src/api/BamWriter.cpp

   1 // ***************************************************************************\r
   2 // BamWriter.cpp (c) 2009 Michael Str�mberg, Derek Barnett\r
   3 // Marth Lab, Department of Biology, Boston College\r
   4 // All rights reserved.\r
   5 // ---------------------------------------------------------------------------\r
   6 // Last modified: 16 September 2010 (DB)\r
   7 // ---------------------------------------------------------------------------\r
   8 // Uses BGZF routines were adapted from the bgzf.c code developed at the Broad\r
   9 // Institute.\r
  10 // ---------------------------------------------------------------------------\r
  11 // Provides the basic functionality for producing BAM files\r
  12 // ***************************************************************************\r
  13 \r
  14 #include <iostream>\r
  15 \r
  16 #include "BGZF.h"\r
  17 #include "BamWriter.h"\r
  18 using namespace BamTools;\r
  19 using namespace std;\r
  20 \r
  21 struct BamWriter::BamWriterPrivate {\r
  22 \r
  23     // data members\r
  24     BgzfData mBGZF;\r
  25     bool IsBigEndian;\r
  26     \r
  27     // constructor / destructor\r
  28     BamWriterPrivate(void) { \r
  29       IsBigEndian = SystemIsBigEndian();  \r
  30     }\r
  31     \r
  32     ~BamWriterPrivate(void) {\r
  33         mBGZF.Close();\r
  34     }\r
  35 \r
  36     // "public" interface\r
  37     void Close(void);\r
  38     bool Open(const string& filename, const string& samHeader, const RefVector& referenceSequences, bool isWriteUncompressed);\r
  39     void SaveAlignment(const BamAlignment& al);\r
  40 \r
  41     // internal methods\r
  42     const unsigned int CalculateMinimumBin(const int begin, int end) const;\r
  43     void CreatePackedCigar(const vector<CigarOp>& cigarOperations, string& packedCigar);\r
  44     void EncodeQuerySequence(const string& query, string& encodedQuery);\r
  45 };\r
  46 \r
  47 // -----------------------------------------------------\r
  48 // BamWriter implementation\r
  49 // -----------------------------------------------------\r
  50 \r
  51 // constructor\r
  52 BamWriter::BamWriter(void) {\r
  53     d = new BamWriterPrivate;\r
  54 }\r
  55 \r
  56 // destructor\r
  57 BamWriter::~BamWriter(void) {\r
  58     delete d;\r
  59     d = 0;\r
  60 }\r
  61 \r
  62 // closes the alignment archive\r
  63 void BamWriter::Close(void) { \r
  64   d->Close(); \r
  65 }\r
  66 \r
  67 // opens the alignment archive\r
  68 bool BamWriter::Open(const string& filename, const string& samHeader, const RefVector& referenceSequences, bool isWriteUncompressed) {\r
  69     return d->Open(filename, samHeader, referenceSequences, isWriteUncompressed);\r
  70 }\r
  71 \r
  72 // saves the alignment to the alignment archive\r
  73 void BamWriter::SaveAlignment(const BamAlignment& al) { \r
  74     d->SaveAlignment(al);\r
  75 }\r
  76 \r
  77 // -----------------------------------------------------\r
  78 // BamWriterPrivate implementation\r
  79 // -----------------------------------------------------\r
  80 \r
  81 // closes the alignment archive\r
  82 void BamWriter::BamWriterPrivate::Close(void) {\r
  83     mBGZF.Close();\r
  84 }\r
  85 \r
  86 // calculates minimum bin for a BAM alignment interval\r
  87 const unsigned int BamWriter::BamWriterPrivate::CalculateMinimumBin(const int begin, int end) const {  \r
  88     --end;\r
  89     if( (begin >> 14) == (end >> 14) ) return 4681 + (begin >> 14);\r
  90     if( (begin >> 17) == (end >> 17) ) return  585 + (begin >> 17);\r
  91     if( (begin >> 20) == (end >> 20) ) return   73 + (begin >> 20);\r
  92     if( (begin >> 23) == (end >> 23) ) return    9 + (begin >> 23);\r
  93     if( (begin >> 26) == (end >> 26) ) return    1 + (begin >> 26);\r
  94     return 0;\r
  95 }\r
  96 \r
  97 // creates a cigar string from the supplied alignment\r
  98 void BamWriter::BamWriterPrivate::CreatePackedCigar(const vector<CigarOp>& cigarOperations, string& packedCigar) {\r
  99 \r
 100     // initialize\r
 101     const unsigned int numCigarOperations = cigarOperations.size();\r
 102     packedCigar.resize(numCigarOperations * BT_SIZEOF_INT);\r
 103 \r
 104     // pack the cigar data into the string\r
 105     unsigned int* pPackedCigar = (unsigned int*)packedCigar.data();\r
 106 \r
 107     unsigned int cigarOp;\r
 108     vector<CigarOp>::const_iterator coIter;\r
 109     for(coIter = cigarOperations.begin(); coIter != cigarOperations.end(); ++coIter) {\r
 110 \r
 111         switch(coIter->Type) {\r
 112             case 'M':\r
 113                   cigarOp = BAM_CMATCH;\r
 114                   break;\r
 115             case 'I':\r
 116                   cigarOp = BAM_CINS;\r
 117                   break;\r
 118             case 'D':\r
 119                   cigarOp = BAM_CDEL;\r
 120                   break;\r
 121             case 'N':\r
 122                   cigarOp = BAM_CREF_SKIP;\r
 123                   break;\r
 124             case 'S':\r
 125                   cigarOp = BAM_CSOFT_CLIP;\r
 126                   break;\r
 127             case 'H':\r
 128                   cigarOp = BAM_CHARD_CLIP;\r
 129                   break;\r
 130             case 'P':\r
 131                   cigarOp = BAM_CPAD;\r
 132                   break;\r
 133             default:\r
 134                   fprintf(stderr, "ERROR: Unknown cigar operation found: %c\n", coIter->Type);\r
 135                   exit(1);\r
 136         }\r
 137 \r
 138         *pPackedCigar = coIter->Length << BAM_CIGAR_SHIFT | cigarOp;\r
 139         pPackedCigar++;\r
 140     }\r
 141 }\r
 142 \r
 143 // encodes the supplied query sequence into 4-bit notation\r
 144 void BamWriter::BamWriterPrivate::EncodeQuerySequence(const string& query, string& encodedQuery) {\r
 145 \r
 146     // prepare the encoded query string\r
 147     const unsigned int queryLen = query.size();\r
 148     const unsigned int encodedQueryLen = (unsigned int)((queryLen / 2.0) + 0.5);\r
 149     encodedQuery.resize(encodedQueryLen);\r
 150     char* pEncodedQuery = (char*)encodedQuery.data();\r
 151     const char* pQuery = (const char*)query.data();\r
 152 \r
 153     unsigned char nucleotideCode;\r
 154     bool useHighWord = true;\r
 155 \r
 156     while(*pQuery) {\r
 157 \r
 158         switch(*pQuery) {\r
 159             \r
 160             case '=':\r
 161                 nucleotideCode = 0;\r
 162                 break;\r
 163                 \r
 164             case 'A':\r
 165                 nucleotideCode = 1;\r
 166                 break;\r
 167             \r
 168             case 'C':\r
 169                 nucleotideCode = 2;\r
 170                 break;\r
 171             \r
 172             case 'G':\r
 173                 nucleotideCode = 4;\r
 174                 break;\r
 175             \r
 176             case 'T':\r
 177                 nucleotideCode = 8;\r
 178                 break;\r
 179             \r
 180             case 'N':\r
 181                 nucleotideCode = 15;\r
 182                 break;\r
 183             \r
 184             default:\r
 185                 fprintf(stderr, "ERROR: Only the following bases are supported in the BAM format: {=, A, C, G, T, N}. Found [%c]\n", *pQuery);\r
 186                 exit(1);\r
 187         }\r
 188 \r
 189         // pack the nucleotide code\r
 190         if(useHighWord) {\r
 191             *pEncodedQuery = nucleotideCode << 4;\r
 192             useHighWord = false;\r
 193         } else {\r
 194             *pEncodedQuery |= nucleotideCode;\r
 195             pEncodedQuery++;\r
 196             useHighWord = true;\r
 197         }\r
 198 \r
 199         // increment the query position\r
 200         pQuery++;\r
 201     }\r
 202 }\r
 203 \r
 204 // opens the alignment archive\r
 205 bool BamWriter::BamWriterPrivate::Open(const string& filename, const string& samHeader, const RefVector& referenceSequences, bool isWriteUncompressed) {\r
 206 \r
 207     // open the BGZF file for writing, return failure if error\r
 208     if ( !mBGZF.Open(filename, "wb", isWriteUncompressed) )\r
 209         return false;\r
 210 \r
 211     // ================\r
 212     // write the header\r
 213     // ================\r
 214 \r
 215     // write the BAM signature\r
 216     const unsigned char SIGNATURE_LENGTH = 4;\r
 217     const char* BAM_SIGNATURE = "BAM\1";\r
 218     mBGZF.Write(BAM_SIGNATURE, SIGNATURE_LENGTH);\r
 219 \r
 220     // write the SAM header text length\r
 221     uint32_t samHeaderLen = samHeader.size();\r
 222     if (IsBigEndian) SwapEndian_32(samHeaderLen);\r
 223     mBGZF.Write((char*)&samHeaderLen, BT_SIZEOF_INT);\r
 224 \r
 225     // write the SAM header text\r
 226     if(samHeaderLen > 0) \r
 227         mBGZF.Write(samHeader.data(), samHeaderLen);\r
 228 \r
 229     // write the number of reference sequences\r
 230     uint32_t numReferenceSequences = referenceSequences.size();\r
 231     if (IsBigEndian) SwapEndian_32(numReferenceSequences);\r
 232     mBGZF.Write((char*)&numReferenceSequences, BT_SIZEOF_INT);\r
 233 \r
 234     // =============================\r
 235     // write the sequence dictionary\r
 236     // =============================\r
 237 \r
 238     RefVector::const_iterator rsIter;\r
 239     for(rsIter = referenceSequences.begin(); rsIter != referenceSequences.end(); rsIter++) {\r
 240 \r
 241         // write the reference sequence name length\r
 242         uint32_t referenceSequenceNameLen = rsIter->RefName.size() + 1;\r
 243         if (IsBigEndian) SwapEndian_32(referenceSequenceNameLen);\r
 244         mBGZF.Write((char*)&referenceSequenceNameLen, BT_SIZEOF_INT);\r
 245 \r
 246         // write the reference sequence name\r
 247         mBGZF.Write(rsIter->RefName.c_str(), referenceSequenceNameLen);\r
 248 \r
 249         // write the reference sequence length\r
 250         int32_t referenceLength = rsIter->RefLength;\r
 251         if (IsBigEndian) SwapEndian_32(referenceLength);\r
 252         mBGZF.Write((char*)&referenceLength, BT_SIZEOF_INT);\r
 253     }\r
 254     \r
 255     // return success\r
 256     return true;\r
 257 }\r
 258 \r
 259 // saves the alignment to the alignment archive\r
 260 void BamWriter::BamWriterPrivate::SaveAlignment(const BamAlignment& al) {\r
 261 \r
 262     // if BamAlignment contains only the core data and a raw char data buffer\r
 263     // (as a result of BamReader::GetNextAlignmentCore())\r
 264     if ( al.SupportData.HasCoreOnly ) {\r
 265       \r
 266         // write the block size\r
 267         unsigned int blockSize = al.SupportData.BlockLength;\r
 268         if (IsBigEndian) SwapEndian_32(blockSize);\r
 269         mBGZF.Write((char*)&blockSize, BT_SIZEOF_INT);\r
 270 \r
 271         // assign the BAM core data\r
 272         uint32_t buffer[8];\r
 273         buffer[0] = al.RefID;\r
 274         buffer[1] = al.Position;\r
 275         buffer[2] = (al.Bin << 16) | (al.MapQuality << 8) | al.SupportData.QueryNameLength;\r
 276         buffer[3] = (al.AlignmentFlag << 16) | al.SupportData.NumCigarOperations;\r
 277         buffer[4] = al.SupportData.QuerySequenceLength;\r
 278         buffer[5] = al.MateRefID;\r
 279         buffer[6] = al.MatePosition;\r
 280         buffer[7] = al.InsertSize;\r
 281         \r
 282         // swap BAM core endian-ness, if necessary\r
 283         if ( IsBigEndian ) { \r
 284             for ( int i = 0; i < 8; ++i )\r
 285                 SwapEndian_32(buffer[i]); \r
 286         }\r
 287         \r
 288         // write the BAM core\r
 289         mBGZF.Write((char*)&buffer, BAM_CORE_SIZE);\r
 290         \r
 291         // write the raw char data\r
 292         mBGZF.Write((char*)al.SupportData.AllCharData.data(), al.SupportData.BlockLength-BAM_CORE_SIZE); \r
 293     }\r
 294     \r
 295     // otherwise, BamAlignment should contain character in the standard fields: Name, QueryBases, etc\r
 296     // ( resulting from BamReader::GetNextAlignment() *OR* being generated directly by client code )\r
 297     else {\r
 298         \r
 299         // calculate char lengths\r
 300         const unsigned int nameLength         = al.Name.size() + 1;\r
 301         const unsigned int numCigarOperations = al.CigarData.size();\r
 302         const unsigned int queryLength        = al.QueryBases.size();\r
 303         const unsigned int tagDataLength      = al.TagData.size();\r
 304         \r
 305         // no way to tell if BamAlignment.Bin is already defined (no default, invalid value)\r
 306         // force calculation of Bin before storing\r
 307         const int endPosition = al.GetEndPosition();\r
 308         const unsigned int alignmentBin = CalculateMinimumBin(al.Position, endPosition);\r
 309       \r
 310         // create our packed cigar string\r
 311         string packedCigar;\r
 312         CreatePackedCigar(al.CigarData, packedCigar);\r
 313         const unsigned int packedCigarLength = packedCigar.size();\r
 314 \r
 315         // encode the query\r
 316         string encodedQuery;\r
 317         EncodeQuerySequence(al.QueryBases, encodedQuery);\r
 318         const unsigned int encodedQueryLength = encodedQuery.size(); \r
 319       \r
 320         // write the block size\r
 321         const unsigned int dataBlockSize = nameLength + packedCigarLength + encodedQueryLength + queryLength + tagDataLength;\r
 322         unsigned int blockSize = BAM_CORE_SIZE + dataBlockSize;\r
 323         if (IsBigEndian) SwapEndian_32(blockSize);\r
 324         mBGZF.Write((char*)&blockSize, BT_SIZEOF_INT);\r
 325 \r
 326         // assign the BAM core data\r
 327         uint32_t buffer[8];\r
 328         buffer[0] = al.RefID;\r
 329         buffer[1] = al.Position;\r
 330         buffer[2] = (alignmentBin << 16) | (al.MapQuality << 8) | nameLength;\r
 331         buffer[3] = (al.AlignmentFlag << 16) | numCigarOperations;\r
 332         buffer[4] = queryLength;\r
 333         buffer[5] = al.MateRefID;\r
 334         buffer[6] = al.MatePosition;\r
 335         buffer[7] = al.InsertSize;\r
 336         \r
 337         // swap BAM core endian-ness, if necessary\r
 338         if ( IsBigEndian ) { \r
 339             for ( int i = 0; i < 8; ++i )\r
 340                 SwapEndian_32(buffer[i]); \r
 341         }\r
 342         \r
 343         // write the BAM core\r
 344         mBGZF.Write((char*)&buffer, BAM_CORE_SIZE);\r
 345         \r
 346         // write the query name\r
 347         mBGZF.Write(al.Name.c_str(), nameLength);\r
 348 \r
 349         // write the packed cigar\r
 350         if ( IsBigEndian ) {\r
 351           \r
 352             char* cigarData = (char*)calloc(sizeof(char), packedCigarLength);\r
 353             memcpy(cigarData, packedCigar.data(), packedCigarLength);\r
 354             \r
 355             for (unsigned int i = 0; i < packedCigarLength; ++i) {\r
 356                 if ( IsBigEndian )\r
 357                   SwapEndian_32p(&cigarData[i]); \r
 358             }\r
 359             \r
 360             mBGZF.Write(cigarData, packedCigarLength);\r
 361             free(cigarData);    \r
 362         } \r
 363         else \r
 364             mBGZF.Write(packedCigar.data(), packedCigarLength);\r
 365 \r
 366         // write the encoded query sequence\r
 367         mBGZF.Write(encodedQuery.data(), encodedQueryLength);\r
 368 \r
 369         // write the base qualities\r
 370         string baseQualities(al.Qualities);\r
 371         char* pBaseQualities = (char*)al.Qualities.data();\r
 372         for(unsigned int i = 0; i < queryLength; i++) { \r
 373             pBaseQualities[i] -= 33; \r
 374         }\r
 375         mBGZF.Write(pBaseQualities, queryLength);\r
 376 \r
 377         // write the read group tag\r
 378         if ( IsBigEndian ) {\r
 379           \r
 380             char* tagData = (char*)calloc(sizeof(char), tagDataLength);\r
 381             memcpy(tagData, al.TagData.data(), tagDataLength);\r
 382           \r
 383             int i = 0;\r
 384             while ( (unsigned int)i < tagDataLength ) {\r
 385                 \r
 386                 i += 2;                                 // skip tag type (e.g. "RG", "NM", etc)\r
 387                 uint8_t type = toupper(tagData[i]);     // lower & upper case letters have same meaning \r
 388                 ++i;                                    // skip value type\r
 389                 \r
 390                 switch (type) {\r
 391                   \r
 392                     case('A') :\r
 393                     case('C') : \r
 394                         ++i;\r
 395                         break;\r
 396                                 \r
 397                     case('S') : \r
 398                         SwapEndian_16p(&tagData[i]); \r
 399                         i+=2; // sizeof(uint16_t)\r
 400                         break;\r
 401                                 \r
 402                     case('F') :\r
 403                     case('I') : \r
 404                         SwapEndian_32p(&tagData[i]);\r
 405                         i+=4; // sizeof(uint32_t)\r
 406                         break;\r
 407                                 \r
 408                     case('D') : \r
 409                         SwapEndian_64p(&tagData[i]);\r
 410                         i+=8; // sizeof(uint64_t)\r
 411                         break;\r
 412                                 \r
 413                     case('H') :\r
 414                     case('Z') : \r
 415                         while (tagData[i]) { ++i; }\r
 416                         ++i; // increment one more for null terminator\r
 417                         break;\r
 418                                 \r
 419                     default : \r
 420                         fprintf(stderr, "ERROR: Invalid tag value type\n"); // shouldn't get here\r
 421                         free(tagData);\r
 422                         exit(1); \r
 423                 }\r
 424             }\r
 425             \r
 426             mBGZF.Write(tagData, tagDataLength);\r
 427             free(tagData);\r
 428         } \r
 429         else \r
 430             mBGZF.Write(al.TagData.data(), tagDataLength);      \r
 431     }\r
 432 }\r