// Marth Lab, Department of Biology, Boston College\r
// All rights reserved.\r
// ---------------------------------------------------------------------------\r
-// Last modified: 30 March 2010 (DB)\r
+// Last modified: 15 July 2010 (DB)\r
// ---------------------------------------------------------------------------\r
// Uses BGZF routines were adapted from the bgzf.c code developed at the Broad\r
// Institute.\r
// Provides the basic functionality for producing BAM files\r
// ***************************************************************************\r
\r
-// BGZF includes\r
+#include <iostream>\r
+\r
#include "BGZF.h"\r
#include "BamWriter.h"\r
using namespace BamTools;\r
BgzfData mBGZF;\r
bool IsBigEndian;\r
\r
- \r
// constructor / destructor\r
BamWriterPrivate(void) { \r
IsBigEndian = SystemIsBigEndian(); \r
void Close(void);\r
void Open(const string& filename, const string& samHeader, const RefVector& referenceSequences);\r
void SaveAlignment(const BamAlignment& al);\r
- void SaveAlignment(const BamAlignment& al, const BamAlignmentSupportData& supportData);\r
\r
// internal methods\r
+ const unsigned int CalculateMinimumBin(const int begin, int end) const;\r
void CreatePackedCigar(const vector<CigarOp>& cigarOperations, string& packedCigar);\r
void EncodeQuerySequence(const string& query, string& encodedQuery);\r
};\r
d->SaveAlignment(al);\r
}\r
\r
-void BamWriter::SaveAlignment(const BamAlignment& al, const BamAlignmentSupportData& supportData) {\r
- d->SaveAlignment(al, supportData);\r
-}\r
-\r
// -----------------------------------------------------\r
// BamWriterPrivate implementation\r
// -----------------------------------------------------\r
mBGZF.Close();\r
}\r
\r
+// calculates minimum bin for a BAM alignment interval\r
+const unsigned int BamWriter::BamWriterPrivate::CalculateMinimumBin(const int begin, int end) const { \r
+ --end;\r
+ if( (begin >> 14) == (end >> 14) ) return 4681 + (begin >> 14);\r
+ if( (begin >> 17) == (end >> 17) ) return 585 + (begin >> 17);\r
+ if( (begin >> 20) == (end >> 20) ) return 73 + (begin >> 20);\r
+ if( (begin >> 23) == (end >> 23) ) return 9 + (begin >> 23);\r
+ if( (begin >> 26) == (end >> 26) ) return 1 + (begin >> 26);\r
+ return 0;\r
+}\r
+\r
// creates a cigar string from the supplied alignment\r
void BamWriter::BamWriterPrivate::CreatePackedCigar(const vector<CigarOp>& cigarOperations, string& packedCigar) {\r
\r
\r
unsigned int cigarOp;\r
vector<CigarOp>::const_iterator coIter;\r
- for(coIter = cigarOperations.begin(); coIter != cigarOperations.end(); coIter++) {\r
+ for(coIter = cigarOperations.begin(); coIter != cigarOperations.end(); ++coIter) {\r
\r
switch(coIter->Type) {\r
case 'M':\r
\r
// write the SAM header text length\r
uint32_t samHeaderLen = samHeader.size();\r
- if ( IsBigEndian ) { SwapEndian_32(samHeaderLen); }\r
+ if (IsBigEndian) SwapEndian_32(samHeaderLen);\r
mBGZF.Write((char*)&samHeaderLen, BT_SIZEOF_INT);\r
\r
// write the SAM header text\r
- if(samHeaderLen > 0) {\r
+ if(samHeaderLen > 0) \r
mBGZF.Write(samHeader.data(), samHeaderLen);\r
- }\r
\r
// write the number of reference sequences\r
uint32_t numReferenceSequences = referenceSequences.size();\r
- if ( IsBigEndian ) { SwapEndian_32(numReferenceSequences); }\r
+ if (IsBigEndian) SwapEndian_32(numReferenceSequences);\r
mBGZF.Write((char*)&numReferenceSequences, BT_SIZEOF_INT);\r
\r
// =============================\r
\r
// write the reference sequence name length\r
uint32_t referenceSequenceNameLen = rsIter->RefName.size() + 1;\r
- if ( IsBigEndian ) { SwapEndian_32(referenceSequenceNameLen); }\r
+ if (IsBigEndian) SwapEndian_32(referenceSequenceNameLen);\r
mBGZF.Write((char*)&referenceSequenceNameLen, BT_SIZEOF_INT);\r
\r
// write the reference sequence name\r
\r
// write the reference sequence length\r
int32_t referenceLength = rsIter->RefLength;\r
- if ( IsBigEndian ) { SwapEndian_32(referenceLength); }\r
+ if (IsBigEndian) SwapEndian_32(referenceLength);\r
mBGZF.Write((char*)&referenceLength, BT_SIZEOF_INT);\r
}\r
}\r
// saves the alignment to the alignment archive\r
void BamWriter::BamWriterPrivate::SaveAlignment(const BamAlignment& al) {\r
\r
- // initialize\r
- const unsigned int nameLen = al.Name.size() + 1;\r
- const unsigned int queryLen = al.QueryBases.size();\r
- const unsigned int numCigarOperations = al.CigarData.size();\r
-\r
- // create our packed cigar string\r
- string packedCigar;\r
- CreatePackedCigar(al.CigarData, packedCigar);\r
- const unsigned int packedCigarLen = packedCigar.size();\r
-\r
- // encode the query\r
- string encodedQuery;\r
- EncodeQuerySequence(al.QueryBases, encodedQuery);\r
- const unsigned int encodedQueryLen = encodedQuery.size();\r
-\r
- // store the tag data length\r
- // -------------------------------------------\r
- // Modified: 3-25-2010 DWB\r
- // Contributed: ARQ\r
- // Fixed: "off by one" error when parsing tags in files produced by BamWriter\r
- const unsigned int tagDataLength = al.TagData.size();\r
- // original line: \r
- // const unsigned int tagDataLength = al.TagData.size() + 1; \r
- // -------------------------------------------\r
- \r
- // assign the BAM core data\r
- uint32_t buffer[8];\r
- buffer[0] = al.RefID;\r
- buffer[1] = al.Position;\r
- buffer[2] = (al.Bin << 16) | (al.MapQuality << 8) | nameLen;\r
- buffer[3] = (al.AlignmentFlag << 16) | numCigarOperations;\r
- buffer[4] = queryLen;\r
- buffer[5] = al.MateRefID;\r
- buffer[6] = al.MatePosition;\r
- buffer[7] = al.InsertSize;\r
-\r
- // write the block size\r
- unsigned int dataBlockSize = nameLen + packedCigarLen + encodedQueryLen + queryLen + tagDataLength;\r
- unsigned int blockSize = BAM_CORE_SIZE + dataBlockSize;\r
- if ( IsBigEndian ) { SwapEndian_32(blockSize); }\r
- mBGZF.Write((char*)&blockSize, BT_SIZEOF_INT);\r
-\r
- // write the BAM core\r
- if ( IsBigEndian ) { \r
- for ( int i = 0; i < 8; ++i ) { \r
- SwapEndian_32(buffer[i]); \r
- } \r
- }\r
- mBGZF.Write((char*)&buffer, BAM_CORE_SIZE);\r
-\r
- // write the query name\r
- mBGZF.Write(al.Name.c_str(), nameLen);\r
-\r
- // write the packed cigar\r
- if ( IsBigEndian ) {\r
+ // if BamAlignment contains only the core data and a raw char data buffer\r
+ // (as a result of BamReader::GetNextAlignmentCore())\r
+ if ( al.SupportData.HasCoreOnly ) {\r
\r
- char* cigarData = (char*)calloc(sizeof(char), packedCigarLen);\r
- memcpy(cigarData, packedCigar.data(), packedCigarLen);\r
+ // write the block size\r
+ unsigned int blockSize = al.SupportData.BlockLength;\r
+ if (IsBigEndian) SwapEndian_32(blockSize);\r
+ mBGZF.Write((char*)&blockSize, BT_SIZEOF_INT);\r
+\r
+ // assign the BAM core data\r
+ uint32_t buffer[8];\r
+ buffer[0] = al.RefID;\r
+ buffer[1] = al.Position;\r
+ buffer[2] = (al.Bin << 16) | (al.MapQuality << 8) | al.SupportData.QueryNameLength;\r
+ buffer[3] = (al.AlignmentFlag << 16) | al.SupportData.NumCigarOperations;\r
+ buffer[4] = al.SupportData.QuerySequenceLength;\r
+ buffer[5] = al.MateRefID;\r
+ buffer[6] = al.MatePosition;\r
+ buffer[7] = al.InsertSize;\r
\r
- for (unsigned int i = 0; i < packedCigarLen; ++i) {\r
- if ( IsBigEndian ) { \r
- SwapEndian_32p(&cigarData[i]); \r
- }\r
+ // swap BAM core endian-ness, if necessary\r
+ if ( IsBigEndian ) { \r
+ for ( int i = 0; i < 8; ++i )\r
+ SwapEndian_32(buffer[i]); \r
}\r
\r
- mBGZF.Write(cigarData, packedCigarLen);\r
- free(cigarData);\r
+ // write the BAM core\r
+ mBGZF.Write((char*)&buffer, BAM_CORE_SIZE);\r
\r
- } else { \r
- mBGZF.Write(packedCigar.data(), packedCigarLen);\r
+ // write the raw char data\r
+ mBGZF.Write((char*)al.SupportData.AllCharData.data(), al.SupportData.BlockLength-BAM_CORE_SIZE); \r
}\r
-\r
- // write the encoded query sequence\r
- mBGZF.Write(encodedQuery.data(), encodedQueryLen);\r
-\r
- // write the base qualities\r
- string baseQualities = al.Qualities;\r
- char* pBaseQualities = (char*)al.Qualities.data();\r
- for(unsigned int i = 0; i < queryLen; i++) { pBaseQualities[i] -= 33; }\r
- mBGZF.Write(pBaseQualities, queryLen);\r
-\r
- // write the read group tag\r
- if ( IsBigEndian ) {\r
+ \r
+ // otherwise, BamAlignment should contain character in the standard fields: Name, QueryBases, etc\r
+ // ( resulting from BamReader::GetNextAlignment() *OR* being generated directly by client code )\r
+ else {\r
+ \r
+ // calculate char lengths\r
+ const unsigned int nameLength = al.Name.size() + 1;\r
+ const unsigned int numCigarOperations = al.CigarData.size();\r
+ const unsigned int queryLength = al.QueryBases.size();\r
+ const unsigned int tagDataLength = al.TagData.size();\r
+ \r
+ // no way to tell if BamAlignment.Bin is already defined (no default, invalid value)\r
+ // force calculation of Bin before storing\r
+ const int endPosition = al.GetEndPosition();\r
+ const unsigned int alignmentBin = CalculateMinimumBin(al.Position, endPosition);\r
\r
- char* tagData = (char*)calloc(sizeof(char), tagDataLength);\r
- memcpy(tagData, al.TagData.data(), tagDataLength);\r
+ // create our packed cigar string\r
+ string packedCigar;\r
+ CreatePackedCigar(al.CigarData, packedCigar);\r
+ const unsigned int packedCigarLength = packedCigar.size();\r
+\r
+ // encode the query\r
+ string encodedQuery;\r
+ EncodeQuerySequence(al.QueryBases, encodedQuery);\r
+ const unsigned int encodedQueryLength = encodedQuery.size(); \r
\r
- int i = 0;\r
- while ( (unsigned int)i < tagDataLength ) {\r
- \r
- i += 2; // skip tag type (e.g. "RG", "NM", etc)\r
- uint8_t type = toupper(tagData[i]); // lower & upper case letters have same meaning \r
- ++i; // skip value type\r
- \r
- switch (type) {\r
- \r
- case('A') :\r
- case('C') : \r
- ++i;\r
- break;\r
- \r
- case('S') : \r
- SwapEndian_16p(&tagData[i]); \r
- i+=2; // sizeof(uint16_t)\r
- break;\r
- \r
- case('F') :\r
- case('I') : \r
- SwapEndian_32p(&tagData[i]);\r
- i+=4; // sizeof(uint32_t)\r
- break;\r
- \r
- case('D') : \r
- SwapEndian_64p(&tagData[i]);\r
- i+=8; // sizeof(uint64_t)\r
- break;\r
- \r
- case('H') :\r
- case('Z') : \r
- while (tagData[i]) { ++i; }\r
- ++i; // increment one more for null terminator\r
- break;\r
- \r
- default : \r
- printf("ERROR: Invalid tag value type\n"); // shouldn't get here\r
- free(tagData);\r
- exit(1); \r
- }\r
+ // write the block size\r
+ const unsigned int dataBlockSize = nameLength + packedCigarLength + encodedQueryLength + queryLength + tagDataLength;\r
+ unsigned int blockSize = BAM_CORE_SIZE + dataBlockSize;\r
+ if (IsBigEndian) SwapEndian_32(blockSize);\r
+ mBGZF.Write((char*)&blockSize, BT_SIZEOF_INT);\r
+\r
+ // assign the BAM core data\r
+ uint32_t buffer[8];\r
+ buffer[0] = al.RefID;\r
+ buffer[1] = al.Position;\r
+ buffer[2] = (alignmentBin << 16) | (al.MapQuality << 8) | nameLength;\r
+ buffer[3] = (al.AlignmentFlag << 16) | numCigarOperations;\r
+ buffer[4] = queryLength;\r
+ buffer[5] = al.MateRefID;\r
+ buffer[6] = al.MatePosition;\r
+ buffer[7] = al.InsertSize;\r
+ \r
+ // swap BAM core endian-ness, if necessary\r
+ if ( IsBigEndian ) { \r
+ for ( int i = 0; i < 8; ++i )\r
+ SwapEndian_32(buffer[i]); \r
}\r
\r
- mBGZF.Write(tagData, tagDataLength);\r
- free(tagData);\r
- } else {\r
- mBGZF.Write(al.TagData.data(), tagDataLength);\r
- }\r
-}\r
+ // write the BAM core\r
+ mBGZF.Write((char*)&buffer, BAM_CORE_SIZE);\r
+ \r
+ // write the query name\r
+ mBGZF.Write(al.Name.c_str(), nameLength);\r
+\r
+ // write the packed cigar\r
+ if ( IsBigEndian ) {\r
+ \r
+ char* cigarData = (char*)calloc(sizeof(char), packedCigarLength);\r
+ memcpy(cigarData, packedCigar.data(), packedCigarLength);\r
+ \r
+ for (unsigned int i = 0; i < packedCigarLength; ++i) {\r
+ if ( IsBigEndian )\r
+ SwapEndian_32p(&cigarData[i]); \r
+ }\r
+ \r
+ mBGZF.Write(cigarData, packedCigarLength);\r
+ free(cigarData); \r
+ } \r
+ else \r
+ mBGZF.Write(packedCigar.data(), packedCigarLength);\r
+\r
+ // write the encoded query sequence\r
+ mBGZF.Write(encodedQuery.data(), encodedQueryLength);\r
\r
-void BamWriter::BamWriterPrivate::SaveAlignment(const BamAlignment& al, const BamAlignmentSupportData& supportData) {\r
- \r
- // assign the BAM core data\r
- uint32_t buffer[8];\r
- buffer[0] = al.RefID;\r
- buffer[1] = al.Position;\r
- buffer[2] = (al.Bin << 16) | (al.MapQuality << 8) | supportData.QueryNameLength;\r
- buffer[3] = (al.AlignmentFlag << 16) | supportData.NumCigarOperations;\r
- buffer[4] = supportData.QuerySequenceLength;\r
- buffer[5] = al.MateRefID;\r
- buffer[6] = al.MatePosition;\r
- buffer[7] = al.InsertSize;\r
-\r
- // write the block size\r
- unsigned int blockSize = supportData.BlockLength;\r
- if ( IsBigEndian ) { SwapEndian_32(blockSize); }\r
- mBGZF.Write((char*)&blockSize, BT_SIZEOF_INT);\r
-\r
- // write the BAM core\r
- if ( IsBigEndian ) { \r
- for ( int i = 0; i < 8; ++i ) { \r
- SwapEndian_32(buffer[i]); \r
+ // write the base qualities\r
+ string baseQualities(al.Qualities);\r
+ char* pBaseQualities = (char*)al.Qualities.data();\r
+ for(unsigned int i = 0; i < queryLength; i++) { \r
+ pBaseQualities[i] -= 33; \r
+ }\r
+ mBGZF.Write(pBaseQualities, queryLength);\r
+\r
+ // write the read group tag\r
+ if ( IsBigEndian ) {\r
+ \r
+ char* tagData = (char*)calloc(sizeof(char), tagDataLength);\r
+ memcpy(tagData, al.TagData.data(), tagDataLength);\r
+ \r
+ int i = 0;\r
+ while ( (unsigned int)i < tagDataLength ) {\r
+ \r
+ i += 2; // skip tag type (e.g. "RG", "NM", etc)\r
+ uint8_t type = toupper(tagData[i]); // lower & upper case letters have same meaning \r
+ ++i; // skip value type\r
+ \r
+ switch (type) {\r
+ \r
+ case('A') :\r
+ case('C') : \r
+ ++i;\r
+ break;\r
+ \r
+ case('S') : \r
+ SwapEndian_16p(&tagData[i]); \r
+ i+=2; // sizeof(uint16_t)\r
+ break;\r
+ \r
+ case('F') :\r
+ case('I') : \r
+ SwapEndian_32p(&tagData[i]);\r
+ i+=4; // sizeof(uint32_t)\r
+ break;\r
+ \r
+ case('D') : \r
+ SwapEndian_64p(&tagData[i]);\r
+ i+=8; // sizeof(uint64_t)\r
+ break;\r
+ \r
+ case('H') :\r
+ case('Z') : \r
+ while (tagData[i]) { ++i; }\r
+ ++i; // increment one more for null terminator\r
+ break;\r
+ \r
+ default : \r
+ printf("ERROR: Invalid tag value type\n"); // shouldn't get here\r
+ free(tagData);\r
+ exit(1); \r
+ }\r
+ }\r
+ \r
+ mBGZF.Write(tagData, tagDataLength);\r
+ free(tagData);\r
} \r
+ else \r
+ mBGZF.Write(al.TagData.data(), tagDataLength); \r
}\r
- mBGZF.Write((char*)&buffer, BAM_CORE_SIZE);\r
-\r
- // write the raw char data\r
- mBGZF.Write((char*)supportData.AllCharData.data(), supportData.BlockLength-BAM_CORE_SIZE);\r
}\r
-\r
projects / bamtools.git / blobdiff