+++ /dev/null
-// ***************************************************************************
-// BamWriter_p.cpp (c) 2010 Derek Barnett
-// Marth Lab, Department of Biology, Boston College
-// ---------------------------------------------------------------------------
-// Last modified: 10 October 2011 (DB)
-// ---------------------------------------------------------------------------
-// Provides the basic functionality for producing BAM files
-// ***************************************************************************
-
-#include "api/BamAlignment.h"
-#include "api/BamConstants.h"
-#include "api/IBamIODevice.h"
-#include "api/internal/BamException_p.h"
-#include "api/internal/BamWriter_p.h"
-using namespace BamTools;
-using namespace BamTools::Internal;
-
-#include <cstdlib>
-#include <cstring>
-using namespace std;
-
-// ctor
-BamWriterPrivate::BamWriterPrivate(void)
- : m_isBigEndian( BamTools::SystemIsBigEndian() )
-{ }
-
-// dtor
-BamWriterPrivate::~BamWriterPrivate(void) {
- Close();
-}
-
-// calculates minimum bin for a BAM alignment interval [begin, end)
-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);
- return 0;
-}
-
-// closes the alignment archive
-void BamWriterPrivate::Close(void) {
-
- // 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 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();
-
- // 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:
- const string message = string("invalid CIGAR operation type") + coIter->Type;
- throw BamException("BamWriter::CreatePackedCigar", message);
- }
-
- *pPackedCigar = coIter->Length << Constants::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 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 (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:
- const string message = string("invalid base: ") + *pQuery;
- throw BamException("BamWriter::EncodeQuerySequence", message);
- }
-
- // pack the nucleotide code
- if ( useHighWord ) {
- *pEncodedQuery = nucleotideCode << 4;
- useHighWord = false;
- } else {
- *pEncodedQuery |= nucleotideCode;
- ++pEncodedQuery;
- useHighWord = true;
- }
-
- // increment the query position
- ++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& samHeaderText,
- const RefVector& referenceSequences)
-{
- try {
-
- // open the BGZF file for writing
- m_stream.Open(filename, IBamIODevice::WriteOnly);
-
- // write BAM file 'metadata' components
- WriteMagicNumber();
- WriteSamHeaderText(samHeaderText);
- WriteReferences(referenceSequences);
-
- // return success
- return true;
-
- } catch ( BamException& e ) {
- m_errorString = e.what();
- return false;
- }
-}
-
-// saves the alignment to the alignment archive
-bool BamWriterPrivate::SaveAlignment(const BamAlignment& al) {
-
- try {
-
- // 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);
-
- // 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);
-
- // if we get here, everything OK
- return true;
-
- } catch ( BamException& e ) {
- m_errorString = e.what();
- return false;
- }
-}
-
-void BamWriterPrivate::SetWriteCompressed(bool ok) {
- // modifying compression is not allowed if BAM file is open
- if ( !IsOpen() )
- m_stream.SetWriteCompressed(ok);
-}
-
-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 alignment's bin is already defined (there is no default, invalid value)
- // so we'll go ahead calculate its bin ID before storing
- const uint32_t alignmentBin = CalculateMinimumBin(al.Position, al.GetEndPosition());
-
- // 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
- m_stream.Write((char*)&buffer, Constants::BAM_CORE_SIZE);
-
- // write the query name
- m_stream.Write(al.Name.c_str(), nameLength);
-
- // 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;
- }
-
- default :
- delete[] tagData;
- const string message = string("invalid tag type: ") + type;
- throw BamException("BamWriter::SaveAlignment", message);
- }
- }
-
- m_stream.Write(tagData, tagDataLength);
- delete[] tagData; // TODO: cleanup on Write exception thrown?
- }
- else
- m_stream.Write(al.TagData.data(), tagDataLength);
-}
-
-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]);
- }
-
- // write the BAM core
- m_stream.Write((char*)&buffer, Constants::BAM_CORE_SIZE);
-
- // write the raw char data
- m_stream.Write((char*)al.SupportData.AllCharData.data(),
- al.SupportData.BlockLength-Constants::BAM_CORE_SIZE);
-}
-
-void BamWriterPrivate::WriteMagicNumber(void) {
- // write BAM file 'magic number'
- m_stream.Write(Constants::BAM_HEADER_MAGIC, Constants::BAM_HEADER_MAGIC_LENGTH);
-}
-
-void BamWriterPrivate::WriteReferences(const BamTools::RefVector& referenceSequences) {
-
- // 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);
-
- // foreach reference sequence
- RefVector::const_iterator rsIter = referenceSequences.begin();
- RefVector::const_iterator rsEnd = referenceSequences.end();
- for ( ; rsIter != rsEnd; ++rsIter ) {
-
- // 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);
-
- // write the reference sequence name
- m_stream.Write(rsIter->RefName.c_str(), referenceSequenceNameLen);
-
- // 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);
- }
-}
-
-void BamWriterPrivate::WriteSamHeaderText(const std::string& samHeaderText) {
-
- // 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);
-
- // write the SAM header text
- if ( samHeaderLen > 0 )
- m_stream.Write(samHeaderText.data(), samHeaderLen);
-}
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