+\r
+// swaps endianness of 16-bit value 'in place'\r
+inline void SwapEndian_16(int16_t& x) {\r
+ x = ((x >> 8) | (x << 8));\r
+}\r
+\r
+inline void SwapEndian_16(uint16_t& x) {\r
+ x = ((x >> 8) | (x << 8));\r
+}\r
+\r
+// swaps endianness of 32-bit value 'in-place'\r
+inline void SwapEndian_32(int32_t& x) {\r
+ x = ( (x >> 24) | \r
+ ((x << 8) & 0x00FF0000) | \r
+ ((x >> 8) & 0x0000FF00) | \r
+ (x << 24)\r
+ );\r
+}\r
+\r
+inline void SwapEndian_32(uint32_t& x) {\r
+ x = ( (x >> 24) | \r
+ ((x << 8) & 0x00FF0000) | \r
+ ((x >> 8) & 0x0000FF00) | \r
+ (x << 24)\r
+ );\r
+}\r
+\r
+// swaps endianness of 64-bit value 'in-place'\r
+inline void SwapEndian_64(int64_t& x) {\r
+ x = ( (x >> 56) | \r
+ ((x << 40) & 0x00FF000000000000ll) |\r
+ ((x << 24) & 0x0000FF0000000000ll) |\r
+ ((x << 8) & 0x000000FF00000000ll) |\r
+ ((x >> 8) & 0x00000000FF000000ll) |\r
+ ((x >> 24) & 0x0000000000FF0000ll) |\r
+ ((x >> 40) & 0x000000000000FF00ll) |\r
+ (x << 56)\r
+ );\r
+}\r
+\r
+inline void SwapEndian_64(uint64_t& x) {\r
+ x = ( (x >> 56) | \r
+ ((x << 40) & 0x00FF000000000000ll) |\r
+ ((x << 24) & 0x0000FF0000000000ll) |\r
+ ((x << 8) & 0x000000FF00000000ll) |\r
+ ((x >> 8) & 0x00000000FF000000ll) |\r
+ ((x >> 24) & 0x0000000000FF0000ll) |\r
+ ((x >> 40) & 0x000000000000FF00ll) |\r
+ (x << 56)\r
+ );\r
+}\r
+\r
+// swaps endianness of 'next 2 bytes' in a char buffer (in-place)\r
+inline void SwapEndian_16p(char* data) {\r
+ uint16_t& value = (uint16_t&)*data; \r
+ SwapEndian_16(value);\r
+}\r
+\r
+// swaps endianness of 'next 4 bytes' in a char buffer (in-place)\r
+inline void SwapEndian_32p(char* data) {\r
+ uint32_t& value = (uint32_t&)*data; \r
+ SwapEndian_32(value);\r
+}\r
+\r
+// swaps endianness of 'next 8 bytes' in a char buffer (in-place)\r
+inline void SwapEndian_64p(char* data) {\r
+ uint64_t& value = (uint64_t&)*data; \r
+ SwapEndian_64(value);\r
+}\r
+\r
+// ----------------------------------------------------------------\r
+// BamAlignment member methods\r
+\r
+// constructors & destructor\r
+inline BamAlignment::BamAlignment(void) { }\r
+\r
+inline BamAlignment::BamAlignment(const BamAlignment& other)\r
+ : Name(other.Name)\r
+ , Length(other.Length)\r
+ , QueryBases(other.QueryBases)\r
+ , AlignedBases(other.AlignedBases)\r
+ , Qualities(other.Qualities)\r
+ , TagData(other.TagData)\r
+ , RefID(other.RefID)\r
+ , Position(other.Position)\r
+ , Bin(other.Bin)\r
+ , MapQuality(other.MapQuality)\r
+ , AlignmentFlag(other.AlignmentFlag)\r
+ , CigarData(other.CigarData)\r
+ , MateRefID(other.MateRefID)\r
+ , MatePosition(other.MatePosition)\r
+ , InsertSize(other.InsertSize)\r
+ , SupportData(other.SupportData)\r
+{ }\r
+\r
+inline BamAlignment::~BamAlignment(void) { }\r
+\r
+// Queries against alignment flags\r
+inline bool BamAlignment::IsDuplicate(void) const { return ( (AlignmentFlag & DUPLICATE) != 0 ); }\r
+inline bool BamAlignment::IsFailedQC(void) const { return ( (AlignmentFlag & QC_FAILED) != 0 ); }\r
+inline bool BamAlignment::IsFirstMate(void) const { return ( (AlignmentFlag & READ_1) != 0 ); }\r
+inline bool BamAlignment::IsMapped(void) const { return ( (AlignmentFlag & UNMAPPED) == 0 ); }\r
+inline bool BamAlignment::IsMateMapped(void) const { return ( (AlignmentFlag & MATE_UNMAPPED) == 0 ); }\r
+inline bool BamAlignment::IsMateReverseStrand(void) const { return ( (AlignmentFlag & MATE_REVERSE) != 0 ); }\r
+inline bool BamAlignment::IsPaired(void) const { return ( (AlignmentFlag & PAIRED) != 0 ); }\r
+inline bool BamAlignment::IsPrimaryAlignment(void) const { return ( (AlignmentFlag & SECONDARY) == 0 ); }\r
+inline bool BamAlignment::IsProperPair(void) const { return ( (AlignmentFlag & PROPER_PAIR) != 0 ); }\r
+inline bool BamAlignment::IsReverseStrand(void) const { return ( (AlignmentFlag & REVERSE) != 0 ); }\r
+inline bool BamAlignment::IsSecondMate(void) const { return ( (AlignmentFlag & READ_2) != 0 ); }\r
+\r
+// Manipulate alignment flags \r
+inline void BamAlignment::SetIsDuplicate(bool ok) { if (ok) AlignmentFlag |= DUPLICATE; else AlignmentFlag &= ~DUPLICATE; }\r
+inline void BamAlignment::SetIsFailedQC(bool ok) { if (ok) AlignmentFlag |= QC_FAILED; else AlignmentFlag &= ~QC_FAILED; }\r
+inline void BamAlignment::SetIsFirstMate(bool ok) { if (ok) AlignmentFlag |= READ_1; else AlignmentFlag &= ~READ_1; }\r
+inline void BamAlignment::SetIsMateUnmapped(bool ok) { if (ok) AlignmentFlag |= MATE_UNMAPPED; else AlignmentFlag &= ~MATE_UNMAPPED; }\r
+inline void BamAlignment::SetIsMateReverseStrand(bool ok) { if (ok) AlignmentFlag |= MATE_REVERSE; else AlignmentFlag &= ~MATE_REVERSE; }\r
+inline void BamAlignment::SetIsPaired(bool ok) { if (ok) AlignmentFlag |= PAIRED; else AlignmentFlag &= ~PAIRED; }\r
+inline void BamAlignment::SetIsProperPair(bool ok) { if (ok) AlignmentFlag |= PROPER_PAIR; else AlignmentFlag &= ~PROPER_PAIR; }\r
+inline void BamAlignment::SetIsReverseStrand(bool ok) { if (ok) AlignmentFlag |= REVERSE; else AlignmentFlag &= ~REVERSE; }\r
+inline void BamAlignment::SetIsSecondaryAlignment(bool ok) { if (ok) AlignmentFlag |= SECONDARY; else AlignmentFlag &= ~SECONDARY; }\r
+inline void BamAlignment::SetIsSecondMate(bool ok) { if (ok) AlignmentFlag |= READ_2; else AlignmentFlag &= ~READ_2; }\r
+inline void BamAlignment::SetIsUnmapped(bool ok) { if (ok) AlignmentFlag |= UNMAPPED; else AlignmentFlag &= ~UNMAPPED; }\r
+\r
+// calculates alignment end position, based on starting position and CIGAR operations\r
+inline \r
+int BamAlignment::GetEndPosition(bool usePadded) const {\r
+\r
+ // initialize alignment end to starting position\r
+ int alignEnd = Position;\r
+\r
+ // iterate over cigar operations\r
+ std::vector<CigarOp>::const_iterator cigarIter = CigarData.begin();\r
+ std::vector<CigarOp>::const_iterator cigarEnd = CigarData.end();\r
+ for ( ; cigarIter != cigarEnd; ++cigarIter) {\r
+ const char cigarType = (*cigarIter).Type;\r
+ if ( cigarType == 'M' || cigarType == 'D' || cigarType == 'N' ) {\r
+ alignEnd += (*cigarIter).Length;\r
+ } \r
+ else if ( usePadded && cigarType == 'I' ) {\r
+ alignEnd += (*cigarIter).Length;\r
+ }\r
+ }\r
+ return alignEnd;\r
+}\r
+\r
+inline\r
+bool BamAlignment::AddTag(const std::string& tag, const std::string& type, const std::string& value) {\r
+ \r
+ if ( SupportData.HasCoreOnly ) return false;\r
+ if ( tag.size() != 2 || type.size() != 1 ) return false;\r
+ if ( type != "Z" && type != "H" ) return false;\r
+ \r
+ // localize the tag data\r
+ char* pTagData = (char*)TagData.data();\r
+ const unsigned int tagDataLength = TagData.size();\r
+ unsigned int numBytesParsed = 0;\r
+ \r
+ // if tag already exists, return false\r
+ // use EditTag explicitly instead\r
+ if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) return false;\r
+ \r
+ // otherwise, copy tag data to temp buffer\r
+ std::string newTag = tag + type + value;\r
+ const int newTagDataLength = tagDataLength + newTag.size() + 1; // leave room for null-term\r
+ char originalTagData[newTagDataLength];\r
+ memcpy(originalTagData, TagData.c_str(), tagDataLength + 1); // '+1' for TagData null-term\r
+ \r
+ // append newTag\r
+ strcat(originalTagData + tagDataLength, newTag.data()); // removes original null-term, appends newTag + null-term\r
+ \r
+ // store temp buffer back in TagData\r
+ const char* newTagData = (const char*)originalTagData;\r
+ TagData.assign(newTagData, newTagDataLength);\r
+ \r
+ // return success\r
+ return true;\r
+}\r
+\r
+inline\r
+bool BamAlignment::AddTag(const std::string& tag, const std::string& type, const uint32_t& value) {\r
+ \r
+ if ( SupportData.HasCoreOnly ) return false;\r
+ if ( tag.size() != 2 || type.size() != 1 ) return false;\r
+ if ( type == "f" || type == "Z" || type == "H" ) return false;\r
+ \r
+ // localize the tag data\r
+ char* pTagData = (char*)TagData.data();\r
+ const unsigned int tagDataLength = TagData.size();\r
+ unsigned int numBytesParsed = 0;\r
+ \r
+ // if tag already exists, return false\r
+ // use EditTag explicitly instead\r
+ if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) return false;\r
+ \r
+ // otherwise, convert value to string\r
+ union { unsigned int value; char valueBuffer[sizeof(unsigned int)]; } un;\r
+ un.value = value;\r
+\r
+ // copy original tag data to temp buffer\r
+ std::string newTag = tag + type;\r
+ const int newTagDataLength = tagDataLength + newTag.size() + 4; // leave room for new integer\r
+ char originalTagData[newTagDataLength];\r
+ memcpy(originalTagData, TagData.c_str(), tagDataLength + 1); // '+1' for TagData null-term\r
+ \r
+ // append newTag\r
+ strcat(originalTagData + tagDataLength, newTag.data());\r
+ memcpy(originalTagData + tagDataLength + newTag.size(), un.valueBuffer, sizeof(unsigned int));\r
+ \r
+ // store temp buffer back in TagData\r
+ const char* newTagData = (const char*)originalTagData;\r
+ TagData.assign(newTagData, newTagDataLength);\r
+ \r
+ // return success\r
+ return true;\r
+}\r
+\r
+inline\r
+bool BamAlignment::AddTag(const std::string& tag, const std::string& type, const int32_t& value) {\r
+ return AddTag(tag, type, (const uint32_t&)value);\r
+}\r
+\r
+inline\r
+bool BamAlignment::AddTag(const std::string& tag, const std::string& type, const float& value) {\r
+ \r
+ if ( SupportData.HasCoreOnly ) return false;\r
+ if ( tag.size() != 2 || type.size() != 1 ) return false;\r
+ if ( type == "Z" || type == "H" ) return false;\r
+ \r
+ // localize the tag data\r
+ char* pTagData = (char*)TagData.data();\r
+ const unsigned int tagDataLength = TagData.size();\r
+ unsigned int numBytesParsed = 0;\r
+ \r
+ // if tag already exists, return false\r
+ // use EditTag explicitly instead\r
+ if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) return false;\r
+ \r
+ // otherwise, convert value to string\r
+ union { float value; char valueBuffer[sizeof(float)]; } un;\r
+ un.value = value;\r
+\r
+ // copy original tag data to temp buffer\r
+ std::string newTag = tag + type;\r
+ const int newTagDataLength = tagDataLength + newTag.size() + 4; // leave room for new float\r
+ char originalTagData[newTagDataLength];\r
+ memcpy(originalTagData, TagData.c_str(), tagDataLength + 1); // '+1' for TagData null-term\r
+ \r
+ // append newTag\r
+ strcat(originalTagData + tagDataLength, newTag.data());\r
+ memcpy(originalTagData + tagDataLength + newTag.size(), un.valueBuffer, sizeof(float));\r
+ \r
+ // store temp buffer back in TagData\r
+ const char* newTagData = (const char*)originalTagData;\r
+ TagData.assign(newTagData, newTagDataLength);\r
+ \r
+ // return success\r
+ return true;\r
+}\r
+\r
+inline\r
+bool BamAlignment::EditTag(const std::string& tag, const std::string& type, const std::string& value) {\r
+ \r
+ if ( SupportData.HasCoreOnly ) return false;\r
+ if ( tag.size() != 2 || type.size() != 1 ) return false;\r
+ if ( type != "Z" && type != "H" ) return false;\r
+ \r
+ // localize the tag data\r
+ char* pOriginalTagData = (char*)TagData.data();\r
+ char* pTagData = pOriginalTagData;\r
+ const unsigned int originalTagDataLength = TagData.size();\r
+ \r
+ unsigned int newTagDataLength = 0;\r
+ unsigned int numBytesParsed = 0;\r
+ \r
+ // if tag found, store data in readGroup, return success\r
+ if ( FindTag(tag, pTagData, originalTagDataLength, numBytesParsed) ) {\r
+ \r
+ // make sure array is more than big enough\r
+ char newTagData[originalTagDataLength + value.size()]; \r
+\r
+ // copy original tag data up til desired tag\r
+ const unsigned int beginningTagDataLength = numBytesParsed;\r
+ newTagDataLength += beginningTagDataLength;\r
+ memcpy(newTagData, pOriginalTagData, numBytesParsed);\r
+ \r
+ // copy new VALUE in place of current tag data\r
+ const unsigned int dataLength = strlen(value.c_str());\r
+ memcpy(newTagData + beginningTagDataLength, (char*)value.c_str(), dataLength+1 );\r
+ \r
+ // skip to next tag (if tag for removal is last, return true) \r
+ const char* pTagStorageType = pTagData - 1;\r
+ if ( !SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed) ) return true;\r
+ \r
+ // copy everything from current tag (the next one after tag for removal) to end\r
+ const unsigned int skippedDataLength = (numBytesParsed - beginningTagDataLength);\r
+ const unsigned int endTagOffset = beginningTagDataLength + dataLength + 1;\r
+ const unsigned int endTagDataLength = originalTagDataLength - beginningTagDataLength - skippedDataLength;\r
+ memcpy(newTagData + endTagOffset, pTagData, endTagDataLength);\r
+ \r
+ // ensure null-terminator\r
+ newTagData[ endTagOffset + endTagDataLength + 1 ] = 0;\r
+ \r
+ // save new tag data\r
+ TagData.assign(newTagData, endTagOffset + endTagDataLength);\r
+ return true;\r
+ }\r
+ \r
+ // tag not found, attempt AddTag\r
+ else return AddTag(tag, type, value);\r
+}\r
+\r
+inline\r
+bool BamAlignment::EditTag(const std::string& tag, const std::string& type, const uint32_t& value) {\r
+ \r
+ if ( SupportData.HasCoreOnly ) return false;\r
+ if ( tag.size() != 2 || type.size() != 1 ) return false;\r
+ if ( type == "f" || type == "Z" || type == "H" ) return false;\r
+ \r
+ // localize the tag data\r
+ char* pOriginalTagData = (char*)TagData.data();\r
+ char* pTagData = pOriginalTagData;\r
+ const unsigned int originalTagDataLength = TagData.size();\r
+ \r
+ unsigned int newTagDataLength = 0;\r
+ unsigned int numBytesParsed = 0;\r
+ \r
+ // if tag found, store data in readGroup, return success\r
+ if ( FindTag(tag, pTagData, originalTagDataLength, numBytesParsed) ) {\r
+ \r
+ // make sure array is more than big enough\r
+ char newTagData[originalTagDataLength + sizeof(value)]; \r
+\r
+ // copy original tag data up til desired tag\r
+ const unsigned int beginningTagDataLength = numBytesParsed;\r
+ newTagDataLength += beginningTagDataLength;\r
+ memcpy(newTagData, pOriginalTagData, numBytesParsed);\r
+ \r
+ // copy new VALUE in place of current tag data\r
+ union { unsigned int value; char valueBuffer[sizeof(unsigned int)]; } un;\r
+ un.value = value;\r
+ memcpy(newTagData + beginningTagDataLength, un.valueBuffer, sizeof(unsigned int));\r
+ \r
+ // skip to next tag (if tag for removal is last, return true) \r
+ const char* pTagStorageType = pTagData - 1;\r
+ if ( !SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed) ) return true;\r
+ \r
+ // copy everything from current tag (the next one after tag for removal) to end\r
+ const unsigned int skippedDataLength = (numBytesParsed - beginningTagDataLength);\r
+ const unsigned int endTagOffset = beginningTagDataLength + sizeof(unsigned int);\r
+ const unsigned int endTagDataLength = originalTagDataLength - beginningTagDataLength - skippedDataLength;\r
+ memcpy(newTagData + endTagOffset, pTagData, endTagDataLength);\r
+ \r
+ // ensure null-terminator\r
+ newTagData[ endTagOffset + endTagDataLength + 1 ] = 0;\r
+ \r
+ // save new tag data\r
+ TagData.assign(newTagData, endTagOffset + endTagDataLength);\r
+ return true;\r
+ }\r
+ \r
+ // tag not found, attempt AddTag\r
+ else return AddTag(tag, type, value);\r
+}\r
+\r
+inline\r
+bool BamAlignment::EditTag(const std::string& tag, const std::string& type, const int32_t& value) {\r
+ return EditTag(tag, type, (const uint32_t&)value);\r
+}\r
+\r
+inline\r
+bool BamAlignment::EditTag(const std::string& tag, const std::string& type, const float& value) {\r
+ \r
+ if ( SupportData.HasCoreOnly ) return false;\r
+ if ( tag.size() != 2 || type.size() != 1 ) return false;\r
+ if ( type == "Z" || type == "H" ) return false;\r
+ \r
+ // localize the tag data\r
+ char* pOriginalTagData = (char*)TagData.data();\r
+ char* pTagData = pOriginalTagData;\r
+ const unsigned int originalTagDataLength = TagData.size();\r
+ \r
+ unsigned int newTagDataLength = 0;\r
+ unsigned int numBytesParsed = 0;\r
+ \r
+ // if tag found, store data in readGroup, return success\r
+ if ( FindTag(tag, pTagData, originalTagDataLength, numBytesParsed) ) {\r
+ \r
+ // make sure array is more than big enough\r
+ char newTagData[originalTagDataLength + sizeof(value)]; \r
+\r
+ // copy original tag data up til desired tag\r
+ const unsigned int beginningTagDataLength = numBytesParsed;\r
+ newTagDataLength += beginningTagDataLength;\r
+ memcpy(newTagData, pOriginalTagData, numBytesParsed);\r
+ \r
+ // copy new VALUE in place of current tag data\r
+ union { float value; char valueBuffer[sizeof(float)]; } un;\r
+ un.value = value;\r
+ memcpy(newTagData + beginningTagDataLength, un.valueBuffer, sizeof(float));\r
+ \r
+ // skip to next tag (if tag for removal is last, return true) \r
+ const char* pTagStorageType = pTagData - 1;\r
+ if ( !SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed) ) return true;\r
+ \r
+ // copy everything from current tag (the next one after tag for removal) to end\r
+ const unsigned int skippedDataLength = (numBytesParsed - beginningTagDataLength);\r
+ const unsigned int endTagOffset = beginningTagDataLength + sizeof(float);\r
+ const unsigned int endTagDataLength = originalTagDataLength - beginningTagDataLength - skippedDataLength;\r
+ memcpy(newTagData + endTagOffset, pTagData, endTagDataLength);\r
+ \r
+ // ensure null-terminator\r
+ newTagData[ endTagOffset + endTagDataLength + 1 ] = 0;\r
+ \r
+ // save new tag data\r
+ TagData.assign(newTagData, endTagOffset + endTagDataLength);\r
+ return true;\r
+ }\r
+ \r
+ // tag not found, attempt AddTag\r
+ else return AddTag(tag, type, value);\r
+}\r
+\r
+// get "NM" tag data - originally contributed by Aaron Quinlan\r
+// stores data in 'editDistance', returns success/fail\r
+inline \r
+bool BamAlignment::GetEditDistance(uint32_t& editDistance) const { \r
+ return GetTag("NM", (uint32_t&)editDistance);\r
+}\r
+\r
+// get "RG" tag data\r
+// stores data in 'readGroup', returns success/fail\r
+inline \r
+bool BamAlignment::GetReadGroup(std::string& readGroup) const {\r
+ return GetTag("RG", readGroup);\r
+}\r
+\r
+inline\r
+bool BamAlignment::GetTag(const std::string& tag, std::string& destination) const {\r
+\r
+ // make sure tag data exists\r
+ if ( SupportData.HasCoreOnly || TagData.empty() ) \r
+ return false;\r
+\r
+ // localize the tag data\r
+ char* pTagData = (char*)TagData.data();\r
+ const unsigned int tagDataLength = TagData.size();\r
+ unsigned int numBytesParsed = 0;\r
+ \r
+ // if tag found, store data in readGroup, return success\r
+ if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {\r
+ const unsigned int dataLength = strlen(pTagData);\r
+ destination.clear();\r
+ destination.resize(dataLength);\r
+ memcpy( (char*)destination.data(), pTagData, dataLength );\r
+ return true;\r
+ }\r
+ \r
+ // tag not found, return failure\r
+ return false;\r
+}\r
+\r
+inline\r
+bool BamAlignment::GetTag(const std::string& tag, uint32_t& destination) const {\r
+ \r
+ // make sure tag data exists\r
+ if ( SupportData.HasCoreOnly || TagData.empty() ) \r
+ return false;\r
+\r
+ // localize the tag data\r
+ char* pTagData = (char*)TagData.data();\r
+ const unsigned int tagDataLength = TagData.size();\r
+ unsigned int numBytesParsed = 0;\r
+ \r
+ // if tag found, determine data byte-length, store data in readGroup, return success\r
+ if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {\r
+ \r
+ // determine data byte-length\r
+ const char type = *(pTagData - 1);\r
+ int destinationLength = 0;\r
+ switch (type) {\r
+ // 1 byte data\r
+ case 'A':\r
+ case 'c':\r
+ case 'C':\r
+ destinationLength = 1;\r
+ break;\r
+\r
+ // 2 byte data\r
+ case 's':\r
+ case 'S':\r
+ destinationLength = 2;\r
+ break;\r
+\r
+ // 4 byte data\r
+ case 'i':\r
+ case 'I':\r
+ destinationLength = 4;\r
+ break;\r
+\r
+ // unsupported type for integer destination (float or var-length strings)\r
+ case 'f':\r
+ case 'Z':\r
+ case 'H':\r
+ printf("ERROR: Cannot store tag of type %c in integer destination\n", type);\r
+ return false;\r
+\r
+ // unknown tag type\r
+ default:\r
+ printf("ERROR: Unknown tag storage class encountered: [%c]\n", type);\r
+ return false;\r
+ }\r
+ \r
+ // store in destination\r
+ destination = 0;\r
+ memcpy(&destination, pTagData, destinationLength);\r
+ return true;\r
+ }\r
+ \r
+ // tag not found, return failure\r
+ return false;\r
+}\r
+\r
+inline\r
+bool BamAlignment::GetTag(const std::string& tag, int32_t& destination) const {\r
+ return GetTag(tag, (uint32_t&)destination);\r
+}\r
+\r
+inline\r
+bool BamAlignment::GetTag(const std::string& tag, float& destination) const {\r
+ \r
+ // make sure tag data exists\r
+ if ( SupportData.HasCoreOnly || TagData.empty() ) \r
+ return false;\r
+\r
+ // localize the tag data\r
+ char* pTagData = (char*)TagData.data();\r
+ const unsigned int tagDataLength = TagData.size();\r
+ unsigned int numBytesParsed = 0;\r
+ \r
+ // if tag found, determine data byte-length, store data in readGroup, return success\r
+ if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {\r
+ //pTagData += numBytesParsed;\r
+ \r
+ // determine data byte-length\r
+ const char type = *(pTagData - 1);\r
+ int destinationLength = 0;\r
+ switch(type) {\r
+\r
+ // 1 byte data\r
+ case 'A':\r
+ case 'c':\r
+ case 'C':\r
+ destinationLength = 1;\r
+ break;\r
+\r
+ // 2 byte data\r
+ case 's':\r
+ case 'S':\r
+ destinationLength = 2;\r
+ break;\r
+\r
+ // 4 byte data\r
+ case 'f':\r
+ case 'i':\r
+ case 'I':\r
+ destinationLength = 4;\r
+ break;\r
+ \r
+ // unsupported type (var-length strings)\r
+ case 'Z':\r
+ case 'H':\r
+ printf("ERROR: Cannot store tag of type %c in integer destination\n", type);\r
+ return false;\r
+\r
+ // unknown tag type\r
+ default:\r
+ printf("ERROR: Unknown tag storage class encountered: [%c]\n", type);\r
+ return false;\r
+ }\r
+ \r
+ // store in destination\r
+ destination = 0.0;\r
+ memcpy(&destination, pTagData, destinationLength);\r
+ return true;\r
+ }\r
+ \r
+ // tag not found, return failure\r
+ return false;\r
+}\r
+\r
+inline\r
+bool BamAlignment::RemoveTag(const std::string& tag) {\r
+ \r
+ // BamAlignments fetched using BamReader::GetNextAlignmentCore() are not allowed\r
+ // also, return false if no data present to remove\r
+ if ( SupportData.HasCoreOnly || TagData.empty() ) return false;\r
+ \r
+ // localize the tag data\r
+ char* pOriginalTagData = (char*)TagData.data();\r
+ char* pTagData = pOriginalTagData;\r
+ const unsigned int originalTagDataLength = TagData.size();\r
+ unsigned int newTagDataLength = 0;\r
+ unsigned int numBytesParsed = 0;\r
+ \r
+ // if tag found, store data in readGroup, return success\r
+ if ( FindTag(tag, pTagData, originalTagDataLength, numBytesParsed) ) {\r
+ \r
+ char newTagData[originalTagDataLength];\r
+\r
+ // copy original tag data up til desired tag\r
+ pTagData -= 3;\r
+ numBytesParsed -= 3;\r
+ const unsigned int beginningTagDataLength = numBytesParsed;\r
+ newTagDataLength += beginningTagDataLength;\r
+ memcpy(newTagData, pOriginalTagData, numBytesParsed);\r
+ \r
+ // skip to next tag (if tag for removal is last, return true) \r
+ const char* pTagStorageType = pTagData + 2;\r
+ pTagData += 3;\r
+ numBytesParsed += 3;\r
+ if ( !SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed) ) return true;\r
+ \r
+ // copy everything from current tag (the next one after tag for removal) to end\r
+ const unsigned int skippedDataLength = (numBytesParsed - beginningTagDataLength);\r
+ const unsigned int endTagDataLength = originalTagDataLength - beginningTagDataLength - skippedDataLength;\r
+ memcpy(newTagData + beginningTagDataLength, pTagData, endTagDataLength );\r
+ \r
+ // save new tag data\r
+ TagData.assign(newTagData, beginningTagDataLength + endTagDataLength);\r
+ return true;\r
+ }\r
+ \r
+ // tag not found, no removal - return failure\r
+ return false;\r
+}\r
+\r
+inline\r
+bool BamAlignment::FindTag(const std::string& tag, char* &pTagData, const unsigned int& tagDataLength, unsigned int& numBytesParsed) {\r
+\r
+ while ( numBytesParsed < tagDataLength ) {\r
+\r
+ const char* pTagType = pTagData;\r
+ const char* pTagStorageType = pTagData + 2;\r
+ pTagData += 3;\r
+ numBytesParsed += 3;\r
+\r
+ // check the current tag, return true on match\r
+ if ( std::strncmp(pTagType, tag.c_str(), 2) == 0 ) \r
+ return true;\r
+\r
+ // get the storage class and find the next tag\r
+ if ( *pTagStorageType == '\0' ) return false; \r
+ if ( !SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed) ) return false;\r
+ if ( *pTagData == '\0' ) return false;\r
+ }\r
+ \r
+ // checked all tags, none match\r
+ return false;\r
+}\r
+\r
+inline\r
+bool BamAlignment::SkipToNextTag(const char storageType, char* &pTagData, unsigned int& numBytesParsed) {\r
+ \r
+ switch(storageType) {\r
+\r
+ case 'A':\r
+ case 'c':\r
+ case 'C':\r
+ ++numBytesParsed;\r
+ ++pTagData;\r
+ break;\r
+\r
+ case 's':\r
+ case 'S':\r
+ numBytesParsed += 2;\r
+ pTagData += 2;\r
+ break;\r
+\r
+ case 'f':\r
+ case 'i':\r
+ case 'I':\r
+ numBytesParsed += 4;\r
+ pTagData += 4;\r
+ break;\r
+\r
+ case 'Z':\r
+ case 'H':\r
+ while(*pTagData) {\r
+ ++numBytesParsed;\r
+ ++pTagData;\r
+ }\r
+ // increment for null-terminator\r
+ ++numBytesParsed;\r
+ ++pTagData;\r
+ break;\r
+\r
+ default: \r
+ // error case\r
+ printf("ERROR: Unknown tag storage class encountered: [%c]\n", storageType);\r
+ return false;\r
+ }\r
+ \r
+ // return success\r
+ return true;\r
+}\r
+\r
+} // namespace BamTools\r
+\r
+#endif // BAMAUX_H\r