X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2FBamAlignment.cpp;h=980303ae6050f116b4e9197de9d10d5e259af9ec;hb=11fabb69eb8c86635dd9498679b72bf78b3af3d1;hp=0077f64a9eb5306033811a6e49261cebfacb5969;hpb=525fc971414d7f7b8b6022e741ebb275d3f68b6b;p=bamtools.git diff --git a/src/api/BamAlignment.cpp b/src/api/BamAlignment.cpp index 0077f64..980303a 100644 --- a/src/api/BamAlignment.cpp +++ b/src/api/BamAlignment.cpp @@ -1,9 +1,8 @@ // *************************************************************************** // BamAlignment.cpp (c) 2009 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- -// Last modified: 22 April 2011 (DB) +// Last modified: 4 October 2011 (DB) // --------------------------------------------------------------------------- // Provides the BamAlignment data structure // *************************************************************************** @@ -115,667 +114,30 @@ BamAlignment::BamAlignment(const BamAlignment& other) */ BamAlignment::~BamAlignment(void) { } -/*! \fn bool BamAlignment::AddTag(const std::string& tag, const std::string& type, const std::string& value) - \brief Adds a field with string data to the BAM tags. +///*! \fn bool BamAlignment::AddTag(const std::string& tag, const std::string& type, const std::string& value) +// \brief Adds a field with string data to the BAM tags. - Does NOT modify an existing tag - use \link BamAlignment::EditTag() \endlink instead. +// Does NOT modify an existing tag - use \link BamAlignment::EditTag() \endlink instead. - \param tag 2-character tag name - \param type 1-character tag type (must be "Z" or "H") - \param value string data to store +// \param[in] tag 2-character tag name +// \param[in] type 1-character tag type (must be "Z" or "H") +// \param[in] value string data to store +// \return \c true if the \b new tag was added successfully +// \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +//*/ - \return \c true if the \b new tag was added successfully - \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. -*/ -bool BamAlignment::AddTag(const std::string& tag, const std::string& type, const std::string& value) { - - // skip if core data not parsed - if ( SupportData.HasCoreOnly ) return false; - - // validate tag/type size & that type is OK for string value - if ( !IsValidSize(tag, type) ) return false; - if ( type.at(0) != Constants::BAM_TAG_TYPE_STRING && - type.at(0) != Constants::BAM_TAG_TYPE_HEX - ) - { - return false; - } - - // localize the tag data - char* pTagData = (char*)TagData.data(); - const unsigned int tagDataLength = TagData.size(); - unsigned int numBytesParsed = 0; - - // if tag already exists, return false - // use EditTag explicitly instead - if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) - return false; - - // otherwise, copy tag data to temp buffer - string newTag = tag + type + value; - const int newTagDataLength = tagDataLength + newTag.size() + 1; // leave room for null-term - char* originalTagData = new char[newTagDataLength]; - memcpy(originalTagData, TagData.c_str(), tagDataLength + 1); // '+1' for TagData null-term - - // append newTag - strcat(originalTagData + tagDataLength, newTag.data()); // removes original null-term, appends newTag + null-term - - // store temp buffer back in TagData - const char* newTagData = (const char*)originalTagData; - TagData.assign(newTagData, newTagDataLength); - - delete[] originalTagData; - - // return success - return true; -} - -/*! \fn bool BamAlignment::AddTag(const std::string& tag, const std::string& type, const uint32_t& value) - \brief Adds a field with unsigned integer data to the BAM tags. - - Does NOT modify an existing tag - use \link BamAlignment::EditTag() \endlink instead. - - \param tag 2-character tag name - \param type 1-character tag type (must NOT be "f", "Z", "H", or "B") - \param value unsigned int data to store - - \return \c true if the \b new tag was added successfully - \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. -*/ -bool BamAlignment::AddTag(const std::string& tag, const std::string& type, const uint32_t& value) { - - // skip if core data not parsed - if ( SupportData.HasCoreOnly ) return false; - - // validate tag/type size & that type is OK for uint32_t value - if ( !IsValidSize(tag, type) ) return false; - if ( type.at(0) == Constants::BAM_TAG_TYPE_FLOAT || - type.at(0) == Constants::BAM_TAG_TYPE_STRING || - type.at(0) == Constants::BAM_TAG_TYPE_HEX || - type.at(0) == Constants::BAM_TAG_TYPE_ARRAY - ) - { - return false; - } - - // localize the tag data - char* pTagData = (char*)TagData.data(); - const unsigned int tagDataLength = TagData.size(); - unsigned int numBytesParsed = 0; - - // if tag already exists, return false - // use EditTag explicitly instead - if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) - return false; - - // otherwise, convert value to string - union { uint32_t value; char valueBuffer[sizeof(uint32_t)]; } un; - un.value = value; - - // copy original tag data to temp buffer - string newTag = tag + type; - const int newTagDataLength = tagDataLength + newTag.size() + 4; // leave room for new integer - char* originalTagData = new char[newTagDataLength]; - memcpy(originalTagData, TagData.c_str(), tagDataLength + 1); // '+1' for TagData null-term - - // append newTag - strcat(originalTagData + tagDataLength, newTag.data()); - memcpy(originalTagData + tagDataLength + newTag.size(), un.valueBuffer, sizeof(uint32_t)); - - // store temp buffer back in TagData - const char* newTagData = (const char*)originalTagData; - TagData.assign(newTagData, newTagDataLength); - delete[] originalTagData; - - // return success - return true; -} - -/*! \fn bool BamAlignment::AddTag(const std::string& tag, const std::string& type, const int32_t& value) - \brief Adds a field with signed integer data to the BAM tags. - - Does NOT modify an existing tag - use \link BamAlignment::EditTag() \endlink instead. - - \param tag 2-character tag name - \param type 1-character tag type (must NOT be "f", "Z", "H", or "B") - \param value signed int data to store - - \return \c true if the \b new tag was added successfully - \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. -*/ -bool BamAlignment::AddTag(const std::string& tag, const std::string& type, const int32_t& value) { - return AddTag(tag, type, (const uint32_t&)value); -} - -/*! \fn bool BamAlignment::AddTag(const std::string& tag, const std::string& type, const float& value) - \brief Adds a field with floating-point data to the BAM tags. - - Does NOT modify an existing tag - use \link BamAlignment::EditTag() \endlink instead. - - \param tag 2-character tag name - \param type 1-character tag type (must NOT be "Z", "H", or "B") - \param value float data to store - - \return \c true if the \b new tag was added successfully - \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. -*/ -bool BamAlignment::AddTag(const std::string& tag, const std::string& type, const float& value) { - - // skip if core data not parsed - if ( SupportData.HasCoreOnly ) return false; - - // validate tag/type size & that type is OK for float value - if ( !IsValidSize(tag, type) ) return false; - if ( type.at(0) == Constants::BAM_TAG_TYPE_STRING || - type.at(0) == Constants::BAM_TAG_TYPE_HEX || - type.at(0) == Constants::BAM_TAG_TYPE_ARRAY - ) - { - return false; - } - - // localize the tag data - char* pTagData = (char*)TagData.data(); - const unsigned int tagDataLength = TagData.size(); - unsigned int numBytesParsed = 0; - - // if tag already exists, return false - // use EditTag explicitly instead - if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) - return false; - - // otherwise, convert value to string - union { float value; char valueBuffer[sizeof(float)]; } un; - un.value = value; - - // copy original tag data to temp buffer - string newTag = tag + type; - const int newTagDataLength = tagDataLength + newTag.size() + 4; // leave room for new float - char* originalTagData = new char[newTagDataLength]; - memcpy(originalTagData, TagData.c_str(), tagDataLength + 1); // '+1' for TagData null-term - - // append newTag - strcat(originalTagData + tagDataLength, newTag.data()); - memcpy(originalTagData + tagDataLength + newTag.size(), un.valueBuffer, sizeof(float)); - - // store temp buffer back in TagData - const char* newTagData = (const char*)originalTagData; - TagData.assign(newTagData, newTagDataLength); - - delete[] originalTagData; - - // return success - return true; -} - -/*! \fn bool AddTag(const std::string& tag, const std::vector& values); - \brief Adds a numeric array field to the BAM tags. - - Does NOT modify an existing tag - use \link BamAlignment::EditTag() \endlink instead. - - \param tag 2-character tag name - \param values vector of uint8_t values to store - - \return \c true if the \b new tag was added successfully - \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. -*/ -bool BamAlignment::AddTag(const std::string& tag, const std::vector& values) { - - // skip if core data not parsed - if ( SupportData.HasCoreOnly ) return false; - - // check for valid tag length - if ( tag.size() != Constants::BAM_TAG_TAGSIZE ) return false; - - // localize the tag data - char* pTagData = (char*)TagData.data(); - const unsigned int tagDataLength = TagData.size(); - unsigned int numBytesParsed = 0; - - // if tag already exists, return false - // use EditTag explicitly instead - if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) - return false; - - // build new tag's base information - char newTagBase[Constants::BAM_TAG_ARRAYBASE_SIZE]; - memcpy( newTagBase, tag.c_str(), Constants::BAM_TAG_TAGSIZE ); - newTagBase[2] = Constants::BAM_TAG_TYPE_ARRAY; - newTagBase[3] = Constants::BAM_TAG_TYPE_UINT8; - - // add number of array elements to newTagBase - const int32_t numElements = values.size(); - memcpy(newTagBase + 4, &numElements, sizeof(int32_t)); - - // copy current TagData string to temp buffer, leaving room for new tag's contents - const int newTagDataLength = tagDataLength + - Constants::BAM_TAG_ARRAYBASE_SIZE + - numElements*sizeof(uint8_t); - char* originalTagData = new char[newTagDataLength]; - memcpy(originalTagData, TagData.c_str(), tagDataLength+1); // '+1' for TagData's null-term - - // write newTagBase (removes old null term) - strcat(originalTagData + tagDataLength, (const char*)newTagBase); - - // add vector elements to tag - int elementsBeginOffset = tagDataLength + Constants::BAM_TAG_ARRAYBASE_SIZE; - for ( int i = 0 ; i < numElements; ++i ) { - const uint8_t value = values.at(i); - memcpy(originalTagData + elementsBeginOffset + i*sizeof(uint8_t), - &value, sizeof(uint8_t)); - } - - // store temp buffer back in TagData - const char* newTagData = (const char*)originalTagData; - TagData.assign(newTagData, newTagDataLength); - - delete[] originalTagData; - - // return success - return true; -} - -/*! \fn bool AddTag(const std::string& tag, const std::vector& values); - \brief Adds a numeric array field to the BAM tags. - - Does NOT modify an existing tag - use \link BamAlignment::EditTag() \endlink instead. - - \param tag 2-character tag name - \param values vector of int8_t values to store - - \return \c true if the \b new tag was added successfully - \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. -*/ -bool BamAlignment::AddTag(const std::string& tag, const std::vector& values) { - - // skip if core data not parsed - if ( SupportData.HasCoreOnly ) return false; - - // check for valid tag length - if ( tag.size() != Constants::BAM_TAG_TAGSIZE ) return false; - - // localize the tag data - char* pTagData = (char*)TagData.data(); - const unsigned int tagDataLength = TagData.size(); - unsigned int numBytesParsed = 0; - - // if tag already exists, return false - // use EditTag explicitly instead - if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) - return false; - - // build new tag's base information - char newTagBase[Constants::BAM_TAG_ARRAYBASE_SIZE]; - memcpy( newTagBase, tag.c_str(), Constants::BAM_TAG_TAGSIZE ); - newTagBase[2] = Constants::BAM_TAG_TYPE_ARRAY; - newTagBase[3] = Constants::BAM_TAG_TYPE_INT8; - - // add number of array elements to newTagBase - const int32_t numElements = values.size(); - memcpy(newTagBase + 4, &numElements, sizeof(int32_t)); - - // copy current TagData string to temp buffer, leaving room for new tag's contents - const int newTagDataLength = tagDataLength + - Constants::BAM_TAG_ARRAYBASE_SIZE + - numElements*sizeof(int8_t); - char* originalTagData = new char[newTagDataLength]; - memcpy(originalTagData, TagData.c_str(), tagDataLength+1); // '+1' for TagData's null-term - - // write newTagBase (removes old null term) - strcat(originalTagData + tagDataLength, (const char*)newTagBase); - - // add vector elements to tag - int elementsBeginOffset = tagDataLength + Constants::BAM_TAG_ARRAYBASE_SIZE; - for ( int i = 0 ; i < numElements; ++i ) { - const int8_t value = values.at(i); - memcpy(originalTagData + elementsBeginOffset + i*sizeof(int8_t), - &value, sizeof(int8_t)); - } - - // store temp buffer back in TagData - const char* newTagData = (const char*)originalTagData; - TagData.assign(newTagData, newTagDataLength); - - delete[] originalTagData; - - // return success - return true; -} - -/*! \fn bool AddTag(const std::string& tag, const std::vector& values); - \brief Adds a numeric array field to the BAM tags. - - Does NOT modify an existing tag - use \link BamAlignment::EditTag() \endlink instead. - - \param tag 2-character tag name - \param values vector of uint16_t values to store - - \return \c true if the \b new tag was added successfully - \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. -*/ -bool BamAlignment::AddTag(const std::string& tag, const std::vector& values) { - - // skip if core data not parsed - if ( SupportData.HasCoreOnly ) return false; - - // check for valid tag length - if ( tag.size() != Constants::BAM_TAG_TAGSIZE ) return false; - - // localize the tag data - char* pTagData = (char*)TagData.data(); - const unsigned int tagDataLength = TagData.size(); - unsigned int numBytesParsed = 0; - - // if tag already exists, return false - // use EditTag explicitly instead - if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) - return false; - - // build new tag's base information - char newTagBase[Constants::BAM_TAG_ARRAYBASE_SIZE]; - memcpy( newTagBase, tag.c_str(), Constants::BAM_TAG_TAGSIZE ); - newTagBase[2] = Constants::BAM_TAG_TYPE_ARRAY; - newTagBase[3] = Constants::BAM_TAG_TYPE_UINT16; - - // add number of array elements to newTagBase - const int32_t numElements = values.size(); - memcpy(newTagBase + 4, &numElements, sizeof(int32_t)); - - // copy current TagData string to temp buffer, leaving room for new tag's contents - const int newTagDataLength = tagDataLength + - Constants::BAM_TAG_ARRAYBASE_SIZE + - numElements*sizeof(uint16_t); - char* originalTagData = new char[newTagDataLength]; - memcpy(originalTagData, TagData.c_str(), tagDataLength+1); // '+1' for TagData's null-term - - // write newTagBase (removes old null term) - strcat(originalTagData + tagDataLength, (const char*)newTagBase); - - // add vector elements to tag - int elementsBeginOffset = tagDataLength + Constants::BAM_TAG_ARRAYBASE_SIZE; - for ( int i = 0 ; i < numElements; ++i ) { - const uint16_t value = values.at(i); - memcpy(originalTagData + elementsBeginOffset + i*sizeof(uint16_t), - &value, sizeof(uint16_t)); - } - - // store temp buffer back in TagData - const char* newTagData = (const char*)originalTagData; - TagData.assign(newTagData, newTagDataLength); - - delete[] originalTagData; - - // return success - return true; -} - -/*! \fn bool AddTag(const std::string& tag, const std::vector& values); - \brief Adds a numeric array field to the BAM tags. - - Does NOT modify an existing tag - use \link BamAlignment::EditTag() \endlink instead. - - \param tag 2-character tag name - \param values vector of int16_t values to store - - \return \c true if the \b new tag was added successfully - \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. -*/ -bool BamAlignment::AddTag(const std::string& tag, const std::vector& values) { - - // skip if core data not parsed - if ( SupportData.HasCoreOnly ) return false; - - // check for valid tag length - if ( tag.size() != Constants::BAM_TAG_TAGSIZE ) return false; - - // localize the tag data - char* pTagData = (char*)TagData.data(); - const unsigned int tagDataLength = TagData.size(); - unsigned int numBytesParsed = 0; - - // if tag already exists, return false - // use EditTag explicitly instead - if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) - return false; - - // build new tag's base information - char newTagBase[Constants::BAM_TAG_ARRAYBASE_SIZE]; - memcpy( newTagBase, tag.c_str(), Constants::BAM_TAG_TAGSIZE ); - newTagBase[2] = Constants::BAM_TAG_TYPE_ARRAY; - newTagBase[3] = Constants::BAM_TAG_TYPE_INT16; - - // add number of array elements to newTagBase - const int32_t numElements = values.size(); - memcpy(newTagBase + 4, &numElements, sizeof(int32_t)); - - // copy current TagData string to temp buffer, leaving room for new tag's contents - const int newTagDataLength = tagDataLength + - Constants::BAM_TAG_ARRAYBASE_SIZE + - numElements*sizeof(int16_t); - char* originalTagData = new char[newTagDataLength]; - memcpy(originalTagData, TagData.c_str(), tagDataLength+1); // '+1' for TagData's null-term - - // write newTagBase (removes old null term) - strcat(originalTagData + tagDataLength, (const char*)newTagBase); - - // add vector elements to tag - int elementsBeginOffset = tagDataLength + Constants::BAM_TAG_ARRAYBASE_SIZE; - for ( int i = 0 ; i < numElements; ++i ) { - const int16_t value = values.at(i); - memcpy(originalTagData + elementsBeginOffset + i*sizeof(int16_t), - &value, sizeof(int16_t)); - } - - // store temp buffer back in TagData - const char* newTagData = (const char*)originalTagData; - TagData.assign(newTagData, newTagDataLength); - - delete[] originalTagData; - - // return success - return true; -} - -/*! \fn bool AddTag(const std::string& tag, const std::vector& values); - \brief Adds a numeric array field to the BAM tags. - - Does NOT modify an existing tag - use \link BamAlignment::EditTag() \endlink instead. - - \param tag 2-character tag name - \param values vector of uint32_t values to store - - \return \c true if the \b new tag was added successfully - \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. -*/ -bool BamAlignment::AddTag(const std::string& tag, const std::vector& values) { - - // skip if core data not parsed - if ( SupportData.HasCoreOnly ) return false; - - // check for valid tag length - if ( tag.size() != Constants::BAM_TAG_TAGSIZE ) return false; - - // localize the tag data - char* pTagData = (char*)TagData.data(); - const unsigned int tagDataLength = TagData.size(); - unsigned int numBytesParsed = 0; - - // if tag already exists, return false - // use EditTag explicitly instead - if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) - return false; - - // build new tag's base information - char newTagBase[Constants::BAM_TAG_ARRAYBASE_SIZE]; - memcpy( newTagBase, tag.c_str(), Constants::BAM_TAG_TAGSIZE ); - newTagBase[2] = Constants::BAM_TAG_TYPE_ARRAY; - newTagBase[3] = Constants::BAM_TAG_TYPE_UINT32; - - // add number of array elements to newTagBase - const int32_t numElements = values.size(); - memcpy(newTagBase + 4, &numElements, sizeof(int32_t)); - - // copy current TagData string to temp buffer, leaving room for new tag's contents - const int newTagDataLength = tagDataLength + - Constants::BAM_TAG_ARRAYBASE_SIZE + - numElements*sizeof(uint32_t); - char* originalTagData = new char[newTagDataLength]; - memcpy(originalTagData, TagData.c_str(), tagDataLength+1); // '+1' for TagData's null-term - - // write newTagBase (removes old null term) - strcat(originalTagData + tagDataLength, (const char*)newTagBase); - - // add vector elements to tag - int elementsBeginOffset = tagDataLength + Constants::BAM_TAG_ARRAYBASE_SIZE; - for ( int i = 0 ; i < numElements; ++i ) { - const uint32_t value = values.at(i); - memcpy(originalTagData + elementsBeginOffset + i*sizeof(uint32_t), - &value, sizeof(uint32_t)); - } - - // store temp buffer back in TagData - const char* newTagData = (const char*)originalTagData; - TagData.assign(newTagData, newTagDataLength); - - delete[] originalTagData; - - // return success - return true; -} - -/*! \fn bool AddTag(const std::string& tag, const std::vector& values); - \brief Adds a numeric array field to the BAM tags. - - Does NOT modify an existing tag - use \link BamAlignment::EditTag() \endlink instead. - - \param tag 2-character tag name - \param values vector of int32_t values to store - - \return \c true if the \b new tag was added successfully - \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. -*/ -bool BamAlignment::AddTag(const std::string& tag, const std::vector& values) { - - // skip if core data not parsed - if ( SupportData.HasCoreOnly ) return false; - - // check for valid tag length - if ( tag.size() != Constants::BAM_TAG_TAGSIZE ) return false; - - // localize the tag data - char* pTagData = (char*)TagData.data(); - const unsigned int tagDataLength = TagData.size(); - unsigned int numBytesParsed = 0; - - // if tag already exists, return false - // use EditTag explicitly instead - if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) - return false; - - // build new tag's base information - char newTagBase[Constants::BAM_TAG_ARRAYBASE_SIZE]; - memcpy( newTagBase, tag.c_str(), Constants::BAM_TAG_TAGSIZE ); - newTagBase[2] = Constants::BAM_TAG_TYPE_ARRAY; - newTagBase[3] = Constants::BAM_TAG_TYPE_INT32; - - // add number of array elements to newTagBase - const int32_t numElements = values.size(); - memcpy(newTagBase + 4, &numElements, sizeof(int32_t)); - - // copy current TagData string to temp buffer, leaving room for new tag's contents - const int newTagDataLength = tagDataLength + - Constants::BAM_TAG_ARRAYBASE_SIZE + - numElements*sizeof(int32_t); - char* originalTagData = new char[newTagDataLength]; - memcpy(originalTagData, TagData.c_str(), tagDataLength+1); // '+1' for TagData's null-term - - // write newTagBase (removes old null term) - strcat(originalTagData + tagDataLength, (const char*)newTagBase); - - // add vector elements to tag - int elementsBeginOffset = tagDataLength + Constants::BAM_TAG_ARRAYBASE_SIZE; - for ( int i = 0 ; i < numElements; ++i ) { - const int32_t value = values.at(i); - memcpy(originalTagData + elementsBeginOffset + i*sizeof(int32_t), - &value, sizeof(int32_t)); - } - - // store temp buffer back in TagData - const char* newTagData = (const char*)originalTagData; - TagData.assign(newTagData, newTagDataLength); - - delete[] originalTagData; - - // return success - return true; -} - -/*! \fn bool AddTag(const std::string& tag, const std::vector& values); - \brief Adds a numeric array field to the BAM tags. - - Does NOT modify an existing tag - use \link BamAlignment::EditTag() \endlink instead. - - \param tag 2-character tag name - \param values vector of float values to store - - \return \c true if the \b new tag was added successfully - \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. -*/ -bool BamAlignment::AddTag(const std::string& tag, const std::vector& values) { - - // skip if core data not parsed - if ( SupportData.HasCoreOnly ) return false; - - // check for valid tag length - if ( tag.size() != Constants::BAM_TAG_TAGSIZE ) return false; - - // localize the tag data - char* pTagData = (char*)TagData.data(); - const unsigned int tagDataLength = TagData.size(); - unsigned int numBytesParsed = 0; - // if tag already exists, return false - // use EditTag explicitly instead - if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) - return false; +///*! \fn bool AddTag(const std::string& tag, const std::vector& values); +// \brief Adds a numeric array field to the BAM tags. - // build new tag's base information - char newTagBase[Constants::BAM_TAG_ARRAYBASE_SIZE]; - memcpy( newTagBase, tag.c_str(), Constants::BAM_TAG_TAGSIZE ); - newTagBase[2] = Constants::BAM_TAG_TYPE_ARRAY; - newTagBase[3] = Constants::BAM_TAG_TYPE_FLOAT; - - // add number of array elements to newTagBase - const int32_t numElements = values.size(); - memcpy(newTagBase + 4, &numElements, sizeof(int32_t)); - - // copy current TagData string to temp buffer, leaving room for new tag's contents - const int newTagDataLength = tagDataLength + - Constants::BAM_TAG_ARRAYBASE_SIZE + - numElements*sizeof(float); - char* originalTagData = new char[newTagDataLength]; - memcpy(originalTagData, TagData.c_str(), tagDataLength+1); // '+1' for TagData's null-term - - // write newTagBase (removes old null term) - strcat(originalTagData + tagDataLength, (const char*)newTagBase); - - // add vector elements to tag - int elementsBeginOffset = tagDataLength + Constants::BAM_TAG_ARRAYBASE_SIZE; - for ( int i = 0 ; i < numElements; ++i ) { - const float value = values.at(i); - memcpy(originalTagData + elementsBeginOffset + i*sizeof(float), - &value, sizeof(float)); - } +// Does NOT modify an existing tag - use \link BamAlignment::EditTag() \endlink instead. - // store temp buffer back in TagData - const char* newTagData = (const char*)originalTagData; - TagData.assign(newTagData, newTagDataLength); +// \param tag 2-character tag name +// \param values vector of uint8_t values to store - delete[] originalTagData; - - // return success - return true; -} +// \return \c true if the \b new tag was added successfully +// \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +//*/ /*! \fn bool BamAlignment::BuildCharData(void) \brief Populates alignment string fields (read name, bases, qualities, tag data). @@ -992,445 +354,46 @@ bool BamAlignment::BuildCharData(void) { exit(1); } } - } - - // store tagData in alignment - TagData.resize(tagDataLength); - memcpy((char*)TagData.data(), tagData, tagDataLength); - } - - // clear the core-only flag - SupportData.HasCoreOnly = false; - - // return success - return true; -} - -/*! \fn bool BamAlignment::EditTag(const std::string& tag, const std::string& type, const std::string& value) - \brief Edits a BAM tag field containing string data. - - If \a tag does not exist, a new entry is created. - - \param tag 2-character tag name - \param type 1-character tag type (must be "Z" or "H") - \param value string data to store - - \return \c true if the tag was modified/created successfully - - \sa BamAlignment::RemoveTag() - \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. -*/ -bool BamAlignment::EditTag(const std::string& tag, const std::string& type, const std::string& value) { - - // skip if core data not parsed - if ( SupportData.HasCoreOnly ) return false; - - // validate tag/type size & that type is OK for string value - if ( !IsValidSize(tag, type) ) return false; - if ( type.at(0) != Constants::BAM_TAG_TYPE_STRING && - type.at(0) != Constants::BAM_TAG_TYPE_HEX ) - return false; - - // localize the tag data - char* pOriginalTagData = (char*)TagData.data(); - char* pTagData = pOriginalTagData; - const unsigned int originalTagDataLength = TagData.size(); - - unsigned int newTagDataLength = 0; - unsigned int numBytesParsed = 0; - - // if tag found - if ( FindTag(tag, pTagData, originalTagDataLength, numBytesParsed) ) { - - // make sure array is more than big enough - char* newTagData = new char[originalTagDataLength + value.size()]; - - // copy original tag data up til desired tag - const unsigned int beginningTagDataLength = numBytesParsed; - newTagDataLength += beginningTagDataLength; - memcpy(newTagData, pOriginalTagData, numBytesParsed); - - // copy new @value in place of current tag data - const unsigned int dataLength = strlen(value.c_str()); - memcpy(newTagData + beginningTagDataLength, (char*)value.c_str(), dataLength+1 ); - - // skip to next tag (if tag for removal is last, return true) - const char* pTagStorageType = pTagData - 1; - if ( !SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed) ) - return true; - - // copy everything from current tag (the next one after tag for removal) to end - const unsigned int skippedDataLength = (numBytesParsed - beginningTagDataLength); - const unsigned int endTagOffset = beginningTagDataLength + dataLength + 1; - const unsigned int endTagDataLength = originalTagDataLength - beginningTagDataLength - skippedDataLength; - memcpy(newTagData + endTagOffset, pTagData, endTagDataLength); - - // ensure null-terminator - newTagData[ endTagOffset + endTagDataLength + 1 ] = 0; - - // save new tag data - TagData.assign(newTagData, endTagOffset + endTagDataLength); - - delete[] newTagData; - - return true; - } - - // tag not found, attempt AddTag - else return AddTag(tag, type, value); -} - -/*! \fn bool BamAlignment::EditTag(const std::string& tag, const std::string& type, const uint32_t& value) - \brief Edits a BAM tag field containing unsigned integer data. - - If \a tag does not exist, a new entry is created. - - \param tag 2-character tag name - \param type 1-character tag type (must NOT be "f", "Z", "H", or "B") - \param value unsigned integer data to store - - \return \c true if the tag was modified/created successfully - - \sa BamAlignment::RemoveTag() - \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. -*/ -bool BamAlignment::EditTag(const std::string& tag, const std::string& type, const uint32_t& value) { - - // skip if core data not parsed - if ( SupportData.HasCoreOnly ) return false; - - // validate tag/type size & that type is OK for uint32_t value - if ( !IsValidSize(tag, type) ) return false; - if ( type.at(0) == Constants::BAM_TAG_TYPE_FLOAT || - type.at(0) == Constants::BAM_TAG_TYPE_STRING || - type.at(0) == Constants::BAM_TAG_TYPE_HEX || - type.at(0) == Constants::BAM_TAG_TYPE_ARRAY - ) - { - return false; - } - - // localize the tag data - char* pOriginalTagData = (char*)TagData.data(); - char* pTagData = pOriginalTagData; - const unsigned int originalTagDataLength = TagData.size(); - - unsigned int newTagDataLength = 0; - unsigned int numBytesParsed = 0; - - // if tag found - if ( FindTag(tag, pTagData, originalTagDataLength, numBytesParsed) ) { - - // make sure array is more than big enough - char* newTagData = new char[originalTagDataLength + sizeof(value)]; - - // copy original tag data up til desired tag - const unsigned int beginningTagDataLength = numBytesParsed; - newTagDataLength += beginningTagDataLength; - memcpy(newTagData, pOriginalTagData, numBytesParsed); - - // copy new @value in place of current tag data - union { uint32_t value; char valueBuffer[sizeof(uint32_t)]; } un; - un.value = value; - memcpy(newTagData + beginningTagDataLength, un.valueBuffer, sizeof(uint32_t)); - - // skip to next tag (if tag for removal is last, return true) - const char* pTagStorageType = pTagData - 1; - if ( !SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed) ) - return true; - - // copy everything from current tag (the next one after tag for removal) to end - const unsigned int skippedDataLength = (numBytesParsed - beginningTagDataLength); - const unsigned int endTagOffset = beginningTagDataLength + sizeof(uint32_t); - const unsigned int endTagDataLength = originalTagDataLength - beginningTagDataLength - skippedDataLength; - memcpy(newTagData + endTagOffset, pTagData, endTagDataLength); - - // ensure null-terminator - newTagData[ endTagOffset + endTagDataLength + 1 ] = 0; - - // save new tag data - TagData.assign(newTagData, endTagOffset + endTagDataLength); - - delete[] newTagData; - - return true; - } - - // tag not found, attempt AddTag - else return AddTag(tag, type, value); -} - -/*! \fn bool BamAlignment::EditTag(const std::string& tag, const std::string& type, const int32_t& value) - \brief Edits a BAM tag field containing signed integer data. - - If \a tag does not exist, a new entry is created. - - \param tag 2-character tag name - \param type 1-character tag type (must NOT be "f", "Z", "H", or "B") - \param value signed integer data to store - - \return \c true if the tag was modified/created successfully - - \sa BamAlignment::RemoveTag() - \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. -*/ -bool BamAlignment::EditTag(const std::string& tag, const std::string& type, const int32_t& value) { - return EditTag(tag, type, (const uint32_t&)value); -} - -/*! \fn bool BamAlignment::EditTag(const std::string& tag, const std::string& type, const float& value) - \brief Edits a BAM tag field containing floating-point data. - - If \a tag does not exist, a new entry is created. - - \param tag 2-character tag name - \param type 1-character tag type (must NOT be "Z", "H", or "B") - \param value float data to store - - \return \c true if the tag was modified/created successfully - - \sa BamAlignment::RemoveTag() - \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. -*/ -bool BamAlignment::EditTag(const std::string& tag, const std::string& type, const float& value) { - - // skip if core data not parsed - if ( SupportData.HasCoreOnly ) return false; - - // validate tag/type size & that type is OK for float value - if ( !IsValidSize(tag, type) ) return false; - if ( type.at(0) == Constants::BAM_TAG_TYPE_STRING || - type.at(0) == Constants::BAM_TAG_TYPE_HEX || - type.at(0) == Constants::BAM_TAG_TYPE_ARRAY - ) - { - return false; - } - - // localize the tag data - char* pOriginalTagData = (char*)TagData.data(); - char* pTagData = pOriginalTagData; - const unsigned int originalTagDataLength = TagData.size(); - - unsigned int newTagDataLength = 0; - unsigned int numBytesParsed = 0; - - // if tag found - if ( FindTag(tag, pTagData, originalTagDataLength, numBytesParsed) ) { - - // make sure array is more than big enough - char* newTagData = new char[originalTagDataLength + sizeof(value)]; - - // copy original tag data up til desired tag - const unsigned int beginningTagDataLength = numBytesParsed; - newTagDataLength += beginningTagDataLength; - memcpy(newTagData, pOriginalTagData, numBytesParsed); - - // copy new @value in place of current tag data - union { float value; char valueBuffer[sizeof(float)]; } un; - un.value = value; - memcpy(newTagData + beginningTagDataLength, un.valueBuffer, sizeof(float)); - - // skip to next tag (if tag for removal is last, return true) - const char* pTagStorageType = pTagData - 1; - if ( !SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed) ) - return true; - - // copy everything from current tag (the next one after tag for removal) to end - const unsigned int skippedDataLength = (numBytesParsed - beginningTagDataLength); - const unsigned int endTagOffset = beginningTagDataLength + sizeof(float); - const unsigned int endTagDataLength = originalTagDataLength - beginningTagDataLength - skippedDataLength; - memcpy(newTagData + endTagOffset, pTagData, endTagDataLength); - - // ensure null-terminator - newTagData[ endTagOffset + endTagDataLength + 1 ] = 0; - - // save new tag data - TagData.assign(newTagData, endTagOffset + endTagDataLength); - - delete[] newTagData; - - return true; - } - - // tag not found, attempt AddTag - else return AddTag(tag, type, value); -} - -/*! \fn bool EditTag(const std::string& tag, const std::vector& values); - \brief Edits a BAM tag field containing a numeric array. - - If \a tag does not exist, a new entry is created. - - \param tag 2-character tag name - \param value vector of uint8_t values to store - - \return \c true if the tag was modified/created successfully - \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. -*/ -bool BamAlignment::EditTag(const std::string& tag, const std::vector& values) { - - // can't do anything if TagData not parsed - if ( SupportData.HasCoreOnly ) - return false; - - // remove existing tag if present - if ( HasTag(tag) ) - RemoveTag(tag); - - // add tag record with new values - return AddTag(tag, values); -} - -/*! \fn bool EditTag(const std::string& tag, const std::vector& values); - \brief Edits a BAM tag field containing a numeric array. - - If \a tag does not exist, a new entry is created. - - \param tag 2-character tag name - \param value vector of int8_t values to store - - \return \c true if the tag was modified/created successfully - \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. -*/ -bool BamAlignment::EditTag(const std::string& tag, const std::vector& values) { - - // can't do anything if TagData not parsed - if ( SupportData.HasCoreOnly ) - return false; - - // remove existing tag if present - if ( HasTag(tag) ) - RemoveTag(tag); - - // add tag record with new values - return AddTag(tag, values); -} - -/*! \fn bool EditTag(const std::string& tag, const std::vector& values); - \brief Edits a BAM tag field containing a numeric array. - - If \a tag does not exist, a new entry is created. - - \param tag 2-character tag name - \param value vector of uint16_t values to store - - \return \c true if the tag was modified/created successfully - \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. -*/ -bool BamAlignment::EditTag(const std::string& tag, const std::vector& values) { - - // can't do anything if TagData not parsed - if ( SupportData.HasCoreOnly ) - return false; - - // remove existing tag if present - if ( HasTag(tag) ) - RemoveTag(tag); - - // add tag record with new values - return AddTag(tag, values); -} - -/*! \fn bool EditTag(const std::string& tag, const std::vector& values); - \brief Edits a BAM tag field containing a numeric array. - - If \a tag does not exist, a new entry is created. - - \param tag 2-character tag name - \param value vector of int16_t values to store - - \return \c true if the tag was modified/created successfully - \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. -*/ -bool BamAlignment::EditTag(const std::string& tag, const std::vector& values) { - - // can't do anything if TagData not parsed - if ( SupportData.HasCoreOnly ) - return false; - - // remove existing tag if present - if ( HasTag(tag) ) - RemoveTag(tag); - - // add tag record with new values - return AddTag(tag, values); -} - -/*! \fn bool EditTag(const std::string& tag, const std::vector& values); - \brief Edits a BAM tag field containing a numeric array. - - If \a tag does not exist, a new entry is created. - - \param tag 2-character tag name - \param value vector of uint32_t values to store - - \return \c true if the tag was modified/created successfully - \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. -*/ -bool BamAlignment::EditTag(const std::string& tag, const std::vector& values) { - - // can't do anything if TagData not parsed - if ( SupportData.HasCoreOnly ) - return false; - - // remove existing tag if present - if ( HasTag(tag) ) - RemoveTag(tag); - - // add tag record with new values - return AddTag(tag, values); -} - -/*! \fn bool EditTag(const std::string& tag, const std::vector& values); - \brief Edits a BAM tag field containing a numeric array. - - If \a tag does not exist, a new entry is created. - - \param tag 2-character tag name - \param value vector of int32_t values to store - - \return \c true if the tag was modified/created successfully - \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. -*/ -bool BamAlignment::EditTag(const std::string& tag, const std::vector& values) { + } - // can't do anything if TagData not parsed - if ( SupportData.HasCoreOnly ) - return false; + // store tagData in alignment + TagData.resize(tagDataLength); + memcpy((char*)TagData.data(), tagData, tagDataLength); + } - // remove existing tag if present - if ( HasTag(tag) ) - RemoveTag(tag); + // clear the core-only flag + SupportData.HasCoreOnly = false; - // add tag record with new values - return AddTag(tag, values); + // return success + return true; } -/*! \fn bool EditTag(const std::string& tag, const std::vector& values); - \brief Edits a BAM tag field containing a numeric array. +///*! \fn bool BamAlignment::EditTag(const std::string& tag, const std::string& type, const std::string& value) +// \brief Edits a BAM tag field containing string data. - If \a tag does not exist, a new entry is created. +// If \a tag does not exist, a new entry is created. - \param tag 2-character tag name - \param value vector of float values to store +// \param tag 2-character tag name +// \param type 1-character tag type (must be "Z" or "H") +// \param value string data to store - \return \c true if the tag was modified/created successfully - \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. -*/ -bool BamAlignment::EditTag(const std::string& tag, const std::vector& values) { +// \return \c true if the tag was modified/created successfully - // can't do anything if TagData not parsed - if ( SupportData.HasCoreOnly ) - return false; +// \sa BamAlignment::RemoveTag() +// \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +//*/ - // remove existing tag if present - if ( HasTag(tag) ) - RemoveTag(tag); +///*! \fn bool EditTag(const std::string& tag, const std::vector& values); +// \brief Edits a BAM tag field containing a numeric array. - // add tag record with new values - return AddTag(tag, values); -} +// If \a tag does not exist, a new entry is created. + +// \param tag 2-character tag name +// \param value vector of uint8_t values to store + +// \return \c true if the tag was modified/created successfully +// \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. +//*/ /*! \fn bool BamAlignment::FindTag(const std::string& tag, char*& pTagData, const unsigned int& tagDataLength, unsigned int& numBytesParsed) \internal @@ -1451,7 +414,7 @@ bool BamAlignment::EditTag(const std::string& tag, const std::vector& val bool BamAlignment::FindTag(const std::string& tag, char*& pTagData, const unsigned int& tagDataLength, - unsigned int& numBytesParsed) const + unsigned int& numBytesParsed) { while ( numBytesParsed < tagDataLength ) { @@ -1487,6 +450,8 @@ bool BamAlignment::FindTag(const std::string& tag, \return \c true if found */ + +// TODO : REMOVE THIS METHOD bool BamAlignment::GetEditDistance(uint32_t& editDistance) const { return GetTag("NM", (uint32_t&)editDistance); } @@ -1540,135 +505,40 @@ int BamAlignment::GetEndPosition(bool usePadded, bool zeroBased) const { \return \c true if found */ + +// TODO : REMOVE THIS METHOD bool BamAlignment::GetReadGroup(std::string& readGroup) const { return GetTag("RG", readGroup); } -/*! \fn bool BamAlignment::GetTag(const std::string& tag, std::string& destination) const - \brief Retrieves the string value associated with a BAM tag. - - \param tag 2-character tag name - \param destination destination for retrieved value - - \return \c true if found -*/ -bool BamAlignment::GetTag(const std::string& tag, std::string& destination) const { - - // make sure tag data exists - if ( SupportData.HasCoreOnly || TagData.empty() ) - return false; - - // localize the tag data - char* pTagData = (char*)TagData.data(); - const unsigned int tagDataLength = TagData.size(); - unsigned int numBytesParsed = 0; - - // if tag found - if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) { - const unsigned int dataLength = strlen(pTagData); - destination.clear(); - destination.resize(dataLength); - memcpy( (char*)destination.data(), pTagData, dataLength ); - return true; - } - - // tag not found, return failure - return false; -} - -/*! \fn bool BamAlignment::GetTag(const std::string& tag, uint32_t& destination) const - \brief Retrieves the unsigned integer value associated with a BAM tag. +///*! \fn bool BamAlignment::GetTag(const std::string& tag, std::string& destination) const +// \brief Retrieves the string value associated with a BAM tag. - \param tag 2-character tag name - \param destination destination for retrieved value +// \param tag 2-character tag name +// \param destination destination for retrieved value - \return \c true if found -*/ -bool BamAlignment::GetTag(const std::string& tag, uint32_t& destination) const { - - // make sure tag data exists - if ( SupportData.HasCoreOnly || TagData.empty() ) - return false; - - // localize the tag data - char* pTagData = (char*)TagData.data(); - const unsigned int tagDataLength = TagData.size(); - unsigned int numBytesParsed = 0; - - // if tag found - if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) { - - // determine data byte-length - const char type = *(pTagData - 1); - int destinationLength = 0; - switch (type) { - - // 1 byte data - case (Constants::BAM_TAG_TYPE_ASCII) : - case (Constants::BAM_TAG_TYPE_INT8) : - case (Constants::BAM_TAG_TYPE_UINT8) : - destinationLength = 1; - break; - - // 2 byte data - case (Constants::BAM_TAG_TYPE_INT16) : - case (Constants::BAM_TAG_TYPE_UINT16) : - destinationLength = 2; - break; - - // 4 byte data - case (Constants::BAM_TAG_TYPE_INT32) : - case (Constants::BAM_TAG_TYPE_UINT32) : - destinationLength = 4; - break; - - // unsupported type for integer destination (float or var-length strings) - case (Constants::BAM_TAG_TYPE_FLOAT) : - case (Constants::BAM_TAG_TYPE_STRING) : - case (Constants::BAM_TAG_TYPE_HEX) : - case (Constants::BAM_TAG_TYPE_ARRAY) : - cerr << "BamAlignment ERROR: cannot store tag of type " << type - << " in integer destination" << endl; - return false; - - // unknown tag type - default: - cerr << "BamAlignment ERROR: unknown tag type encountered: " - << type << endl; - return false; - } - - // store in destination - destination = 0; - memcpy(&destination, pTagData, destinationLength); - return true; - } - - // tag not found, return failure - return false; -} +// \return \c true if found +//*/ -/*! \fn bool BamAlignment::GetTag(const std::string& tag, int32_t& destination) const - \brief Retrieves the signed integer value associated with a BAM tag. +///*! \fn bool BamAlignment::GetTag(const std::string& tag, std::vector& destination) const +// \brief Retrieves the numeric array data associated with a BAM tag - \param tag 2-character tag name - \param destination destination for retrieved value +// \param tag 2-character tag name +// \param destination destination for retrieved data - \return \c true if found -*/ -bool BamAlignment::GetTag(const std::string& tag, int32_t& destination) const { - return GetTag(tag, (uint32_t&)destination); -} +// \return \c true if found +//*/ -/*! \fn bool BamAlignment::GetTag(const std::string& tag, float& destination) const - \brief Retrieves the floating-point value associated with a BAM tag. +/*! \fn bool BamAlignment::GetTagType(const std::string& tag, char& type) const + \brief Retrieves the BAM tag type-code associated with requested tag name. - \param tag 2-character tag name - \param destination destination for retrieved value + \param tag 2-character tag name + \param type destination for the retrieved (1-character) tag type \return \c true if found + \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. */ -bool BamAlignment::GetTag(const std::string& tag, float& destination) const { +bool BamAlignment::GetTagType(const std::string& tag, char& type) const { // make sure tag data exists if ( SupportData.HasCoreOnly || TagData.empty() ) @@ -1679,372 +549,32 @@ bool BamAlignment::GetTag(const std::string& tag, float& destination) const { const unsigned int tagDataLength = TagData.size(); unsigned int numBytesParsed = 0; - // if tag found - if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) { - - // determine data byte-length - const char type = *(pTagData - 1); - int destinationLength = 0; - switch (type) { - - // 1 byte data - case (Constants::BAM_TAG_TYPE_ASCII) : - case (Constants::BAM_TAG_TYPE_INT8) : - case (Constants::BAM_TAG_TYPE_UINT8) : - destinationLength = 1; - break; - - // 2 byte data - case (Constants::BAM_TAG_TYPE_INT16) : - case (Constants::BAM_TAG_TYPE_UINT16) : - destinationLength = 2; - break; - - // 4 byte data - case (Constants::BAM_TAG_TYPE_FLOAT) : - case (Constants::BAM_TAG_TYPE_INT32) : - case (Constants::BAM_TAG_TYPE_UINT32) : - destinationLength = 4; - break; - - // unsupported type (var-length strings) - case (Constants::BAM_TAG_TYPE_STRING) : - case (Constants::BAM_TAG_TYPE_HEX) : - case (Constants::BAM_TAG_TYPE_ARRAY) : - cerr << "BamAlignment ERROR: cannot store tag of type " << type - << " in float destination" << endl; - return false; - - // unknown tag type - default: - cerr << "BamAlignment ERROR: unknown tag type encountered: " - << type << endl; - return false; - } - - // store in destination - destination = 0.0; - memcpy(&destination, pTagData, destinationLength); - return true; - } - - // tag not found, return failure - return false; -} - -/*! \fn bool BamAlignment::GetTag(const std::string& tag, std::vector& destination) const - \brief Retrieves the numeric array data associated with a BAM tag - - \param tag 2-character tag name - \param destination destination for retrieved data - - \return \c true if found -*/ -bool BamAlignment::GetTag(const std::string& tag, std::vector& destination) const { - - // make sure tag data exists - if ( SupportData.HasCoreOnly || TagData.empty() ) - return false; - - // localize the tag data - char* pTagData = (char*)TagData.data(); - const unsigned int tagDataLength = TagData.size(); - unsigned int numBytesParsed = 0; - - // return false if tag not found - if ( !FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) - return false; - - // check that tag is array type - const char tagType = *(pTagData - 1); - if ( tagType != Constants::BAM_TAG_TYPE_ARRAY ) { - cerr << "BamAlignment ERROR: Cannot store non-array data from tag: " - << tag << " in array destination" << endl; - return false; - } - - // calculate length of each element in tag's array - const char elementType = *pTagData; - ++pTagData; - int elementLength = 0; - switch ( elementType ) { - case (Constants::BAM_TAG_TYPE_ASCII) : - case (Constants::BAM_TAG_TYPE_INT8) : - case (Constants::BAM_TAG_TYPE_UINT8) : - elementLength = sizeof(uint8_t); - break; - - case (Constants::BAM_TAG_TYPE_INT16) : - case (Constants::BAM_TAG_TYPE_UINT16) : - elementLength = sizeof(uint16_t); - break; - - case (Constants::BAM_TAG_TYPE_INT32) : - case (Constants::BAM_TAG_TYPE_UINT32) : - elementLength = sizeof(uint32_t); - break; - - // unsupported type for integer destination (float or var-length data) - case (Constants::BAM_TAG_TYPE_FLOAT) : - case (Constants::BAM_TAG_TYPE_STRING) : - case (Constants::BAM_TAG_TYPE_HEX) : - case (Constants::BAM_TAG_TYPE_ARRAY) : - cerr << "BamAlignment ERROR: array element type: " << elementType - << " cannot be stored in integer value" << endl; - return false; - - // unknown tag type - default: - cerr << "BamAlignment ERROR: unknown element type encountered: " - << elementType << endl; - return false; - } - - // get number of elements - int32_t numElements; - memcpy(&numElements, pTagData, sizeof(int32_t)); - pTagData += 4; - destination.clear(); - destination.reserve(numElements); - - // read in elements - uint32_t value; - for ( int i = 0 ; i < numElements; ++i ) { - memcpy(&value, pTagData, sizeof(uint32_t)); - pTagData += sizeof(uint32_t); - destination.push_back(value); - } - - // return success - return false; -} - -/*! \fn bool BamAlignment::GetTag(const std::string& tag, std::vector& destination) const - \brief Retrieves the numeric array data associated with a BAM tag - - \param tag 2-character tag name - \param destination destination for retrieved data - - \return \c true if found -*/ -bool BamAlignment::GetTag(const std::string& tag, std::vector& destination) const { - - // make sure tag data exists - if ( SupportData.HasCoreOnly || TagData.empty() ) - return false; - - // localize the tag data - char* pTagData = (char*)TagData.data(); - const unsigned int tagDataLength = TagData.size(); - unsigned int numBytesParsed = 0; - - // return false if tag not found - if ( !FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) - return false; - - // check that tag is array type - const char tagType = *(pTagData - 1); - if ( tagType != Constants::BAM_TAG_TYPE_ARRAY ) { - cerr << "BamAlignment ERROR: Cannot store non-array data from tag: " - << tag << " in array destination" << endl; - return false; - } - - // calculate length of each element in tag's array - const char elementType = *pTagData; - ++pTagData; - int elementLength = 0; - switch ( elementType ) { - case (Constants::BAM_TAG_TYPE_ASCII) : - case (Constants::BAM_TAG_TYPE_INT8) : - case (Constants::BAM_TAG_TYPE_UINT8) : - elementLength = sizeof(uint8_t); - break; - - case (Constants::BAM_TAG_TYPE_INT16) : - case (Constants::BAM_TAG_TYPE_UINT16) : - elementLength = sizeof(uint16_t); - break; - - case (Constants::BAM_TAG_TYPE_INT32) : - case (Constants::BAM_TAG_TYPE_UINT32) : - elementLength = sizeof(uint32_t); - break; - - // unsupported type for integer destination (float or var-length data) - case (Constants::BAM_TAG_TYPE_FLOAT) : - case (Constants::BAM_TAG_TYPE_STRING) : - case (Constants::BAM_TAG_TYPE_HEX) : - case (Constants::BAM_TAG_TYPE_ARRAY) : - cerr << "BamAlignment ERROR: array element type: " << elementType - << " cannot be stored in integer value" << endl; - return false; - - // unknown tag type - default: - cerr << "BamAlignment ERROR: unknown element type encountered: " - << elementType << endl; - return false; - } - - // get number of elements - int32_t numElements; - memcpy(&numElements, pTagData, sizeof(int32_t)); - pTagData += 4; - destination.clear(); - destination.reserve(numElements); - - // read in elements - int32_t value; - for ( int i = 0 ; i < numElements; ++i ) { - memcpy(&value, pTagData, sizeof(int32_t)); - pTagData += sizeof(int32_t); - destination.push_back(value); - } - - // return success - return false; - -} - -/*! \fn bool BamAlignment::GetTag(const std::string& tag, std::vector& destination) const - \brief Retrieves the numeric array data associated with a BAM tag - - \param tag 2-character tag name - \param destination destination for retrieved data - - \return \c true if found -*/ -bool BamAlignment::GetTag(const std::string& tag, std::vector& destination) const { - - // make sure tag data exists - if ( SupportData.HasCoreOnly || TagData.empty() ) - return false; - - // localize the tag data - char* pTagData = (char*)TagData.data(); - const unsigned int tagDataLength = TagData.size(); - unsigned int numBytesParsed = 0; - - // return false if tag not found + // if tag not found, return failure if ( !FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) return false; - // check that tag is array type - const char tagType = *(pTagData - 1); - if ( tagType != Constants::BAM_TAG_TYPE_ARRAY ) { - cerr << "BamAlignment ERROR: Cannot store non-array data from tag: " - << tag << " in array destination" << endl; - return false; - } - - // calculate length of each element in tag's array - const char elementType = *pTagData; - ++pTagData; - int elementLength = 0; - switch ( elementType ) { - case (Constants::BAM_TAG_TYPE_ASCII) : - case (Constants::BAM_TAG_TYPE_INT8) : - case (Constants::BAM_TAG_TYPE_UINT8) : - elementLength = sizeof(uint8_t); - break; - + // otherwise, retrieve & validate tag type code + type = *(pTagData - 1); + switch ( type ) { + case (Constants::BAM_TAG_TYPE_ASCII) : + case (Constants::BAM_TAG_TYPE_INT8) : + case (Constants::BAM_TAG_TYPE_UINT8) : case (Constants::BAM_TAG_TYPE_INT16) : case (Constants::BAM_TAG_TYPE_UINT16) : - elementLength = sizeof(uint16_t); - break; - case (Constants::BAM_TAG_TYPE_INT32) : case (Constants::BAM_TAG_TYPE_UINT32) : case (Constants::BAM_TAG_TYPE_FLOAT) : - elementLength = sizeof(uint32_t); - break; - - // unsupported type for float destination (var-length data) case (Constants::BAM_TAG_TYPE_STRING) : case (Constants::BAM_TAG_TYPE_HEX) : case (Constants::BAM_TAG_TYPE_ARRAY) : - cerr << "BamAlignment ERROR: array element type: " << elementType - << " cannot be stored in float value" << endl; - return false; + return true; // unknown tag type default: - cerr << "BamAlignment ERROR: unknown element type encountered: " - << elementType << endl; + cerr << "BamAlignment ERROR: unknown tag type encountered: " + << type << endl; return false; } - - // get number of elements - int32_t numElements; - memcpy(&numElements, pTagData, sizeof(int32_t)); - pTagData += 4; - destination.clear(); - destination.reserve(numElements); - - // read in elements - float value; - for ( int i = 0 ; i < numElements; ++i ) { - memcpy(&value, pTagData, sizeof(float)); - pTagData += sizeof(float); - destination.push_back(value); - } - - // return success - return false; -} - -/*! \fn bool BamAlignment::GetTagType(const std::string& tag, char& type) const - \brief Retrieves the BAM tag type-code associated with requested tag name. - - \param tag 2-character tag name - \param type destination for the retrieved (1-character) tag type - - \return \c true if found - \sa \samSpecURL for more details on reserved tag names, supported tag types, etc. -*/ -bool BamAlignment::GetTagType(const std::string& tag, char& type) const { - - // make sure tag data exists - if ( SupportData.HasCoreOnly || TagData.empty() ) - return false; - - // localize the tag data - char* pTagData = (char*)TagData.data(); - const unsigned int tagDataLength = TagData.size(); - unsigned int numBytesParsed = 0; - - // lookup tag - if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) { - - // retrieve tag type code - type = *(pTagData - 1); - - // validate that type is a proper BAM tag type - switch (type) { - case (Constants::BAM_TAG_TYPE_ASCII) : - case (Constants::BAM_TAG_TYPE_INT8) : - case (Constants::BAM_TAG_TYPE_UINT8) : - case (Constants::BAM_TAG_TYPE_INT16) : - case (Constants::BAM_TAG_TYPE_UINT16) : - case (Constants::BAM_TAG_TYPE_INT32) : - case (Constants::BAM_TAG_TYPE_UINT32) : - case (Constants::BAM_TAG_TYPE_FLOAT) : - case (Constants::BAM_TAG_TYPE_STRING) : - case (Constants::BAM_TAG_TYPE_HEX) : - case (Constants::BAM_TAG_TYPE_ARRAY) : - return true; - - // unknown tag type - default: - cerr << "BamAlignment ERROR: unknown tag type encountered: " - << type << endl; - return false; - } - } - - // tag not found, return failure - return false; } /*! \fn bool BamAlignment::HasTag(const std::string& tag) const @@ -2156,7 +686,7 @@ bool BamAlignment::IsSecondMate(void) const { \return \c true if both \a tag and \a type are correct sizes */ -bool BamAlignment::IsValidSize(const string& tag, const string& type) const { +bool BamAlignment::IsValidSize(const string& tag, const string& type) { return (tag.size() == Constants::BAM_TAG_TAGSIZE) && (type.size() == Constants::BAM_TAG_TYPESIZE); } @@ -2168,8 +698,12 @@ bool BamAlignment::IsValidSize(const string& tag, const string& type) const { */ bool BamAlignment::RemoveTag(const std::string& tag) { - // skip if no tag data available - if ( SupportData.HasCoreOnly || TagData.empty() ) + // if char data not populated, do that first + if ( SupportData.HasCoreOnly ) + BuildCharData(); + + // skip if no tags available + if ( TagData.empty() ) return false; // localize the tag data @@ -2178,41 +712,39 @@ bool BamAlignment::RemoveTag(const std::string& tag) { const unsigned int originalTagDataLength = TagData.size(); unsigned int newTagDataLength = 0; unsigned int numBytesParsed = 0; - - // if tag found - if ( FindTag(tag, pTagData, originalTagDataLength, numBytesParsed) ) { - - char* newTagData = new char[originalTagDataLength]; - - // copy original tag data up til desired tag - pTagData -= 3; - numBytesParsed -= 3; - const unsigned int beginningTagDataLength = numBytesParsed; - newTagDataLength += beginningTagDataLength; - memcpy(newTagData, pOriginalTagData, numBytesParsed); - - // skip to next tag (if tag for removal is last, return true) - const char* pTagStorageType = pTagData + 2; - pTagData += 3; - numBytesParsed += 3; - if ( !SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed) ) - return true; - - // copy everything from current tag (the next one after tag for removal) to end + + // if tag not found, simply return true + if ( !FindTag(tag, pTagData, originalTagDataLength, numBytesParsed) ) + return true; + + // otherwise, remove it + char* newTagData = new char[originalTagDataLength]; + + // copy original tag data up til desired tag + pTagData -= 3; + numBytesParsed -= 3; + const unsigned int beginningTagDataLength = numBytesParsed; + newTagDataLength += beginningTagDataLength; + memcpy(newTagData, pOriginalTagData, numBytesParsed); + + // attemp to skip to next tag + const char* pTagStorageType = pTagData + 2; + pTagData += 3; + numBytesParsed += 3; + if ( SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed) ) { + + // squeeze remaining tag data const unsigned int skippedDataLength = (numBytesParsed - beginningTagDataLength); const unsigned int endTagDataLength = originalTagDataLength - beginningTagDataLength - skippedDataLength; memcpy(newTagData + beginningTagDataLength, pTagData, endTagDataLength ); - - // save new tag data - TagData.assign(newTagData, beginningTagDataLength + endTagDataLength); - - delete[] newTagData; - return true; + // save modified tag data in alignment + TagData.assign(newTagData, beginningTagDataLength + endTagDataLength); } - - // tag not found, no removal - return failure - return false; + + // clean up & return success + delete[] newTagData; + return true; } /*! \fn void BamAlignment::SetIsDuplicate(bool ok) @@ -2345,7 +877,7 @@ void BamAlignment::SetIsUnmapped(bool ok) { */ bool BamAlignment::SkipToNextTag(const char storageType, char*& pTagData, - unsigned int& numBytesParsed) const + unsigned int& numBytesParsed) { switch (storageType) {