) {
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471 switch(storageType) {
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482 numBytesParsed += 2;
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489 numBytesParsed += 4;
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499 // ---------------------------
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500 // Added: 3-25-2010 DWB
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501 // Contributed: ARQ
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502 // Fixed: error parsing variable length tag data
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504 // ---------------------------
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508 printf("ERROR: Unknown tag storage class encountered: [%c]\n", *pTagData);
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513 // ----------------------------------------------------------------
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514 // Added: 3-35-2010 DWB
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515 // Fixed: Routines to provide endian-correctness
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516 // ----------------------------------------------------------------
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518 // returns true if system is big endian
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519 inline bool SystemIsBigEndian(void) {
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520 const uint16_t one = 0x0001;
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521 return ((*(char*) &one) == 0 );
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524 // swaps endianness of 16-bit value 'in place'
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525 inline void SwapEndian_16(int16_t& x) {
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526 x = ((x >> 8) | (x << 8));
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529 inline void SwapEndian_16(uint16_t& x) {
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530 x = ((x >> 8) | (x << 8));
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533 // swaps endianness of 32-bit value 'in-place'
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534 inline void SwapEndian_32(int32_t& x) {
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536 ((x << 8) & 0x00FF0000) |
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537 ((x >> 8) & 0x0000FF00) |
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542 inline void SwapEndian_32(uint32_t& x) {
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544 ((x << 8) & 0x00FF0000) |
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545 ((x >> 8) & 0x0000FF00) |
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550 // swaps endianness of 64-bit value 'in-place'
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551 inline void SwapEndian_64(int64_t& x) {
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553 ((x << 40) & 0x00FF000000000000ll) |
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554 ((x << 24) & 0x0000FF0000000000ll) |
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555 ((x << 8) & 0x000000FF00000000ll) |
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556 ((x >> 8) & 0x00000000FF000000ll) |
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557 ((x >> 24) & 0x0000000000FF0000ll) |
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558 ((x >> 40) & 0x000000000000FF00ll) |
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563 inline void SwapEndian_64(uint64_t& x) {
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565 ((x << 40) & 0x00FF000000000000ll) |
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566 ((x << 24) & 0x0000FF0000000000ll) |
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567 ((x << 8) & 0x000000FF00000000ll) |
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568 ((x >> 8) & 0x00000000FF000000ll) |
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569 ((x >> 24) & 0x0000000000FF0000ll) |
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570 ((x >> 40) & 0x000000000000FF00ll) |
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575 // swaps endianness of 'next 2 bytes' in a char buffer (in-place)
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576 inline void SwapEndian_16p(char* data) {
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577 uint16_t& value = (uint16_t&)*data;
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578 SwapEndian_16(value);
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581 // swaps endianness of 'next 4 bytes' in a char buffer (in-place)
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582 inline void SwapEndian_32p(char* data) {
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583 uint32_t& value = (uint32_t&)*data;
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584 SwapEndian_32(value);
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587 // swaps endianness of 'next 8 bytes' in a char buffer (in-place)
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588 inline void SwapEndian_64p(char* data) {
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589 uint64_t& value = (uint64_t&)*data;
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590 SwapEndian_64(value);
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593 } // namespace BamTools
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