--- /dev/null
+// ***************************************************************************
+// BamWriter_p.cpp (c) 2010 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 22 November 2010 (DB)
+// ---------------------------------------------------------------------------
+// Provides the basic functionality for producing BAM files
+// ***************************************************************************
+
+#include <api/BamAlignment.h>
+#include <api/internal/BamWriter_p.h>
+using namespace BamTools;
+using namespace BamTools::Internal;
+using namespace std;
+
+BamWriterPrivate::BamWriterPrivate(void) {
+ IsBigEndian = SystemIsBigEndian();
+}
+
+BamWriterPrivate::~BamWriterPrivate(void) {
+ mBGZF.Close();
+}
+
+// closes the alignment archive
+void BamWriterPrivate::Close(void) {
+ mBGZF.Close();
+}
+
+// calculates minimum bin for a BAM alignment interval
+const unsigned int BamWriterPrivate::CalculateMinimumBin(const int begin, int end) const {
+ --end;
+ if( (begin >> 14) == (end >> 14) ) return 4681 + (begin >> 14);
+ if( (begin >> 17) == (end >> 17) ) return 585 + (begin >> 17);
+ if( (begin >> 20) == (end >> 20) ) return 73 + (begin >> 20);
+ if( (begin >> 23) == (end >> 23) ) return 9 + (begin >> 23);
+ if( (begin >> 26) == (end >> 26) ) return 1 + (begin >> 26);
+ return 0;
+}
+
+// creates a cigar string from the supplied alignment
+void BamWriterPrivate::CreatePackedCigar(const vector<CigarOp>& cigarOperations, string& packedCigar) {
+
+ // initialize
+ const unsigned int numCigarOperations = cigarOperations.size();
+ packedCigar.resize(numCigarOperations * BT_SIZEOF_INT);
+
+ // pack the cigar data into the string
+ unsigned int* pPackedCigar = (unsigned int*)packedCigar.data();
+
+ unsigned int cigarOp;
+ vector<CigarOp>::const_iterator coIter;
+ for(coIter = cigarOperations.begin(); coIter != cigarOperations.end(); ++coIter) {
+
+ switch(coIter->Type) {
+ case 'M':
+ cigarOp = BAM_CMATCH;
+ break;
+ case 'I':
+ cigarOp = BAM_CINS;
+ break;
+ case 'D':
+ cigarOp = BAM_CDEL;
+ break;
+ case 'N':
+ cigarOp = BAM_CREF_SKIP;
+ break;
+ case 'S':
+ cigarOp = BAM_CSOFT_CLIP;
+ break;
+ case 'H':
+ cigarOp = BAM_CHARD_CLIP;
+ break;
+ case 'P':
+ cigarOp = BAM_CPAD;
+ break;
+ default:
+ fprintf(stderr, "ERROR: Unknown cigar operation found: %c\n", coIter->Type);
+ exit(1);
+ }
+
+ *pPackedCigar = coIter->Length << BAM_CIGAR_SHIFT | cigarOp;
+ pPackedCigar++;
+ }
+}
+
+// encodes the supplied query sequence into 4-bit notation
+void BamWriterPrivate::EncodeQuerySequence(const string& query, string& encodedQuery) {
+
+ // prepare the encoded query string
+ const unsigned int queryLen = query.size();
+ const unsigned int encodedQueryLen = (unsigned int)((queryLen / 2.0) + 0.5);
+ encodedQuery.resize(encodedQueryLen);
+ char* pEncodedQuery = (char*)encodedQuery.data();
+ const char* pQuery = (const char*)query.data();
+
+ unsigned char nucleotideCode;
+ bool useHighWord = true;
+
+ while(*pQuery) {
+
+ switch(*pQuery) {
+
+ case '=':
+ nucleotideCode = 0;
+ break;
+
+ case 'A':
+ nucleotideCode = 1;
+ break;
+
+ case 'C':
+ nucleotideCode = 2;
+ break;
+
+ case 'G':
+ nucleotideCode = 4;
+ break;
+
+ case 'T':
+ nucleotideCode = 8;
+ break;
+
+ case 'N':
+ nucleotideCode = 15;
+ break;
+
+ default:
+ fprintf(stderr, "ERROR: Only the following bases are supported in the BAM format: {=, A, C, G, T, N}. Found [%c]\n", *pQuery);
+ exit(1);
+ }
+
+ // pack the nucleotide code
+ if(useHighWord) {
+ *pEncodedQuery = nucleotideCode << 4;
+ useHighWord = false;
+ } else {
+ *pEncodedQuery |= nucleotideCode;
+ pEncodedQuery++;
+ useHighWord = true;
+ }
+
+ // increment the query position
+ pQuery++;
+ }
+}
+
+// opens the alignment archive
+bool BamWriterPrivate::Open(const string& filename,
+ const string& samHeader,
+ const RefVector& referenceSequences,
+ bool isWriteUncompressed)
+{
+ // open the BGZF file for writing, return failure if error
+ if ( !mBGZF.Open(filename, "wb", isWriteUncompressed) )
+ return false;
+
+ // ================
+ // write the header
+ // ================
+
+ // write the BAM signature
+ const unsigned char SIGNATURE_LENGTH = 4;
+ const char* BAM_SIGNATURE = "BAM\1";
+ mBGZF.Write(BAM_SIGNATURE, SIGNATURE_LENGTH);
+
+ // write the SAM header text length
+ uint32_t samHeaderLen = samHeader.size();
+ if (IsBigEndian) SwapEndian_32(samHeaderLen);
+ mBGZF.Write((char*)&samHeaderLen, BT_SIZEOF_INT);
+
+ // write the SAM header text
+ if(samHeaderLen > 0)
+ mBGZF.Write(samHeader.data(), samHeaderLen);
+
+ // write the number of reference sequences
+ uint32_t numReferenceSequences = referenceSequences.size();
+ if (IsBigEndian) SwapEndian_32(numReferenceSequences);
+ mBGZF.Write((char*)&numReferenceSequences, BT_SIZEOF_INT);
+
+ // =============================
+ // write the sequence dictionary
+ // =============================
+
+ RefVector::const_iterator rsIter;
+ for(rsIter = referenceSequences.begin(); rsIter != referenceSequences.end(); rsIter++) {
+
+ // write the reference sequence name length
+ uint32_t referenceSequenceNameLen = rsIter->RefName.size() + 1;
+ if (IsBigEndian) SwapEndian_32(referenceSequenceNameLen);
+ mBGZF.Write((char*)&referenceSequenceNameLen, BT_SIZEOF_INT);
+
+ // write the reference sequence name
+ mBGZF.Write(rsIter->RefName.c_str(), referenceSequenceNameLen);
+
+ // write the reference sequence length
+ int32_t referenceLength = rsIter->RefLength;
+ if (IsBigEndian) SwapEndian_32(referenceLength);
+ mBGZF.Write((char*)&referenceLength, BT_SIZEOF_INT);
+ }
+
+ // return success
+ return true;
+}
+
+// saves the alignment to the alignment archive
+void BamWriterPrivate::SaveAlignment(const BamAlignment& al) {
+
+ // if BamAlignment contains only the core data and a raw char data buffer
+ // (as a result of BamReader::GetNextAlignmentCore())
+ if ( al.SupportData.HasCoreOnly ) {
+
+ // write the block size
+ unsigned int blockSize = al.SupportData.BlockLength;
+ if (IsBigEndian) SwapEndian_32(blockSize);
+ mBGZF.Write((char*)&blockSize, BT_SIZEOF_INT);
+
+ // assign the BAM core data
+ uint32_t buffer[8];
+ buffer[0] = al.RefID;
+ buffer[1] = al.Position;
+ buffer[2] = (al.Bin << 16) | (al.MapQuality << 8) | al.SupportData.QueryNameLength;
+ buffer[3] = (al.AlignmentFlag << 16) | al.SupportData.NumCigarOperations;
+ buffer[4] = al.SupportData.QuerySequenceLength;
+ buffer[5] = al.MateRefID;
+ buffer[6] = al.MatePosition;
+ buffer[7] = al.InsertSize;
+
+ // swap BAM core endian-ness, if necessary
+ if ( IsBigEndian ) {
+ for ( int i = 0; i < 8; ++i )
+ SwapEndian_32(buffer[i]);
+ }
+
+ // write the BAM core
+ mBGZF.Write((char*)&buffer, BAM_CORE_SIZE);
+
+ // write the raw char data
+ mBGZF.Write((char*)al.SupportData.AllCharData.data(), al.SupportData.BlockLength-BAM_CORE_SIZE);
+ }
+
+ // otherwise, BamAlignment should contain character in the standard fields: Name, QueryBases, etc
+ // ( resulting from BamReader::GetNextAlignment() *OR* being generated directly by client code )
+ else {
+
+ // calculate char lengths
+ const unsigned int nameLength = al.Name.size() + 1;
+ const unsigned int numCigarOperations = al.CigarData.size();
+ const unsigned int queryLength = al.QueryBases.size();
+ const unsigned int tagDataLength = al.TagData.size();
+
+ // no way to tell if BamAlignment.Bin is already defined (no default, invalid value)
+ // force calculation of Bin before storing
+ const int endPosition = al.GetEndPosition();
+ const unsigned int alignmentBin = CalculateMinimumBin(al.Position, endPosition);
+
+ // create our packed cigar string
+ string packedCigar;
+ CreatePackedCigar(al.CigarData, packedCigar);
+ const unsigned int packedCigarLength = packedCigar.size();
+
+ // encode the query
+ string encodedQuery;
+ EncodeQuerySequence(al.QueryBases, encodedQuery);
+ const unsigned int encodedQueryLength = encodedQuery.size();
+
+ // write the block size
+ const unsigned int dataBlockSize = nameLength + packedCigarLength + encodedQueryLength + queryLength + tagDataLength;
+ unsigned int blockSize = BAM_CORE_SIZE + dataBlockSize;
+ if (IsBigEndian) SwapEndian_32(blockSize);
+ mBGZF.Write((char*)&blockSize, BT_SIZEOF_INT);
+
+ // assign the BAM core data
+ uint32_t buffer[8];
+ buffer[0] = al.RefID;
+ buffer[1] = al.Position;
+ buffer[2] = (alignmentBin << 16) | (al.MapQuality << 8) | nameLength;
+ buffer[3] = (al.AlignmentFlag << 16) | numCigarOperations;
+ buffer[4] = queryLength;
+ buffer[5] = al.MateRefID;
+ buffer[6] = al.MatePosition;
+ buffer[7] = al.InsertSize;
+
+ // swap BAM core endian-ness, if necessary
+ if ( IsBigEndian ) {
+ for ( int i = 0; i < 8; ++i )
+ SwapEndian_32(buffer[i]);
+ }
+
+ // write the BAM core
+ mBGZF.Write((char*)&buffer, BAM_CORE_SIZE);
+
+ // write the query name
+ mBGZF.Write(al.Name.c_str(), nameLength);
+
+ // write the packed cigar
+ if ( IsBigEndian ) {
+
+ char* cigarData = (char*)calloc(sizeof(char), packedCigarLength);
+ memcpy(cigarData, packedCigar.data(), packedCigarLength);
+
+ for (unsigned int i = 0; i < packedCigarLength; ++i) {
+ if ( IsBigEndian )
+ SwapEndian_32p(&cigarData[i]);
+ }
+
+ mBGZF.Write(cigarData, packedCigarLength);
+ free(cigarData);
+ }
+ else
+ mBGZF.Write(packedCigar.data(), packedCigarLength);
+
+ // write the encoded query sequence
+ mBGZF.Write(encodedQuery.data(), encodedQueryLength);
+
+ // write the base qualities
+ string baseQualities(al.Qualities);
+ char* pBaseQualities = (char*)al.Qualities.data();
+ for(unsigned int i = 0; i < queryLength; i++) {
+ pBaseQualities[i] -= 33;
+ }
+ mBGZF.Write(pBaseQualities, queryLength);
+
+ // write the read group tag
+ if ( IsBigEndian ) {
+
+ char* tagData = (char*)calloc(sizeof(char), tagDataLength);
+ memcpy(tagData, al.TagData.data(), tagDataLength);
+
+ int i = 0;
+ while ( (unsigned int)i < tagDataLength ) {
+
+ i += 2; // skip tag type (e.g. "RG", "NM", etc)
+ uint8_t type = toupper(tagData[i]); // lower & upper case letters have same meaning
+ ++i; // skip value type
+
+ switch (type) {
+
+ case('A') :
+ case('C') :
+ ++i;
+ break;
+
+ case('S') :
+ SwapEndian_16p(&tagData[i]);
+ i+=2; // sizeof(uint16_t)
+ break;
+
+ case('F') :
+ case('I') :
+ SwapEndian_32p(&tagData[i]);
+ i+=4; // sizeof(uint32_t)
+ break;
+
+ case('D') :
+ SwapEndian_64p(&tagData[i]);
+ i+=8; // sizeof(uint64_t)
+ break;
+
+ case('H') :
+ case('Z') :
+ while (tagData[i]) { ++i; }
+ ++i; // increment one more for null terminator
+ break;
+
+ default :
+ fprintf(stderr, "ERROR: Invalid tag value type\n"); // shouldn't get here
+ free(tagData);
+ exit(1);
+ }
+ }
+
+ mBGZF.Write(tagData, tagDataLength);
+ free(tagData);
+ }
+ else
+ mBGZF.Write(al.TagData.data(), tagDataLength);
+ }
+}
projects / bamtools.git / blobdiff