X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2FBamAlignment.cpp;h=0b13fb4121786277de72218c676fc29f38c4d648;hb=8b4c010999a8d0c482d84bbf17c98dc4bbae02b7;hp=91ca8ad68fafab2d0f84375459d7cc72c1c226b0;hpb=1a93ff03d7e40d97c32e6f5966045ceaeb2f038a;p=bamtools.git diff --git a/src/api/BamAlignment.cpp b/src/api/BamAlignment.cpp index 91ca8ad..0b13fb4 100644 --- a/src/api/BamAlignment.cpp +++ b/src/api/BamAlignment.cpp @@ -2,23 +2,14 @@ // BamAlignment.cpp (c) 2009 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 22 April 2011 (DB) +// Last modified: 17 October 2011 (DB) // --------------------------------------------------------------------------- // Provides the BamAlignment data structure // *************************************************************************** -#include -#include +#include "api/BamAlignment.h" +#include "api/BamConstants.h" using namespace BamTools; - -#include -#include -#include -#include -#include -#include -#include -#include using namespace std; /*! \class BamTools::BamAlignment @@ -114,668 +105,6 @@ 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. - - 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 - - \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; - - // 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)); - } - - // 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::BuildCharData(void) \brief Populates alignment string fields (read name, bases, qualities, tag data). @@ -799,7 +128,7 @@ bool BamAlignment::BuildCharData(void) { // calculate character lengths/offsets const unsigned int dataLength = SupportData.BlockLength - Constants::BAM_CORE_SIZE; - const unsigned int seqDataOffset = SupportData.QueryNameLength + (SupportData.NumCigarOperations * 4); + const unsigned int seqDataOffset = SupportData.QueryNameLength + (SupportData.NumCigarOperations*4); const unsigned int qualDataOffset = seqDataOffset + (SupportData.QuerySequenceLength+1)/2; const unsigned int tagDataOffset = qualDataOffset + SupportData.QuerySequenceLength; const unsigned int tagDataLength = dataLength - tagDataOffset; @@ -822,8 +151,8 @@ bool BamAlignment::BuildCharData(void) { QueryBases.clear(); if ( hasSeqData ) { QueryBases.reserve(SupportData.QuerySequenceLength); - for (unsigned int i = 0; i < SupportData.QuerySequenceLength; ++i) { - char singleBase = Constants::BAM_DNA_LOOKUP[ ( (seqData[(i/2)] >> (4*(1-(i%2)))) & 0xf ) ]; + for ( size_t i = 0; i < SupportData.QuerySequenceLength; ++i ) { + const char singleBase = Constants::BAM_DNA_LOOKUP[ ( (seqData[(i/2)] >> (4*(1-(i%2)))) & 0xf ) ]; QueryBases.append(1, singleBase); } } @@ -832,8 +161,8 @@ bool BamAlignment::BuildCharData(void) { Qualities.clear(); if ( hasQualData ) { Qualities.reserve(SupportData.QuerySequenceLength); - for (unsigned int i = 0; i < SupportData.QuerySequenceLength; ++i) { - char singleQuality = (char)(qualData[i]+33); + for ( size_t i = 0; i < SupportData.QuerySequenceLength; ++i ) { + const char singleQuality = static_cast(qualData[i]+33); Qualities.append(1, singleQuality); } } @@ -855,7 +184,7 @@ bool BamAlignment::BuildCharData(void) { for ( ; cigarIter != cigarEnd; ++cigarIter ) { const CigarOp& op = (*cigarIter); - switch (op.Type) { + switch ( op.Type ) { // for 'M', 'I', '=', 'X' - write bases case (Constants::BAM_CIGAR_MATCH_CHAR) : @@ -890,11 +219,11 @@ bool BamAlignment::BuildCharData(void) { case (Constants::BAM_CIGAR_HARDCLIP_CHAR) : break; - // shouldn't get here + // invalid CIGAR op-code default: - cerr << "BamAlignment ERROR: invalid CIGAR operation type: " - << op.Type << endl; - exit(1); + const string message = string("invalid CIGAR operation type: ") + op.Type; + SetErrorString("BamAlignment::BuildCharData", message); + return false; } } } @@ -903,8 +232,8 @@ bool BamAlignment::BuildCharData(void) { TagData.clear(); if ( hasTagData ) { if ( IsBigEndian ) { - int i = 0; - while ( (unsigned int)i < tagDataLength ) { + size_t i = 0; + while ( i < tagDataLength ) { i += Constants::BAM_TAG_TAGSIZE; // skip tag chars (e.g. "RG", "NM", etc.) const char type = tagData[i]; // get tag type at position i @@ -950,12 +279,12 @@ bool BamAlignment::BuildCharData(void) { // swap endian-ness of number of elements in place, then retrieve for loop BamTools::SwapEndian_32p(&tagData[i]); - int32_t numElements; + uint32_t numElements; memcpy(&numElements, &tagData[i], sizeof(uint32_t)); i += sizeof(uint32_t); // swap endian-ness of array elements - for ( int j = 0; j < numElements; ++j ) { + for ( size_t j = 0; j < numElements; ++j ) { switch (arrayType) { case (Constants::BAM_TAG_TYPE_INT8) : case (Constants::BAM_TAG_TYPE_UINT8) : @@ -974,9 +303,8 @@ bool BamAlignment::BuildCharData(void) { i += sizeof(uint32_t); break; default: - // error case - cerr << "BamAlignment ERROR: unknown binary array type encountered: " - << arrayType << endl; + const string message = string("invalid binary array type: ") + arrayType; + SetErrorString("BamAlignment::BuildCharData", message); return false; } } @@ -984,462 +312,34 @@ bool BamAlignment::BuildCharData(void) { break; } - // shouldn't get here + // invalid tag type-code default : - cerr << "BamAlignment ERROR: invalid tag value type: " - << type << endl; - 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; - - // 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 float 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; + const string message = string("invalid tag type: ") + type; + SetErrorString("BamAlignment::BuildCharData", message); + return false; + } + } + } - // remove existing tag if present - if ( HasTag(tag) ) - RemoveTag(tag); + // store tagData in alignment + TagData.resize(tagDataLength); + memcpy((char*)(TagData.data()), tagData, tagDataLength); + } - // add tag record with new values - return AddTag(tag, values); + // clear core-only flag & return success + SupportData.HasCoreOnly = false; + return true; } -/*! \fn bool BamAlignment::FindTag(const std::string& tag, char*& pTagData, const unsigned int& tagDataLength, unsigned int& numBytesParsed) +/*! \fn bool BamAlignment::FindTag(const std::string& tag, char*& pTagData, const unsigned int& tagDataLength, unsigned int& numBytesParsed) const \internal Searches for requested tag in BAM tag data. - \param tag requested 2-character tag name - \param pTagData pointer to current position in BamAlignment::TagData - \param tagDataLength length of BamAlignment::TagData - \param numBytesParsed number of bytes parsed so far + \param[in] tag requested 2-character tag name + \param[in,out] pTagData pointer to current position in BamAlignment::TagData + \param[in] tagDataLength length of BamAlignment::TagData + \param[in,out] numBytesParsed number of bytes parsed so far \return \c true if found @@ -1474,33 +374,22 @@ bool BamAlignment::FindTag(const std::string& tag, return false; } -/*! \fn bool BamAlignment::GetEditDistance(uint32_t& editDistance) const - \brief Retrieves value of edit distance tag ("NM"). +/*! \fn int BamAlignment::GetEndPosition(bool usePadded = false, bool closedInterval = false) const + \brief Calculates alignment end position, based on its starting position and CIGAR data. - \deprecated Instead use BamAlignment::GetTag() - \code - BamAlignment::GetTag("NM", editDistance); - \endcode + \warning The position returned now represents a zero-based, HALF-OPEN interval. + In previous versions of BamTools (0.x & 1.x) all intervals were treated + as zero-based, CLOSED. - \param editDistance destination for retrieved value - - \return \c true if found -*/ -bool BamAlignment::GetEditDistance(uint32_t& editDistance) const { - return GetTag("NM", (uint32_t&)editDistance); -} - -/*! \fn int BamAlignment::GetEndPosition(bool usePadded = false, bool zeroBased = true) const - \brief Calculates alignment end position, based on starting position and CIGAR data. - - \param usePadded Inserted bases affect reported position. Default is false, so that reported - position stays 'sync-ed' with reference coordinates. - \param zeroBased Return (BAM standard) 0-based coordinate. Setting this to false can be useful - when using BAM data with half-open formats (e.g. BED). + \param[in] usePadded Allow inserted bases to affect the reported position. Default is + false, so that reported position stays synced with reference + coordinates. + \param[in] closedInterval Setting this to true will return a 0-based end coordinate. Default is + false, so that his value represents a standard, half-open interval. \return alignment end position */ -int BamAlignment::GetEndPosition(bool usePadded, bool zeroBased) const { +int BamAlignment::GetEndPosition(bool usePadded, bool closedInterval) const { // initialize alignment end to starting position int alignEnd = Position; @@ -1509,546 +398,201 @@ int BamAlignment::GetEndPosition(bool usePadded, bool zeroBased) const { vector::const_iterator cigarIter = CigarData.begin(); vector::const_iterator cigarEnd = CigarData.end(); for ( ; cigarIter != cigarEnd; ++cigarIter) { - const char cigarType = (*cigarIter).Type; - const uint32_t& cigarLength = (*cigarIter).Length; - - if ( cigarType == Constants::BAM_CIGAR_MATCH_CHAR || - cigarType == Constants::BAM_CIGAR_DEL_CHAR || - cigarType == Constants::BAM_CIGAR_REFSKIP_CHAR ) - alignEnd += cigarLength; - else if ( usePadded && cigarType == Constants::BAM_CIGAR_INS_CHAR ) - alignEnd += cigarLength; - } - - // adjust for zero-based coordinates, if requested - if ( zeroBased ) alignEnd -= 1; - - // return result - return alignEnd; -} - -/*! \fn bool BamAlignment::GetReadGroup(std::string& readGroup) const - \brief Retrieves value of read group tag ("RG"). - - \deprecated Instead use BamAlignment::GetTag() - \code - BamAlignment::GetTag("RG", readGroup); - \endcode - - \param readGroup destination for retrieved value - - \return \c true if found -*/ -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 { + const CigarOp& op = (*cigarIter); - // 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. - - \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; + switch ( op.Type ) { - // 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; + // increase end position on CIGAR chars [DMXN=] + case Constants::BAM_CIGAR_DEL_CHAR : + case Constants::BAM_CIGAR_MATCH_CHAR : + case Constants::BAM_CIGAR_MISMATCH_CHAR : + case Constants::BAM_CIGAR_REFSKIP_CHAR : + case Constants::BAM_CIGAR_SEQMATCH_CHAR : + alignEnd += op.Length; break; - // 2 byte data - case (Constants::BAM_TAG_TYPE_INT16) : - case (Constants::BAM_TAG_TYPE_UINT16) : - destinationLength = 2; + // increase end position on insertion, only if @usePadded is true + case Constants::BAM_CIGAR_INS_CHAR : + if ( usePadded ) + alignEnd += op.Length; break; - // 4 byte data - case (Constants::BAM_TAG_TYPE_INT32) : - case (Constants::BAM_TAG_TYPE_UINT32) : - destinationLength = 4; + // all other CIGAR chars do not affect end position + default : 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; + + // adjust for closedInterval, if requested + if ( closedInterval ) + alignEnd -= 1; + + // return result + return alignEnd; } -/*! \fn bool BamAlignment::GetTag(const std::string& tag, int32_t& destination) const - \brief Retrieves the signed integer value associated with a BAM tag. +/*! \fn std::string BamAlignment::GetErrorString(void) const + \brief Returns a human-readable description of the last error that occurred - \param tag 2-character tag name - \param destination destination for retrieved value + This method allows elimination of STDERR pollution. Developers of client code + may choose how the messages are displayed to the user, if at all. - \return \c true if found + \return error description */ -bool BamAlignment::GetTag(const std::string& tag, int32_t& destination) const { - return GetTag(tag, (uint32_t&)destination); +std::string BamAlignment::GetErrorString(void) const { + return ErrorString; } -/*! \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::GetSoftClips(std::vector& clipSizes, std::vector& readPositions, std::vector& genomePositions, bool usePadded = false) const + \brief Identifies if an alignment has a soft clip. If so, identifies the + sizes of the soft clips, as well as their positions in the read and reference. - \param tag 2-character tag name - \param destination destination for retrieved value + \param[out] clipSizes vector of the sizes of each soft clip in the alignment + \param[out] readPositions vector of the 0-based read locations of each soft clip in the alignment. + These positions are basically indexes within the read, not genomic positions. + \param[out] genomePositions vector of the 0-based genome locations of each soft clip in the alignment + \param[in] usePadded inserted bases affect reported position. Default is false, so that + reported position stays 'sync-ed' with reference coordinates. - \return \c true if found + \return \c true if any soft clips were found in the alignment */ -bool BamAlignment::GetTag(const std::string& tag, float& destination) const { - - // make sure tag data exists - if ( SupportData.HasCoreOnly || TagData.empty() ) - return false; +bool BamAlignment::GetSoftClips(vector& clipSizes, + vector& readPositions, + vector& genomePositions, + bool usePadded) const +{ + // initialize positions & flags + int refPosition = Position; + int readPosition = 0; + bool softClipFound = false; + bool firstCigarOp = true; - // 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; + // iterate over cigar operations + vector::const_iterator cigarIter = CigarData.begin(); + vector::const_iterator cigarEnd = CigarData.end(); + for ( ; cigarIter != cigarEnd; ++cigarIter) { + const CigarOp& op = (*cigarIter); + + switch ( op.Type ) { + + // increase both read & genome positions on CIGAR chars [DMXN=] + case Constants::BAM_CIGAR_DEL_CHAR : + case Constants::BAM_CIGAR_MATCH_CHAR : + case Constants::BAM_CIGAR_MISMATCH_CHAR : + case Constants::BAM_CIGAR_REFSKIP_CHAR : + case Constants::BAM_CIGAR_SEQMATCH_CHAR : + refPosition += op.Length; + readPosition += op.Length; break; - // 2 byte data - case (Constants::BAM_TAG_TYPE_INT16) : - case (Constants::BAM_TAG_TYPE_UINT16) : - destinationLength = 2; + // increase read position on insertion, genome position only if @usePadded is true + case Constants::BAM_CIGAR_INS_CHAR : + readPosition += op.Length; + if ( usePadded ) + refPosition += op.Length; break; - // 4 byte data - case (Constants::BAM_TAG_TYPE_FLOAT) : - case (Constants::BAM_TAG_TYPE_INT32) : - case (Constants::BAM_TAG_TYPE_UINT32) : - destinationLength = 4; + case Constants::BAM_CIGAR_SOFTCLIP_CHAR : + + softClipFound = true; + + ////////////////////////////////////////////////////////////////////////////// + // if we are dealing with the *first* CIGAR operation + // for this alignment, we increment the read position so that + // the read and genome position of the clip are referring to the same base. + // For example, in the alignment below, the ref position would be 4, yet + // the read position would be 0. Thus, to "sync" the two, + // we need to increment the read position by the length of the + // soft clip. + // Read: ATCGTTTCGTCCCTGC + // Ref: GGGATTTCGTCCCTGC + // Cigar: SSSSMMMMMMMMMMMM + // + // NOTE: This only needs to be done if the soft clip is the _first_ CIGAR op. + ////////////////////////////////////////////////////////////////////////////// + if ( firstCigarOp ) + readPosition += op.Length; + + // track the soft clip's size, read position, and genome position + clipSizes.push_back(op.Length); + readPositions.push_back(readPosition); + genomePositions.push_back(refPosition); + + // any other CIGAR operations have no effect + default : 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); + // clear our "first pass" flag + firstCigarOp = false; } - // return success - return false; + // return whether any soft clips found + return softClipFound; } -/*! \fn bool BamAlignment::GetTag(const std::string& tag, std::vector& destination) const - \brief Retrieves the numeric array data 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 data + \param[in] tag 2-character tag name + \param[out] type retrieved (1-character) type-code \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, 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; +bool BamAlignment::GetTagType(const std::string& tag, char& type) const { + + // skip if alignment is core-only + if ( SupportData.HasCoreOnly ) { + // TODO: set error string? 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() ) + // skip if no tags present + if ( TagData.empty() ) { + // TODO: set error string? 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; + + // if tag not found, return failure + if ( !FindTag(tag, pTagData, tagDataLength, numBytesParsed) ){ + // TODO: set error string? 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; + const string message = string("invalid tag type: ") + type; + SetErrorString("BamAlignment::GetTagType", message); 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 \brief Returns true if alignment has a record for requested tag. - \param tag 2-character tag name + + \param[in] tag 2-character tag name \return \c true if alignment has a record for tag */ bool BamAlignment::HasTag(const std::string& tag) const { @@ -2143,33 +687,34 @@ bool BamAlignment::IsSecondMate(void) const { return ( (AlignmentFlag & Constants::BAM_ALIGNMENT_READ_2) != 0 ); } -/*! \fn bool BamAlignment::IsValidSize(const string& tag, const string& type) const +/*! \fn bool BamAlignment::IsValidSize(const std::string& tag, const std::string& type) const \internal Checks that tag name & type strings are expected sizes. - \a tag should have length - \a type should have length 1 - - \param tag BAM tag name - \param type BAM tag type-code - \return \c true if both \a tag and \a type are correct sizes + \param tag[in] BAM tag name + \param type[in] BAM tag type-code + \return \c true if both input strings are valid sizes */ -bool BamAlignment::IsValidSize(const string& tag, const string& type) const { +bool BamAlignment::IsValidSize(const std::string& tag, const std::string& type) const { return (tag.size() == Constants::BAM_TAG_TAGSIZE) && (type.size() == Constants::BAM_TAG_TYPESIZE); } -/*! \fn bool BamAlignment::RemoveTag(const std::string& tag) +/*! \fn void BamAlignment::RemoveTag(const std::string& tag) \brief Removes field from BAM tags. - \return \c true if tag was removed successfully (or didn't exist before) + \param[in] tag 2-character name of field to remove */ -bool BamAlignment::RemoveTag(const std::string& tag) { +void BamAlignment::RemoveTag(const std::string& tag) { - // skip if no tag data available - if ( SupportData.HasCoreOnly || TagData.empty() ) - return false; + // if char data not populated, do that first + if ( SupportData.HasCoreOnly ) + BuildCharData(); + + // skip if no tags available + if ( TagData.empty() ) + return; // localize the tag data char* pOriginalTagData = (char*)TagData.data(); @@ -2177,41 +722,48 @@ 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 + + // skip if tag not found + if ( !FindTag(tag, pTagData, originalTagDataLength, numBytesParsed) ) + return; + + // otherwise, remove it + RaiiBuffer newTagData(originalTagDataLength); + + // copy original tag data up til desired tag + pTagData -= 3; + numBytesParsed -= 3; + const unsigned int beginningTagDataLength = numBytesParsed; + newTagDataLength += beginningTagDataLength; + memcpy(newTagData.Buffer, 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); + memcpy(newTagData.Buffer + beginningTagDataLength, pTagData, endTagDataLength ); - delete[] newTagData; - - return true; + // save modified tag data in alignment + TagData.assign(newTagData.Buffer, beginningTagDataLength + endTagDataLength); } - - // tag not found, no removal - return failure - return false; +} + +/*! \fn void BamAlignment::SetErrorString(const std::string& where, const std::string& what) const + \internal + + Sets a formatted error string for this alignment. + + \param[in] where class/method where error occurred + \param[in] what description of error +*/ +void BamAlignment::SetErrorString(const std::string& where, const std::string& what) const { + static const string SEPARATOR = ": "; + ErrorString = where + SEPARATOR + what; } /*! \fn void BamAlignment::SetIsDuplicate(bool ok) @@ -2254,15 +806,6 @@ void BamAlignment::SetIsMateMapped(bool ok) { else AlignmentFlag |= Constants::BAM_ALIGNMENT_MATE_UNMAPPED; } -/*! \fn void BamAlignment::SetIsMateUnmapped(bool ok) - \brief Complement of using SetIsMateMapped(). - \deprecated For sake of symmetry with the query methods - \sa IsMateMapped(), SetIsMateMapped() -*/ -void BamAlignment::SetIsMateUnmapped(bool ok) { - SetIsMateMapped(!ok); -} - /*! \fn void BamAlignment::SetIsMateReverseStrand(bool ok) \brief Sets "alignment's mate mapped to reverse strand" flag to \a ok. */ @@ -2303,15 +846,6 @@ void BamAlignment::SetIsReverseStrand(bool ok) { else AlignmentFlag &= ~Constants::BAM_ALIGNMENT_REVERSE_STRAND; } -/*! \fn void BamAlignment::SetIsSecondaryAlignment(bool ok) - \brief Complement of using SetIsPrimaryAlignment(). - \deprecated For sake of symmetry with the query methods - \sa IsPrimaryAlignment(), SetIsPrimaryAlignment() -*/ -void BamAlignment::SetIsSecondaryAlignment(bool ok) { - SetIsPrimaryAlignment(!ok); -} - /*! \fn void BamAlignment::SetIsSecondMate(bool ok) \brief Sets "alignment is second mate on read" flag to \a ok. */ @@ -2320,26 +854,18 @@ void BamAlignment::SetIsSecondMate(bool ok) { else AlignmentFlag &= ~Constants::BAM_ALIGNMENT_READ_2; } -/*! \fn void BamAlignment::SetIsUnmapped(bool ok) - \brief Complement of using SetIsMapped(). - \deprecated For sake of symmetry with the query methods - \sa IsMapped(), SetIsMapped() -*/ -void BamAlignment::SetIsUnmapped(bool ok) { - SetIsMapped(!ok); -} - -/*! \fn bool BamAlignment::SkipToNextTag(const char storageType, char*& pTagData, unsigned int& numBytesParsed) +/*! \fn bool BamAlignment::SkipToNextTag(const char storageType, char*& pTagData, unsigned int& numBytesParsed) const \internal Moves to next available tag in tag data string - \param storageType BAM tag type-code that determines how far to move cursor - \param pTagData pointer to current position (cursor) in tag string - \param numBytesParsed report of how many bytes were parsed (cumulatively) + \param[in] storageType BAM tag type-code that determines how far to move cursor + \param[in,out] pTagData pointer to current position (cursor) in tag string + \param[in,out] numBytesParsed report of how many bytes were parsed (cumulatively) \return \c if storageType was a recognized BAM tag type - \post \a pTagData will point to the byte where the next tag data begins. + + \post \a pTagData will point to the byte where the next tag data begins. \a numBytesParsed will correspond to the cursor's position in the full TagData string. */ bool BamAlignment::SkipToNextTag(const char storageType, @@ -2389,7 +915,7 @@ bool BamAlignment::SkipToNextTag(const char storageType, // read number of elements int32_t numElements; - memcpy(&numElements, pTagData, sizeof(uint32_t)); // already endian-swapped if necessary + memcpy(&numElements, pTagData, sizeof(uint32_t)); // already endian-swapped, if needed numBytesParsed += sizeof(uint32_t); pTagData += sizeof(uint32_t); @@ -2410,8 +936,8 @@ bool BamAlignment::SkipToNextTag(const char storageType, bytesToSkip = numElements*sizeof(uint32_t); break; default: - cerr << "BamAlignment ERROR: unknown binary array type encountered: " - << arrayType << endl; + const string message = string("invalid binary array type: ") + arrayType; + SetErrorString("BamAlignment::SkipToNextTag", message); return false; } @@ -2422,11 +948,11 @@ bool BamAlignment::SkipToNextTag(const char storageType, } default: - cerr << "BamAlignment ERROR: unknown tag type encountered" - << storageType << endl; + const string message = string("invalid tag type: ") + storageType; + SetErrorString("BamAlignment::SkipToNextTag", message); return false; } - // return success + // if we get here, tag skipped OK - return success return true; }