1 // ***************************************************************************
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2 // BamReader.cpp (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: 8 June 2010 (DB)
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7 // ---------------------------------------------------------------------------
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8 // Uses BGZF routines were adapted from the bgzf.c code developed at the Broad
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10 // ---------------------------------------------------------------------------
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11 // Provides the basic functionality for reading BAM files
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12 // ***************************************************************************
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15 #include <algorithm>
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20 // BamTools includes
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22 #include "BamReader.h"
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23 using namespace BamTools;
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24 using namespace std;
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26 struct BamReader::BamReaderPrivate {
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28 // -------------------------------
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30 // -------------------------------
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32 // general file data
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36 RefVector References;
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38 int64_t AlignmentsBeginOffset;
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40 string IndexFilename;
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45 // user-specified region values
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46 bool IsRegionSpecified;
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50 // BAM character constants
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51 const char* DNA_LOOKUP;
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52 const char* CIGAR_LOOKUP;
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54 // -------------------------------
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55 // constructor & destructor
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56 // -------------------------------
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57 BamReaderPrivate(void);
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58 ~BamReaderPrivate(void);
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60 // -------------------------------
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61 // "public" interface
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62 // -------------------------------
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66 bool Jump(int refID, int position = 0);
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67 void Open(const string& filename, const string& indexFilename = "");
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70 // access alignment data
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71 bool GetNextAlignment(BamAlignment& bAlignment);
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72 bool GetNextAlignmentCore(BamAlignment& bAlignment, BamAlignmentSupportData& supportData);
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74 // access auxiliary data
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75 int GetReferenceID(const string& refName) const;
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78 bool CreateIndex(void);
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80 // -------------------------------
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82 // -------------------------------
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84 // *** reading alignments and auxiliary data *** //
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86 // calculate bins that overlap region ( left to reference end for now )
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87 int BinsFromRegion(int refID, int left, uint16_t[MAX_BIN]);
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88 // fills out character data for BamAlignment data
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89 bool BuildCharData(BamAlignment& bAlignment, const BamAlignmentSupportData& supportData);
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90 // calculate file offset for first alignment chunk overlapping 'left'
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91 int64_t GetOffset(int refID, int left);
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92 // checks to see if alignment overlaps current region
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93 bool IsOverlap(BamAlignment& bAlignment);
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94 // retrieves header text from BAM file
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95 void LoadHeaderData(void);
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96 // retrieves BAM alignment under file pointer
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97 bool LoadNextAlignment(BamAlignment& bAlignment, BamAlignmentSupportData& supportData);
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98 // builds reference data structure from BAM file
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99 void LoadReferenceData(void);
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101 // *** index file handling *** //
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103 // calculates index for BAM file
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104 bool BuildIndex(void);
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105 // clear out inernal index data structure
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106 void ClearIndex(void);
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107 // saves BAM bin entry for index
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108 void InsertBinEntry(BamBinMap& binMap, const uint32_t& saveBin, const uint64_t& saveOffset, const uint64_t& lastOffset);
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109 // saves linear offset entry for index
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110 void InsertLinearOffset(LinearOffsetVector& offsets, const BamAlignment& bAlignment, const uint64_t& lastOffset);
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111 // loads index from BAM index file
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112 bool LoadIndex(void);
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113 // simplifies index by merging 'chunks'
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114 void MergeChunks(void);
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115 // saves index to BAM index file
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116 bool WriteIndex(void);
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119 // -----------------------------------------------------
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120 // BamReader implementation (wrapper around BRPrivate)
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121 // -----------------------------------------------------
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124 BamReader::BamReader(void) {
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125 d = new BamReaderPrivate;
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129 BamReader::~BamReader(void) {
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135 void BamReader::Close(void) { d->Close(); }
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136 bool BamReader::Jump(int refID, int position) { return d->Jump(refID, position); }
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137 void BamReader::Open(const string& filename, const string& indexFilename) { d->Open(filename, indexFilename); }
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138 bool BamReader::Rewind(void) { return d->Rewind(); }
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140 // access alignment data
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141 bool BamReader::GetNextAlignment(BamAlignment& bAlignment) { return d->GetNextAlignment(bAlignment); }
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142 bool BamReader::GetNextAlignmentCore(BamAlignment& bAlignment, BamAlignmentSupportData& supportData) { return d->GetNextAlignmentCore(bAlignment, supportData); }
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144 // access auxiliary data
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145 const string BamReader::GetHeaderText(void) const { return d->HeaderText; }
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146 int BamReader::GetReferenceCount(void) const { return d->References.size(); }
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147 const RefVector BamReader::GetReferenceData(void) const { return d->References; }
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148 int BamReader::GetReferenceID(const string& refName) const { return d->GetReferenceID(refName); }
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149 const std::string BamReader::GetFilename(void) const { return d->Filename; }
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151 // index operations
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152 bool BamReader::CreateIndex(void) { return d->CreateIndex(); }
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154 // -----------------------------------------------------
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155 // BamReaderPrivate implementation
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156 // -----------------------------------------------------
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159 BamReader::BamReaderPrivate::BamReaderPrivate(void)
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160 : IsIndexLoaded(false)
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161 , AlignmentsBeginOffset(0)
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162 , IsRegionSpecified(false)
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165 , DNA_LOOKUP("=ACMGRSVTWYHKDBN")
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166 , CIGAR_LOOKUP("MIDNSHP")
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168 IsBigEndian = SystemIsBigEndian();
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172 BamReader::BamReaderPrivate::~BamReaderPrivate(void) {
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176 // calculate bins that overlap region ( left to reference end for now )
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177 int BamReader::BamReaderPrivate::BinsFromRegion(int refID, int left, uint16_t list[MAX_BIN]) {
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179 // get region boundaries
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180 uint32_t begin = (unsigned int)left;
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181 uint32_t end = (unsigned int)References.at(refID).RefLength - 1;
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183 // initialize list, bin '0' always a valid bin
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187 // get rest of bins that contain this region
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189 for (k = 1 + (begin>>26); k <= 1 + (end>>26); ++k) { list[i++] = k; }
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190 for (k = 9 + (begin>>23); k <= 9 + (end>>23); ++k) { list[i++] = k; }
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191 for (k = 73 + (begin>>20); k <= 73 + (end>>20); ++k) { list[i++] = k; }
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192 for (k = 585 + (begin>>17); k <= 585 + (end>>17); ++k) { list[i++] = k; }
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193 for (k = 4681 + (begin>>14); k <= 4681 + (end>>14); ++k) { list[i++] = k; }
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195 // return number of bins stored
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199 bool BamReader::BamReaderPrivate::BuildCharData(BamAlignment& bAlignment, const BamAlignmentSupportData& supportData) {
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201 // calculate character lengths/offsets
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202 const unsigned int dataLength = supportData.BlockLength - BAM_CORE_SIZE;
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203 const unsigned int seqDataOffset = supportData.QueryNameLength + (supportData.NumCigarOperations * 4);
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204 const unsigned int qualDataOffset = seqDataOffset + (supportData.QuerySequenceLength+1)/2;
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205 const unsigned int tagDataOffset = qualDataOffset + supportData.QuerySequenceLength;
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206 const unsigned int tagDataLength = dataLength - tagDataOffset;
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208 // set up char buffers
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209 const char* allCharData = supportData.AllCharData.data();
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210 const char* seqData = ((const char*)allCharData) + seqDataOffset;
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211 const char* qualData = ((const char*)allCharData) + qualDataOffset;
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212 char* tagData = ((char*)allCharData) + tagDataOffset;
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214 // save query sequence
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215 bAlignment.QueryBases.clear();
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216 bAlignment.QueryBases.reserve(supportData.QuerySequenceLength);
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217 for (unsigned int i = 0; i < supportData.QuerySequenceLength; ++i) {
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218 char singleBase = DNA_LOOKUP[ ( ( seqData[(i/2)] >> (4*(1-(i%2)))) & 0xf ) ];
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219 bAlignment.QueryBases.append(1, singleBase);
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222 // save qualities, converting from numeric QV to 'FASTQ-style' ASCII character
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223 bAlignment.Qualities.clear();
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224 bAlignment.Qualities.reserve(supportData.QuerySequenceLength);
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225 for (unsigned int i = 0; i < supportData.QuerySequenceLength; ++i) {
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226 char singleQuality = (char)(qualData[i]+33);
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227 bAlignment.Qualities.append(1, singleQuality);
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230 // parse CIGAR to build 'AlignedBases'
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231 bAlignment.AlignedBases.clear();
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232 bAlignment.AlignedBases.reserve(supportData.QuerySequenceLength);
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235 vector<CigarOp>::const_iterator cigarIter = bAlignment.CigarData.begin();
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236 vector<CigarOp>::const_iterator cigarEnd = bAlignment.CigarData.end();
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237 for ( ; cigarIter != cigarEnd; ++cigarIter ) {
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239 const CigarOp& op = (*cigarIter);
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244 bAlignment.AlignedBases.append(bAlignment.QueryBases.substr(k, op.Length)); // for 'M', 'I' - write bases
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248 k += op.Length; // for 'S' - soft clip, skip over query bases
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252 bAlignment.AlignedBases.append(op.Length, '-'); // for 'D' - write gap character
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256 bAlignment.AlignedBases.append( op.Length, '*' ); // for 'P' - write padding character
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260 bAlignment.AlignedBases.append( op.Length, 'N' ); // for 'N' - write N's, skip bases in original query sequence
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265 break; // for 'H' - hard clip, do nothing to AlignedBases, move to next op
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268 printf("ERROR: Invalid Cigar op type\n"); // shouldn't get here
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273 // -----------------------
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274 // Added: 3-25-2010 DWB
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275 // Fixed: endian-correctness for tag data
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276 // -----------------------
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277 if ( IsBigEndian ) {
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279 while ( (unsigned int)i < tagDataLength ) {
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281 i += 2; // skip tag type (e.g. "RG", "NM", etc)
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282 uint8_t type = toupper(tagData[i]); // lower & upper case letters have same meaning
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283 ++i; // skip value type
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293 SwapEndian_16p(&tagData[i]);
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294 i+=2; // sizeof(uint16_t)
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299 SwapEndian_32p(&tagData[i]);
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300 i+=4; // sizeof(uint32_t)
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304 SwapEndian_64p(&tagData[i]);
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305 i+=8; // sizeof(uint64_t)
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310 while (tagData[i]) { ++i; }
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311 ++i; // increment one more for null terminator
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315 printf("ERROR: Invalid tag value type\n"); // shouldn't get here
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322 bAlignment.TagData.clear();
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323 bAlignment.TagData.resize(tagDataLength);
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324 memcpy((char*)bAlignment.TagData.data(), tagData, tagDataLength);
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330 // populates BAM index data structure from BAM file data
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331 bool BamReader::BamReaderPrivate::BuildIndex(void) {
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333 // check to be sure file is open
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334 if (!mBGZF.IsOpen) { return false; }
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336 // move file pointer to beginning of alignments
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339 // get reference count, reserve index space
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340 int numReferences = References.size();
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341 for ( int i = 0; i < numReferences; ++i ) {
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342 Index.push_back(ReferenceIndex());
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345 // sets default constant for bin, ID, offset, coordinate variables
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346 const uint32_t defaultValue = 0xffffffffu;
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349 uint32_t saveBin(defaultValue);
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350 uint32_t lastBin(defaultValue);
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352 // reference ID data
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353 int32_t saveRefID(defaultValue);
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354 int32_t lastRefID(defaultValue);
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357 uint64_t saveOffset = mBGZF.Tell();
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358 uint64_t lastOffset = saveOffset;
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361 int32_t lastCoordinate = defaultValue;
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363 BamAlignment bAlignment;
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364 while( GetNextAlignment(bAlignment) ) {
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366 // change of chromosome, save ID, reset bin
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367 if ( lastRefID != bAlignment.RefID ) {
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368 lastRefID = bAlignment.RefID;
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369 lastBin = defaultValue;
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372 // if lastCoordinate greater than BAM position - file not sorted properly
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373 else if ( lastCoordinate > bAlignment.Position ) {
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374 printf("BAM file not properly sorted:\n");
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375 printf("Alignment %s : %d > %d on reference (id = %d)", bAlignment.Name.c_str(), lastCoordinate, bAlignment.Position, bAlignment.RefID);
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379 // if valid reference && BAM bin spans some minimum cutoff (smaller bin ids span larger regions)
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380 if ( (bAlignment.RefID >= 0) && (bAlignment.Bin < 4681) ) {
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382 // save linear offset entry (matched to BAM entry refID)
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383 ReferenceIndex& refIndex = Index.at(bAlignment.RefID);
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384 LinearOffsetVector& offsets = refIndex.Offsets;
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385 InsertLinearOffset(offsets, bAlignment, lastOffset);
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388 // if current BamAlignment bin != lastBin, "then possibly write the binning index"
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389 if ( bAlignment.Bin != lastBin ) {
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391 // if not first time through
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392 if ( saveBin != defaultValue ) {
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394 // save Bam bin entry
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395 ReferenceIndex& refIndex = Index.at(saveRefID);
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396 BamBinMap& binMap = refIndex.Bins;
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397 InsertBinEntry(binMap, saveBin, saveOffset, lastOffset);
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400 // update saveOffset
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401 saveOffset = lastOffset;
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403 // update bin values
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404 saveBin = bAlignment.Bin;
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405 lastBin = bAlignment.Bin;
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407 // update saveRefID
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408 saveRefID = bAlignment.RefID;
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410 // if invalid RefID, break out (why?)
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411 if ( saveRefID < 0 ) { break; }
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414 // make sure that current file pointer is beyond lastOffset
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415 if ( mBGZF.Tell() <= (int64_t)lastOffset ) {
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416 printf("Error in BGZF offsets.\n");
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420 // update lastOffset
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421 lastOffset = mBGZF.Tell();
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423 // update lastCoordinate
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424 lastCoordinate = bAlignment.Position;
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427 // save any leftover BAM data (as long as refID is valid)
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428 if ( saveRefID >= 0 ) {
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429 // save Bam bin entry
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430 ReferenceIndex& refIndex = Index.at(saveRefID);
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431 BamBinMap& binMap = refIndex.Bins;
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432 InsertBinEntry(binMap, saveBin, saveOffset, lastOffset);
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435 // simplify index by merging chunks
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438 // iterate over references
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439 BamIndex::iterator indexIter = Index.begin();
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440 BamIndex::iterator indexEnd = Index.end();
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441 for ( int i = 0; indexIter != indexEnd; ++indexIter, ++i ) {
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443 // get reference index data
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444 ReferenceIndex& refIndex = (*indexIter);
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445 BamBinMap& binMap = refIndex.Bins;
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446 LinearOffsetVector& offsets = refIndex.Offsets;
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448 // store whether reference has alignments or no
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449 References[i].RefHasAlignments = ( binMap.size() > 0 );
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451 // sort linear offsets
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452 sort(offsets.begin(), offsets.end());
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456 // rewind file pointer to beginning of alignments, return success/fail
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461 // clear index data structure
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462 void BamReader::BamReaderPrivate::ClearIndex(void) {
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463 Index.clear(); // sufficient ??
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466 // closes the BAM file
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467 void BamReader::BamReaderPrivate::Close(void) {
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470 HeaderText.clear();
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471 IsRegionSpecified = false;
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474 // create BAM index from BAM file (keep structure in memory) and write to default index output file
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475 bool BamReader::BamReaderPrivate::CreateIndex(void) {
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480 // build (& save) index from BAM file
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482 ok &= BuildIndex();
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483 ok &= WriteIndex();
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485 // return success/fail
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489 // returns RefID for given RefName (returns References.size() if not found)
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490 int BamReader::BamReaderPrivate::GetReferenceID(const string& refName) const {
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492 // retrieve names from reference data
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493 vector<string> refNames;
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494 RefVector::const_iterator refIter = References.begin();
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495 RefVector::const_iterator refEnd = References.end();
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496 for ( ; refIter != refEnd; ++refIter) {
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497 refNames.push_back( (*refIter).RefName );
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500 // return 'index-of' refName ( if not found, returns refNames.size() )
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501 return distance(refNames.begin(), find(refNames.begin(), refNames.end(), refName));
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504 // get next alignment (from specified region, if given)
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505 bool BamReader::BamReaderPrivate::GetNextAlignment(BamAlignment& bAlignment) {
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507 BamAlignmentSupportData supportData;
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509 // if valid alignment available
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510 if ( LoadNextAlignment(bAlignment, supportData) ) {
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512 // if region not specified, return success
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513 if ( !IsRegionSpecified ) {
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514 bool ok = BuildCharData(bAlignment, supportData);
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518 // load next alignment until region overlap is found
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519 while ( !IsOverlap(bAlignment) ) {
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520 // if no valid alignment available (likely EOF) return failure
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521 if ( !LoadNextAlignment(bAlignment, supportData) ) return false;
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524 // return success (alignment found that overlaps region)
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525 bool ok = BuildCharData(bAlignment, supportData);
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529 // no valid alignment
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534 // retrieves next available alignment core data (returns success/fail)
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535 // ** DOES NOT parse any character data (bases, qualities, tag data)
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536 // these can be accessed, if necessary, from the supportData
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537 // useful for operations requiring ONLY positional or other alignment-related information
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538 bool BamReader::BamReaderPrivate::GetNextAlignmentCore(BamAlignment& bAlignment, BamAlignmentSupportData& supportData) {
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540 // if valid alignment available
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541 if ( LoadNextAlignment(bAlignment, supportData) ) {
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543 // if region not specified, return success
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544 if ( !IsRegionSpecified ) return true;
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546 // load next alignment until region overlap is found
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547 while ( !IsOverlap(bAlignment) ) {
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548 // if no valid alignment available (likely EOF) return failure
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549 if ( !LoadNextAlignment(bAlignment, supportData) ) return false;
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552 // return success (alignment found that overlaps region)
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556 // no valid alignment
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561 // calculate closest indexed file offset for region specified
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562 int64_t BamReader::BamReaderPrivate::GetOffset(int refID, int left) {
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564 // calculate which bins overlap this region
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565 uint16_t* bins = (uint16_t*)calloc(MAX_BIN, 2);
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566 int numBins = BinsFromRegion(refID, left, bins);
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568 // get bins for this reference
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569 const ReferenceIndex& refIndex = Index.at(refID);
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570 const BamBinMap& binMap = refIndex.Bins;
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572 // get minimum offset to consider
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573 const LinearOffsetVector& offsets = refIndex.Offsets;
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574 uint64_t minOffset = ( (unsigned int)(left>>BAM_LIDX_SHIFT) >= offsets.size() ) ? 0 : offsets.at(left>>BAM_LIDX_SHIFT);
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576 // store offsets to beginning of alignment 'chunks'
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577 std::vector<int64_t> chunkStarts;
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579 // store all alignment 'chunk' starts for bins in this region
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580 for (int i = 0; i < numBins; ++i ) {
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581 uint16_t binKey = bins[i];
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583 map<uint32_t, ChunkVector>::const_iterator binIter = binMap.find(binKey);
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584 if ( (binIter != binMap.end()) && ((*binIter).first == binKey) ) {
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586 const ChunkVector& chunks = (*binIter).second;
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587 std::vector<Chunk>::const_iterator chunksIter = chunks.begin();
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588 std::vector<Chunk>::const_iterator chunksEnd = chunks.end();
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589 for ( ; chunksIter != chunksEnd; ++chunksIter) {
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590 const Chunk& chunk = (*chunksIter);
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591 if ( chunk.Stop > minOffset ) {
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592 chunkStarts.push_back( chunk.Start );
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601 // if no alignments found, else return smallest offset for alignment starts
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602 if ( chunkStarts.size() == 0 ) { return -1; }
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603 else { return *min_element(chunkStarts.begin(), chunkStarts.end()); }
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606 // saves BAM bin entry for index
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607 void BamReader::BamReaderPrivate::InsertBinEntry(BamBinMap& binMap,
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608 const uint32_t& saveBin,
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609 const uint64_t& saveOffset,
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610 const uint64_t& lastOffset)
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613 BamBinMap::iterator binIter = binMap.find(saveBin);
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615 // create new chunk
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616 Chunk newChunk(saveOffset, lastOffset);
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618 // if entry doesn't exist
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619 if ( binIter == binMap.end() ) {
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620 ChunkVector newChunks;
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621 newChunks.push_back(newChunk);
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622 binMap.insert( pair<uint32_t, ChunkVector>(saveBin, newChunks));
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627 ChunkVector& binChunks = (*binIter).second;
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628 binChunks.push_back( newChunk );
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632 // saves linear offset entry for index
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633 void BamReader::BamReaderPrivate::InsertLinearOffset(LinearOffsetVector& offsets,
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634 const BamAlignment& bAlignment,
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635 const uint64_t& lastOffset)
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637 // get converted offsets
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638 int beginOffset = bAlignment.Position >> BAM_LIDX_SHIFT;
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639 int endOffset = (bAlignment.GetEndPosition() - 1) >> BAM_LIDX_SHIFT;
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641 // resize vector if necessary
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642 int oldSize = offsets.size();
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643 int newSize = endOffset + 1;
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644 if ( oldSize < newSize ) { offsets.resize(newSize, 0); }
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647 for(int i = beginOffset + 1; i <= endOffset ; ++i) {
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648 if ( offsets[i] == 0) {
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649 offsets[i] = lastOffset;
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654 // returns whether alignment overlaps currently specified region (refID, leftBound)
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655 bool BamReader::BamReaderPrivate::IsOverlap(BamAlignment& bAlignment) {
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657 // if on different reference sequence, quit
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658 if ( bAlignment.RefID != CurrentRefID ) { return false; }
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660 // read starts after left boundary
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661 if ( bAlignment.Position >= CurrentLeft) { return true; }
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663 // return whether alignment end overlaps left boundary
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664 return ( bAlignment.GetEndPosition() >= CurrentLeft );
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667 // jumps to specified region(refID, leftBound) in BAM file, returns success/fail
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668 bool BamReader::BamReaderPrivate::Jump(int refID, int position) {
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670 // if data exists for this reference and position is valid
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671 if ( References.at(refID).RefHasAlignments && (position <= References.at(refID).RefLength) ) {
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673 // set current region
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674 CurrentRefID = refID;
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675 CurrentLeft = position;
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676 IsRegionSpecified = true;
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678 // calculate offset
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679 int64_t offset = GetOffset(CurrentRefID, CurrentLeft);
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681 // if in valid offset, return failure
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682 if ( offset == -1 ) { return false; }
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684 // otherwise return success of seek operation
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685 else { return mBGZF.Seek(offset); }
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688 // invalid jump request parameters, return failure
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692 // load BAM header data
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693 void BamReader::BamReaderPrivate::LoadHeaderData(void) {
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695 // check to see if proper BAM header
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697 if (mBGZF.Read(buffer, 4) != 4) {
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698 printf("Could not read header type\n");
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702 if (strncmp(buffer, "BAM\001", 4)) {
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703 printf("wrong header type!\n");
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707 // get BAM header text length
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708 mBGZF.Read(buffer, 4);
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709 unsigned int headerTextLength = BgzfData::UnpackUnsignedInt(buffer);
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710 if ( IsBigEndian ) { SwapEndian_32(headerTextLength); }
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712 // get BAM header text
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713 char* headerText = (char*)calloc(headerTextLength + 1, 1);
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714 mBGZF.Read(headerText, headerTextLength);
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715 HeaderText = (string)((const char*)headerText);
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717 // clean up calloc-ed temp variable
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721 // load existing index data from BAM index file (".bai"), return success/fail
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722 bool BamReader::BamReaderPrivate::LoadIndex(void) {
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724 // clear out index data
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727 // skip if index file empty
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728 if ( IndexFilename.empty() ) { return false; }
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730 // open index file, abort on error
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731 FILE* indexStream = fopen(IndexFilename.c_str(), "rb");
\r
733 printf("ERROR: Unable to open the BAM index file %s for reading.\n", IndexFilename.c_str() );
\r
737 size_t elementsRead = 0;
\r
739 // see if index is valid BAM index
\r
741 elementsRead = fread(magic, 1, 4, indexStream);
\r
742 if (strncmp(magic, "BAI\1", 4)) {
\r
743 printf("Problem with index file - invalid format.\n");
\r
744 fclose(indexStream);
\r
748 // get number of reference sequences
\r
749 uint32_t numRefSeqs;
\r
750 elementsRead = fread(&numRefSeqs, 4, 1, indexStream);
\r
751 if ( IsBigEndian ) { SwapEndian_32(numRefSeqs); }
\r
753 // intialize space for BamIndex data structure
\r
754 Index.reserve(numRefSeqs);
\r
756 // iterate over reference sequences
\r
757 for (unsigned int i = 0; i < numRefSeqs; ++i) {
\r
759 // get number of bins for this reference sequence
\r
761 elementsRead = fread(&numBins, 4, 1, indexStream);
\r
762 if ( IsBigEndian ) { SwapEndian_32(numBins); }
\r
765 RefData& refEntry = References[i];
\r
766 refEntry.RefHasAlignments = true;
\r
769 // intialize BinVector
\r
772 // iterate over bins for that reference sequence
\r
773 for (int j = 0; j < numBins; ++j) {
\r
777 elementsRead = fread(&binID, 4, 1, indexStream);
\r
779 // get number of regionChunks in this bin
\r
780 uint32_t numChunks;
\r
781 elementsRead = fread(&numChunks, 4, 1, indexStream);
\r
783 if ( IsBigEndian ) {
\r
784 SwapEndian_32(binID);
\r
785 SwapEndian_32(numChunks);
\r
788 // intialize ChunkVector
\r
789 ChunkVector regionChunks;
\r
790 regionChunks.reserve(numChunks);
\r
792 // iterate over regionChunks in this bin
\r
793 for (unsigned int k = 0; k < numChunks; ++k) {
\r
795 // get chunk boundaries (left, right)
\r
798 elementsRead = fread(&left, 8, 1, indexStream);
\r
799 elementsRead = fread(&right, 8, 1, indexStream);
\r
801 if ( IsBigEndian ) {
\r
802 SwapEndian_64(left);
\r
803 SwapEndian_64(right);
\r
807 regionChunks.push_back( Chunk(left, right) );
\r
810 // sort chunks for this bin
\r
811 sort( regionChunks.begin(), regionChunks.end(), ChunkLessThan );
\r
813 // save binID, chunkVector for this bin
\r
814 binMap.insert( pair<uint32_t, ChunkVector>(binID, regionChunks) );
\r
817 // load linear index for this reference sequence
\r
819 // get number of linear offsets
\r
820 int32_t numLinearOffsets;
\r
821 elementsRead = fread(&numLinearOffsets, 4, 1, indexStream);
\r
822 if ( IsBigEndian ) { SwapEndian_32(numLinearOffsets); }
\r
824 // intialize LinearOffsetVector
\r
825 LinearOffsetVector offsets;
\r
826 offsets.reserve(numLinearOffsets);
\r
828 // iterate over linear offsets for this reference sequeence
\r
829 uint64_t linearOffset;
\r
830 for (int j = 0; j < numLinearOffsets; ++j) {
\r
831 // read a linear offset & store
\r
832 elementsRead = fread(&linearOffset, 8, 1, indexStream);
\r
833 if ( IsBigEndian ) { SwapEndian_64(linearOffset); }
\r
834 offsets.push_back(linearOffset);
\r
837 // sort linear offsets
\r
838 sort( offsets.begin(), offsets.end() );
\r
840 // store index data for that reference sequence
\r
841 Index.push_back( ReferenceIndex(binMap, offsets) );
\r
844 // close index file (.bai) and return
\r
845 fclose(indexStream);
\r
849 // populates BamAlignment with alignment data under file pointer, returns success/fail
\r
850 bool BamReader::BamReaderPrivate::LoadNextAlignment(BamAlignment& bAlignment, BamAlignmentSupportData& supportData) {
\r
852 // read in the 'block length' value, make sure it's not zero
\r
854 mBGZF.Read(buffer, 4);
\r
855 supportData.BlockLength = BgzfData::UnpackUnsignedInt(buffer);
\r
856 if ( IsBigEndian ) { SwapEndian_32(supportData.BlockLength); }
\r
857 if ( supportData.BlockLength == 0 ) { return false; }
\r
859 // read in core alignment data, make sure the right size of data was read
\r
860 char x[BAM_CORE_SIZE];
\r
861 if ( mBGZF.Read(x, BAM_CORE_SIZE) != BAM_CORE_SIZE ) { return false; }
\r
863 if ( IsBigEndian ) {
\r
864 for ( int i = 0; i < BAM_CORE_SIZE; i+=sizeof(uint32_t) ) {
\r
865 SwapEndian_32p(&x[i]);
\r
869 // set BamAlignment 'core' and 'support' data
\r
870 bAlignment.RefID = BgzfData::UnpackSignedInt(&x[0]);
\r
871 bAlignment.Position = BgzfData::UnpackSignedInt(&x[4]);
\r
873 unsigned int tempValue = BgzfData::UnpackUnsignedInt(&x[8]);
\r
874 bAlignment.Bin = tempValue >> 16;
\r
875 bAlignment.MapQuality = tempValue >> 8 & 0xff;
\r
876 supportData.QueryNameLength = tempValue & 0xff;
\r
878 tempValue = BgzfData::UnpackUnsignedInt(&x[12]);
\r
879 bAlignment.AlignmentFlag = tempValue >> 16;
\r
880 supportData.NumCigarOperations = tempValue & 0xffff;
\r
882 supportData.QuerySequenceLength = BgzfData::UnpackUnsignedInt(&x[16]);
\r
883 bAlignment.MateRefID = BgzfData::UnpackSignedInt(&x[20]);
\r
884 bAlignment.MatePosition = BgzfData::UnpackSignedInt(&x[24]);
\r
885 bAlignment.InsertSize = BgzfData::UnpackSignedInt(&x[28]);
\r
887 // store 'all char data' and cigar ops
\r
888 const unsigned int dataLength = supportData.BlockLength - BAM_CORE_SIZE;
\r
889 const unsigned int cigarDataOffset = supportData.QueryNameLength;
\r
891 char* allCharData = (char*)calloc(sizeof(char), dataLength);
\r
892 uint32_t* cigarData = (uint32_t*)(allCharData + cigarDataOffset);
\r
894 // read in character data - make sure proper data size was read
\r
895 if ( mBGZF.Read(allCharData, dataLength) != (signed int)dataLength) { return false; }
\r
898 // store alignment name and length
\r
899 bAlignment.Name.assign((const char*)(allCharData));
\r
900 bAlignment.Length = supportData.QuerySequenceLength;
\r
902 // store remaining 'allCharData' in supportData structure
\r
903 supportData.AllCharData.assign((const char*)allCharData, dataLength);
\r
905 // save CigarOps for BamAlignment
\r
906 bAlignment.CigarData.clear();
\r
907 for (unsigned int i = 0; i < supportData.NumCigarOperations; ++i) {
\r
909 // swap if necessary
\r
910 if ( IsBigEndian ) { SwapEndian_32(cigarData[i]); }
\r
912 // build CigarOp structure
\r
914 op.Length = (cigarData[i] >> BAM_CIGAR_SHIFT);
\r
915 op.Type = CIGAR_LOOKUP[ (cigarData[i] & BAM_CIGAR_MASK) ];
\r
918 bAlignment.CigarData.push_back(op);
\r
926 // loads reference data from BAM file
\r
927 void BamReader::BamReaderPrivate::LoadReferenceData(void) {
\r
929 // get number of reference sequences
\r
931 mBGZF.Read(buffer, 4);
\r
932 unsigned int numberRefSeqs = BgzfData::UnpackUnsignedInt(buffer);
\r
933 if ( IsBigEndian ) { SwapEndian_32(numberRefSeqs); }
\r
934 if (numberRefSeqs == 0) { return; }
\r
935 References.reserve((int)numberRefSeqs);
\r
937 // iterate over all references in header
\r
938 for (unsigned int i = 0; i != numberRefSeqs; ++i) {
\r
940 // get length of reference name
\r
941 mBGZF.Read(buffer, 4);
\r
942 unsigned int refNameLength = BgzfData::UnpackUnsignedInt(buffer);
\r
943 if ( IsBigEndian ) { SwapEndian_32(refNameLength); }
\r
944 char* refName = (char*)calloc(refNameLength, 1);
\r
946 // get reference name and reference sequence length
\r
947 mBGZF.Read(refName, refNameLength);
\r
948 mBGZF.Read(buffer, 4);
\r
949 int refLength = BgzfData::UnpackSignedInt(buffer);
\r
950 if ( IsBigEndian ) { SwapEndian_32(refLength); }
\r
952 // store data for reference
\r
953 RefData aReference;
\r
954 aReference.RefName = (string)((const char*)refName);
\r
955 aReference.RefLength = refLength;
\r
956 References.push_back(aReference);
\r
958 // clean up calloc-ed temp variable
\r
963 // merges 'alignment chunks' in BAM bin (used for index building)
\r
964 void BamReader::BamReaderPrivate::MergeChunks(void) {
\r
966 // iterate over reference enties
\r
967 BamIndex::iterator indexIter = Index.begin();
\r
968 BamIndex::iterator indexEnd = Index.end();
\r
969 for ( ; indexIter != indexEnd; ++indexIter ) {
\r
971 // get BAM bin map for this reference
\r
972 ReferenceIndex& refIndex = (*indexIter);
\r
973 BamBinMap& bamBinMap = refIndex.Bins;
\r
975 // iterate over BAM bins
\r
976 BamBinMap::iterator binIter = bamBinMap.begin();
\r
977 BamBinMap::iterator binEnd = bamBinMap.end();
\r
978 for ( ; binIter != binEnd; ++binIter ) {
\r
980 // get chunk vector for this bin
\r
981 ChunkVector& binChunks = (*binIter).second;
\r
982 if ( binChunks.size() == 0 ) { continue; }
\r
984 ChunkVector mergedChunks;
\r
985 mergedChunks.push_back( binChunks[0] );
\r
987 // iterate over chunks
\r
989 ChunkVector::iterator chunkIter = binChunks.begin();
\r
990 ChunkVector::iterator chunkEnd = binChunks.end();
\r
991 for ( ++chunkIter; chunkIter != chunkEnd; ++chunkIter) {
\r
993 // get 'currentChunk' based on numeric index
\r
994 Chunk& currentChunk = mergedChunks[i];
\r
996 // get iteratorChunk based on vector iterator
\r
997 Chunk& iteratorChunk = (*chunkIter);
\r
999 // if currentChunk.Stop(shifted) == iterator Chunk.Start(shifted)
\r
1000 if ( currentChunk.Stop>>16 == iteratorChunk.Start>>16 ) {
\r
1002 // set currentChunk.Stop to iteratorChunk.Stop
\r
1003 currentChunk.Stop = iteratorChunk.Stop;
\r
1008 // set currentChunk + 1 to iteratorChunk
\r
1009 mergedChunks.push_back(iteratorChunk);
\r
1014 // saved merged chunk vector
\r
1015 (*binIter).second = mergedChunks;
\r
1020 // opens BAM file (and index)
\r
1021 void BamReader::BamReaderPrivate::Open(const string& filename, const string& indexFilename) {
\r
1023 Filename = filename;
\r
1024 IndexFilename = indexFilename;
\r
1026 // open the BGZF file for reading, retrieve header text & reference data
\r
1027 mBGZF.Open(filename, "rb");
\r
1029 LoadReferenceData();
\r
1031 // store file offset of first alignment
\r
1032 AlignmentsBeginOffset = mBGZF.Tell();
\r
1034 // open index file & load index data (if exists)
\r
1035 if ( !IndexFilename.empty() ) {
\r
1040 // returns BAM file pointer to beginning of alignment data
\r
1041 bool BamReader::BamReaderPrivate::Rewind(void) {
\r
1043 // find first reference that has alignments in the BAM file
\r
1045 int refCount = References.size();
\r
1046 for ( ; refID < refCount; ++refID ) {
\r
1047 if ( References.at(refID).RefHasAlignments ) { break; }
\r
1050 // store default bounds for first alignment
\r
1051 CurrentRefID = refID;
\r
1053 IsRegionSpecified = false;
\r
1055 // return success/failure of seek
\r
1056 return mBGZF.Seek(AlignmentsBeginOffset);
\r
1059 // saves index data to BAM index file (".bai"), returns success/fail
\r
1060 bool BamReader::BamReaderPrivate::WriteIndex(void) {
\r
1062 IndexFilename = Filename + ".bai";
\r
1063 FILE* indexStream = fopen(IndexFilename.c_str(), "wb");
\r
1064 if ( indexStream == 0 ) {
\r
1065 printf("ERROR: Could not open file to save index\n");
\r
1069 // write BAM index header
\r
1070 fwrite("BAI\1", 1, 4, indexStream);
\r
1072 // write number of reference sequences
\r
1073 int32_t numReferenceSeqs = Index.size();
\r
1074 if ( IsBigEndian ) { SwapEndian_32(numReferenceSeqs); }
\r
1075 fwrite(&numReferenceSeqs, 4, 1, indexStream);
\r
1077 // iterate over reference sequences
\r
1078 BamIndex::const_iterator indexIter = Index.begin();
\r
1079 BamIndex::const_iterator indexEnd = Index.end();
\r
1080 for ( ; indexIter != indexEnd; ++ indexIter ) {
\r
1082 // get reference index data
\r
1083 const ReferenceIndex& refIndex = (*indexIter);
\r
1084 const BamBinMap& binMap = refIndex.Bins;
\r
1085 const LinearOffsetVector& offsets = refIndex.Offsets;
\r
1087 // write number of bins
\r
1088 int32_t binCount = binMap.size();
\r
1089 if ( IsBigEndian ) { SwapEndian_32(binCount); }
\r
1090 fwrite(&binCount, 4, 1, indexStream);
\r
1092 // iterate over bins
\r
1093 BamBinMap::const_iterator binIter = binMap.begin();
\r
1094 BamBinMap::const_iterator binEnd = binMap.end();
\r
1095 for ( ; binIter != binEnd; ++binIter ) {
\r
1097 // get bin data (key and chunk vector)
\r
1098 uint32_t binKey = (*binIter).first;
\r
1099 const ChunkVector& binChunks = (*binIter).second;
\r
1101 // save BAM bin key
\r
1102 if ( IsBigEndian ) { SwapEndian_32(binKey); }
\r
1103 fwrite(&binKey, 4, 1, indexStream);
\r
1105 // save chunk count
\r
1106 int32_t chunkCount = binChunks.size();
\r
1107 if ( IsBigEndian ) { SwapEndian_32(chunkCount); }
\r
1108 fwrite(&chunkCount, 4, 1, indexStream);
\r
1110 // iterate over chunks
\r
1111 ChunkVector::const_iterator chunkIter = binChunks.begin();
\r
1112 ChunkVector::const_iterator chunkEnd = binChunks.end();
\r
1113 for ( ; chunkIter != chunkEnd; ++chunkIter ) {
\r
1115 // get current chunk data
\r
1116 const Chunk& chunk = (*chunkIter);
\r
1117 uint64_t start = chunk.Start;
\r
1118 uint64_t stop = chunk.Stop;
\r
1120 if ( IsBigEndian ) {
\r
1121 SwapEndian_64(start);
\r
1122 SwapEndian_64(stop);
\r
1125 // save chunk offsets
\r
1126 fwrite(&start, 8, 1, indexStream);
\r
1127 fwrite(&stop, 8, 1, indexStream);
\r
1131 // write linear offsets size
\r
1132 int32_t offsetSize = offsets.size();
\r
1133 if ( IsBigEndian ) { SwapEndian_32(offsetSize); }
\r
1134 fwrite(&offsetSize, 4, 1, indexStream);
\r
1136 // iterate over linear offsets
\r
1137 LinearOffsetVector::const_iterator offsetIter = offsets.begin();
\r
1138 LinearOffsetVector::const_iterator offsetEnd = offsets.end();
\r
1139 for ( ; offsetIter != offsetEnd; ++offsetIter ) {
\r
1141 // write linear offset value
\r
1142 uint64_t linearOffset = (*offsetIter);
\r
1143 if ( IsBigEndian ) { SwapEndian_64(linearOffset); }
\r
1144 fwrite(&linearOffset, 8, 1, indexStream);
\r
1148 // flush buffer, close file, and return success
\r
1149 fflush(indexStream);
\r
1150 fclose(indexStream);
\r