// ***************************************************************************
// BamWriter_p.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 11 January 2011 (DB)
+// Last modified: 6 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides the basic functionality for producing BAM files
// ***************************************************************************
#include <api/BamAlignment.h>
+#include <api/BamConstants.h>
+<<<<<<< HEAD
+#include <api/internal/BamException_p.h>
+=======
+#include <api/IBamIODevice.h>
+>>>>>>> iodevice
#include <api/internal/BamWriter_p.h>
using namespace BamTools;
using namespace BamTools::Internal;
+
+#include <cstdlib>
+#include <cstring>
using namespace std;
// ctor
-BamWriterPrivate::BamWriterPrivate(void) {
- IsBigEndian = SystemIsBigEndian();
-}
+BamWriterPrivate::BamWriterPrivate(void)
+ : m_isBigEndian( BamTools::SystemIsBigEndian() )
+{ }
// dtor
BamWriterPrivate::~BamWriterPrivate(void) {
- mBGZF.Close();
+ Close();
}
// calculates minimum bin for a BAM alignment interval
-const unsigned int BamWriterPrivate::CalculateMinimumBin(const int begin, int end) const {
+uint32_t 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);
+ 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;
}
// closes the alignment archive
void BamWriterPrivate::Close(void) {
- mBGZF.Close();
+
+ // skip if file not open
+ if ( !IsOpen() ) return;
+
+ // close output stream
+ try {
+ m_stream.Close();
+ } catch ( BamException& e ) {
+ m_errorString = e.what();
+ }
}
// 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);
+ const size_t numCigarOperations = cigarOperations.size();
+ packedCigar.resize(numCigarOperations * Constants::BAM_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;
+ // iterate over cigar operations
+ vector<CigarOp>::const_iterator coIter = cigarOperations.begin();
+ vector<CigarOp>::const_iterator coEnd = cigarOperations.end();
+ for ( ; coIter != coEnd; ++coIter ) {
+
+ // store op in packedCigar
+ uint8_t cigarOp;
+ switch ( coIter->Type ) {
+ case (Constants::BAM_CIGAR_MATCH_CHAR) : cigarOp = Constants::BAM_CIGAR_MATCH; break;
+ case (Constants::BAM_CIGAR_INS_CHAR) : cigarOp = Constants::BAM_CIGAR_INS; break;
+ case (Constants::BAM_CIGAR_DEL_CHAR) : cigarOp = Constants::BAM_CIGAR_DEL; break;
+ case (Constants::BAM_CIGAR_REFSKIP_CHAR) : cigarOp = Constants::BAM_CIGAR_REFSKIP; break;
+ case (Constants::BAM_CIGAR_SOFTCLIP_CHAR) : cigarOp = Constants::BAM_CIGAR_SOFTCLIP; break;
+ case (Constants::BAM_CIGAR_HARDCLIP_CHAR) : cigarOp = Constants::BAM_CIGAR_HARDCLIP; break;
+ case (Constants::BAM_CIGAR_PAD_CHAR) : cigarOp = Constants::BAM_CIGAR_PAD; break;
+ case (Constants::BAM_CIGAR_SEQMATCH_CHAR) : cigarOp = Constants::BAM_CIGAR_SEQMATCH; break;
+ case (Constants::BAM_CIGAR_MISMATCH_CHAR) : cigarOp = Constants::BAM_CIGAR_MISMATCH; break;
default:
- fprintf(stderr, "ERROR: Unknown cigar operation found: %c\n", coIter->Type);
- exit(1);
+ const string message = string("invalid CIGAR operation type") + coIter->Type;
+ throw BamException("BamWriter::CreatePackedCigar", message);
}
- *pPackedCigar = coIter->Length << BAM_CIGAR_SHIFT | cigarOp;
+ *pPackedCigar = coIter->Length << Constants::BAM_CIGAR_SHIFT | cigarOp;
pPackedCigar++;
}
}
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);
+ const size_t queryLength = query.size();
+ const size_t encodedQueryLength = static_cast<size_t>((queryLength+1)/2);
+ encodedQuery.resize(encodedQueryLength);
char* pEncodedQuery = (char*)encodedQuery.data();
const char* pQuery = (const char*)query.data();
+ // walk through original query sequence, encoding its bases
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;
+ while ( *pQuery ) {
+ switch ( *pQuery ) {
+ case (Constants::BAM_DNA_EQUAL) : nucleotideCode = Constants::BAM_BASECODE_EQUAL; break;
+ case (Constants::BAM_DNA_A) : nucleotideCode = Constants::BAM_BASECODE_A; break;
+ case (Constants::BAM_DNA_C) : nucleotideCode = Constants::BAM_BASECODE_C; break;
+ case (Constants::BAM_DNA_M) : nucleotideCode = Constants::BAM_BASECODE_M; break;
+ case (Constants::BAM_DNA_G) : nucleotideCode = Constants::BAM_BASECODE_G; break;
+ case (Constants::BAM_DNA_R) : nucleotideCode = Constants::BAM_BASECODE_R; break;
+ case (Constants::BAM_DNA_S) : nucleotideCode = Constants::BAM_BASECODE_S; break;
+ case (Constants::BAM_DNA_V) : nucleotideCode = Constants::BAM_BASECODE_V; break;
+ case (Constants::BAM_DNA_T) : nucleotideCode = Constants::BAM_BASECODE_T; break;
+ case (Constants::BAM_DNA_W) : nucleotideCode = Constants::BAM_BASECODE_W; break;
+ case (Constants::BAM_DNA_Y) : nucleotideCode = Constants::BAM_BASECODE_Y; break;
+ case (Constants::BAM_DNA_H) : nucleotideCode = Constants::BAM_BASECODE_H; break;
+ case (Constants::BAM_DNA_K) : nucleotideCode = Constants::BAM_BASECODE_K; break;
+ case (Constants::BAM_DNA_D) : nucleotideCode = Constants::BAM_BASECODE_D; break;
+ case (Constants::BAM_DNA_B) : nucleotideCode = Constants::BAM_BASECODE_B; break;
+ case (Constants::BAM_DNA_N) : nucleotideCode = Constants::BAM_BASECODE_N; 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);
+ const string message = string("invalid base: ") + *pQuery;
+ throw BamException("BamWriter::EncodeQuerySequence", message);
}
// pack the nucleotide code
- if(useHighWord) {
+ if ( useHighWord ) {
*pEncodedQuery = nucleotideCode << 4;
useHighWord = false;
} else {
*pEncodedQuery |= nucleotideCode;
- pEncodedQuery++;
+ ++pEncodedQuery;
useHighWord = true;
}
// increment the query position
- pQuery++;
+ ++pQuery;
}
}
+// returns a description of the last error that occurred
+std::string BamWriterPrivate::GetErrorString(void) const {
+ return m_errorString;
+}
+
+// returns whether BAM file is open for writing or not
+bool BamWriterPrivate::IsOpen(void) const {
+ return m_stream.IsOpen();
+}
+
// opens the alignment archive
bool BamWriterPrivate::Open(const string& filename,
- const string& samHeader,
- const RefVector& referenceSequences,
- bool isWriteUncompressed)
+ const string& samHeaderText,
+ const RefVector& referenceSequences)
{
+<<<<<<< HEAD
+ try {
+=======
// open the BGZF file for writing, return failure if error
- if ( !mBGZF.Open(filename, "wb", isWriteUncompressed) )
+ if ( !m_stream.Open(filename, IBamIODevice::WriteOnly) )
return false;
+>>>>>>> iodevice
- // ================
- // write the header
- // ================
+ // open the BGZF file for writing, return failure if error
+ m_stream.Open(filename, "wb");
- // write the BAM signature
- const unsigned char SIGNATURE_LENGTH = 4;
- const char* BAM_SIGNATURE = "BAM\1";
- mBGZF.Write(BAM_SIGNATURE, SIGNATURE_LENGTH);
+ // write BAM file 'metadata' components
+ WriteMagicNumber();
+ WriteSamHeaderText(samHeaderText);
+ WriteReferences(referenceSequences);
- // write the SAM header text length
- uint32_t samHeaderLen = samHeader.size();
- if (IsBigEndian) SwapEndian_32(samHeaderLen);
- mBGZF.Write((char*)&samHeaderLen, BT_SIZEOF_INT);
+ // return success
+ return true;
- // write the SAM header text
- if(samHeaderLen > 0)
- mBGZF.Write(samHeader.data(), samHeaderLen);
+ } catch ( BamException& e ) {
+ m_errorString = e.what();
+ return false;
+ }
+}
- // write the number of reference sequences
- uint32_t numReferenceSequences = referenceSequences.size();
- if (IsBigEndian) SwapEndian_32(numReferenceSequences);
- mBGZF.Write((char*)&numReferenceSequences, BT_SIZEOF_INT);
+// saves the alignment to the alignment archive
+bool BamWriterPrivate::SaveAlignment(const BamAlignment& al) {
- // =============================
- // write the sequence dictionary
- // =============================
+ try {
- RefVector::const_iterator rsIter = referenceSequences.begin();
- RefVector::const_iterator rsEnd = referenceSequences.end();
- for( ; rsIter != rsEnd; ++rsIter ) {
+ // if BamAlignment contains only the core data and a raw char data buffer
+ // (as a result of BamReader::GetNextAlignmentCore())
+ if ( al.SupportData.HasCoreOnly )
+ WriteCoreAlignment(al);
- // 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);
+ // otherwise, BamAlignment should contain character in the standard fields: Name, QueryBases, etc
+ // (resulting from BamReader::GetNextAlignment() *OR* being generated directly by client code)
+ else WriteAlignment(al);
- // write the reference sequence name
- mBGZF.Write(rsIter->RefName.c_str(), referenceSequenceNameLen);
+ // if we get here, everything OK
+ return true;
- // write the reference sequence length
- int32_t referenceLength = rsIter->RefLength;
- if (IsBigEndian) SwapEndian_32(referenceLength);
- mBGZF.Write((char*)&referenceLength, BT_SIZEOF_INT);
+ } catch ( BamException& e ) {
+ m_errorString = e.what();
+ return false;
}
+}
- // return success
- return true;
+void BamWriterPrivate::SetWriteCompressed(bool ok) {
+ // modifying compression is not allowed if BAM file is open
+ if ( !IsOpen() )
+ m_stream.SetWriteCompressed(ok);
}
-// 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]);
- }
+void BamWriterPrivate::WriteAlignment(const BamAlignment& al) {
+
+ // 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 uint32_t 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 = Constants::BAM_CORE_SIZE + dataBlockSize;
+ if ( m_isBigEndian ) BamTools::SwapEndian_32(blockSize);
+ m_stream.Write((char*)&blockSize, Constants::BAM_SIZEOF_INT);
+
+ // assign the BAM core data
+ uint32_t buffer[Constants::BAM_CORE_BUFFER_SIZE];
+ 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 ( m_isBigEndian ) {
+ for ( int i = 0; i < 8; ++i )
+ BamTools::SwapEndian_32(buffer[i]);
+ }
- // write the BAM core
- mBGZF.Write((char*)&buffer, BAM_CORE_SIZE);
+ // write the BAM core
+ m_stream.Write((char*)&buffer, Constants::BAM_CORE_SIZE);
- // write the raw char data
- mBGZF.Write((char*)al.SupportData.AllCharData.data(), al.SupportData.BlockLength-BAM_CORE_SIZE);
- }
+ // write the query name
+ m_stream.Write(al.Name.c_str(), nameLength);
- // 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 packed cigar
+ if ( m_isBigEndian ) {
+ char* cigarData = new char[packedCigarLength]();
+ memcpy(cigarData, packedCigar.data(), packedCigarLength);
+ if ( m_isBigEndian ) {
+ for ( size_t i = 0; i < packedCigarLength; ++i )
+ BamTools::SwapEndian_32p(&cigarData[i]);
}
+ m_stream.Write(cigarData, packedCigarLength);
+ delete[] cigarData; // TODO: cleanup on Write exception thrown?
+ }
+ else
+ m_stream.Write(packedCigar.data(), packedCigarLength);
+
+ // write the encoded query sequence
+ m_stream.Write(encodedQuery.data(), encodedQueryLength);
+
+ // write the base qualities
+ char* pBaseQualities = (char*)al.Qualities.data();
+ for ( size_t i = 0; i < queryLength; ++i )
+ pBaseQualities[i] -= 33; // FASTQ conversion
+ m_stream.Write(pBaseQualities, queryLength);
+
+ // write the read group tag
+ if ( m_isBigEndian ) {
+
+ char* tagData = new char[tagDataLength]();
+ memcpy(tagData, al.TagData.data(), tagDataLength);
+
+ size_t i = 0;
+ while ( i < tagDataLength ) {
+
+ i += Constants::BAM_TAG_TAGSIZE; // skip tag chars (e.g. "RG", "NM", etc.)
+ const char type = tagData[i]; // get tag type at position i
+ ++i;
+
+ switch ( type ) {
+
+ case(Constants::BAM_TAG_TYPE_ASCII) :
+ case(Constants::BAM_TAG_TYPE_INT8) :
+ case(Constants::BAM_TAG_TYPE_UINT8) :
+ ++i;
+ break;
+
+ case(Constants::BAM_TAG_TYPE_INT16) :
+ case(Constants::BAM_TAG_TYPE_UINT16) :
+ BamTools::SwapEndian_16p(&tagData[i]);
+ i += sizeof(uint16_t);
+ break;
+
+ case(Constants::BAM_TAG_TYPE_FLOAT) :
+ case(Constants::BAM_TAG_TYPE_INT32) :
+ case(Constants::BAM_TAG_TYPE_UINT32) :
+ BamTools::SwapEndian_32p(&tagData[i]);
+ i += sizeof(uint32_t);
+ break;
+
+ case(Constants::BAM_TAG_TYPE_HEX) :
+ case(Constants::BAM_TAG_TYPE_STRING) :
+ // no endian swapping necessary for hex-string/string data
+ while ( tagData[i] )
+ ++i;
+ // increment one more for null terminator
+ ++i;
+ break;
+
+ case(Constants::BAM_TAG_TYPE_ARRAY) :
+
+ {
+ // read array type
+ const char arrayType = tagData[i];
+ ++i;
+
+ // swap endian-ness of number of elements in place, then retrieve for loop
+ BamTools::SwapEndian_32p(&tagData[i]);
+ int32_t numElements;
+ memcpy(&numElements, &tagData[i], sizeof(uint32_t));
+ i += sizeof(uint32_t);
+
+ // swap endian-ness of array elements
+ for ( int j = 0; j < numElements; ++j ) {
+ switch (arrayType) {
+ case (Constants::BAM_TAG_TYPE_INT8) :
+ case (Constants::BAM_TAG_TYPE_UINT8) :
+ // no endian-swapping necessary
+ ++i;
+ break;
+ case (Constants::BAM_TAG_TYPE_INT16) :
+ case (Constants::BAM_TAG_TYPE_UINT16) :
+ BamTools::SwapEndian_16p(&tagData[i]);
+ i += sizeof(uint16_t);
+ break;
+ case (Constants::BAM_TAG_TYPE_FLOAT) :
+ case (Constants::BAM_TAG_TYPE_INT32) :
+ case (Constants::BAM_TAG_TYPE_UINT32) :
+ BamTools::SwapEndian_32p(&tagData[i]);
+ i += sizeof(uint32_t);
+ break;
+ default:
+ delete[] tagData;
+ const string message = string("invalid binary array type: ") + arrayType;
+ throw BamException("BamWriter::SaveAlignment", message);
+ }
+ }
+
+ break;
+ }
- // write the BAM core
- mBGZF.Write((char*)&buffer, BAM_CORE_SIZE);
+ default :
+ delete[] tagData;
+ const string message = string("invalid tag type: ") + type;
+ throw BamException("BamWriter::SaveAlignment", message);
+ }
+ }
- // write the query name
- mBGZF.Write(al.Name.c_str(), nameLength);
+ m_stream.Write(tagData, tagDataLength);
+ delete[] tagData; // TODO: cleanup on Write exception thrown?
+ }
+ else
+ m_stream.Write(al.TagData.data(), tagDataLength);
+}
- // write the packed cigar
- if ( IsBigEndian ) {
+void BamWriterPrivate::WriteCoreAlignment(const BamAlignment& al) {
+
+ // write the block size
+ unsigned int blockSize = al.SupportData.BlockLength;
+ if ( m_isBigEndian ) BamTools::SwapEndian_32(blockSize);
+ m_stream.Write((char*)&blockSize, Constants::BAM_SIZEOF_INT);
+
+ // re-calculate bin (in case BamAlignment's position has been previously modified)
+ const uint32_t alignmentBin = CalculateMinimumBin(al.Position, al.GetEndPosition());
+
+ // assign the BAM core data
+ uint32_t buffer[Constants::BAM_CORE_BUFFER_SIZE];
+ buffer[0] = al.RefID;
+ buffer[1] = al.Position;
+ buffer[2] = (alignmentBin << 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 ( m_isBigEndian ) {
+ for ( int i = 0; i < 8; ++i )
+ BamTools::SwapEndian_32(buffer[i]);
+ }
- char* cigarData = (char*)calloc(sizeof(char), packedCigarLength);
- memcpy(cigarData, packedCigar.data(), packedCigarLength);
+ // write the BAM core
+ m_stream.Write((char*)&buffer, Constants::BAM_CORE_SIZE);
- for (unsigned int i = 0; i < packedCigarLength; ++i) {
- if ( IsBigEndian )
- SwapEndian_32p(&cigarData[i]);
- }
+ // write the raw char data
+ m_stream.Write((char*)al.SupportData.AllCharData.data(),
+ al.SupportData.BlockLength-Constants::BAM_CORE_SIZE);
+}
- mBGZF.Write(cigarData, packedCigarLength);
- free(cigarData);
- }
- else
- mBGZF.Write(packedCigar.data(), packedCigarLength);
+void BamWriterPrivate::WriteMagicNumber(void) {
+ // write BAM file 'magic number'
+ m_stream.Write(Constants::BAM_HEADER_MAGIC, Constants::BAM_HEADER_MAGIC_LENGTH);
+}
- // write the encoded query sequence
- mBGZF.Write(encodedQuery.data(), encodedQueryLength);
+void BamWriterPrivate::WriteReferences(const BamTools::RefVector& referenceSequences) {
- // write the base qualities
- char* pBaseQualities = (char*)al.Qualities.data();
- for(unsigned int i = 0; i < queryLength; i++)
- pBaseQualities[i] -= 33; // FASTQ conversion
- mBGZF.Write(pBaseQualities, queryLength);
+ // write the number of reference sequences
+ uint32_t numReferenceSequences = referenceSequences.size();
+ if ( m_isBigEndian ) BamTools::SwapEndian_32(numReferenceSequences);
+ m_stream.Write((char*)&numReferenceSequences, Constants::BAM_SIZEOF_INT);
- // write the read group tag
- if ( IsBigEndian ) {
+ // foreach reference sequence
+ RefVector::const_iterator rsIter = referenceSequences.begin();
+ RefVector::const_iterator rsEnd = referenceSequences.end();
+ for ( ; rsIter != rsEnd; ++rsIter ) {
- char* tagData = (char*)calloc(sizeof(char), tagDataLength);
- memcpy(tagData, al.TagData.data(), tagDataLength);
+ // write the reference sequence name length
+ uint32_t referenceSequenceNameLen = rsIter->RefName.size() + 1;
+ if ( m_isBigEndian ) BamTools::SwapEndian_32(referenceSequenceNameLen);
+ m_stream.Write((char*)&referenceSequenceNameLen, Constants::BAM_SIZEOF_INT);
- int i = 0;
- while ( (unsigned int)i < tagDataLength ) {
+ // write the reference sequence name
+ m_stream.Write(rsIter->RefName.c_str(), referenceSequenceNameLen);
- 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
+ // write the reference sequence length
+ int32_t referenceLength = rsIter->RefLength;
+ if ( m_isBigEndian ) BamTools::SwapEndian_32(referenceLength);
+ m_stream.Write((char*)&referenceLength, Constants::BAM_SIZEOF_INT);
+ }
+}
- switch (type) {
+void BamWriterPrivate::WriteSamHeaderText(const std::string& samHeaderText) {
- 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);
- }
- }
+ // write the SAM header text length
+ uint32_t samHeaderLen = samHeaderText.size();
+ if ( m_isBigEndian ) BamTools::SwapEndian_32(samHeaderLen);
+ m_stream.Write((char*)&samHeaderLen, Constants::BAM_SIZEOF_INT);
- mBGZF.Write(tagData, tagDataLength);
- free(tagData);
- }
- else
- mBGZF.Write(al.TagData.data(), tagDataLength);
- }
+ // write the SAM header text
+ if ( samHeaderLen > 0 )
+ m_stream.Write(samHeaderText.data(), samHeaderLen);
}
projects / bamtools.git / blobdiff