// BamAlignment.cpp (c) 2009 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 22 April 2011 (DB)
+// Last modified: 4 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides the BamAlignment data structure
// ***************************************************************************
*/
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<uint8_t>& 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<uint8_t>& 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<int8_t>& 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<int8_t>& 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<uint16_t>& 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<uint16_t>& 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<int16_t>& 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<int16_t>& 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<uint32_t>& 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<uint32_t>& 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<int32_t>& 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<int32_t>& 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<float>& 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<float>& 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<uint8_t>& 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).
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<uint8_t>& 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<uint8_t>& 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<int8_t>& 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<int8_t>& 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<uint16_t>& 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<uint16_t>& 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<int16_t>& 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<int16_t>& 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<uint32_t>& 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<uint32_t>& 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<int32_t>& 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<int32_t>& 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<float>& 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<float>& 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<uint8_t>& 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
bool BamAlignment::FindTag(const std::string& tag,
char*& pTagData,
const unsigned int& tagDataLength,
- unsigned int& numBytesParsed) const
+ unsigned int& numBytesParsed)
{
while ( numBytesParsed < tagDataLength ) {
\return \c true if found
*/
+
+// TODO : REMOVE THIS METHOD
bool BamAlignment::GetEditDistance(uint32_t& editDistance) const {
return GetTag("NM", (uint32_t&)editDistance);
}
\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<uint32_t>& 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() )
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<uint32_t>& 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<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;
-
- // 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<int32_t>& 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<int32_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;
-
- // 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<float>& 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<float>& 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
\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);
}
*/
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
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)
*/
bool BamAlignment::SkipToNextTag(const char storageType,
char*& pTagData,
- unsigned int& numBytesParsed) const
+ unsigned int& numBytesParsed)
{
switch (storageType) {
// BamAlignment.h (c) 2009 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 22 April 2011 (DB)
+// Last modified: 4 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides the BamAlignment data structure
// ***************************************************************************
#include <api/api_global.h>
#include <api/BamAux.h>
+#include <api/BamConstants.h>
+#include <cctype>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <iostream>
#include <string>
#include <vector>
// tag data access methods
public:
- // -------------------------------------------------------------------------------------
- // N.B. - The following tag access methods may not be used on BamAlignments fetched
- // using BamReader::GetNextAlignmentCore(). Attempting to use them will not result in
- // error message (to keep output clean) but will ALWAYS return false. Only user-created
- // BamAlignments or those retrieved using BamReader::GetNextAlignment() are valid here.
- //
- // You can call BuildCharData() on such an alignment retrieved by GetNextAlignmentCore().
- // This populates all the character data, and will enable subsequent queries on tag data.
- // -------------------------------------------------------------------------------------
-
- // adds a tag
- bool AddTag(const std::string& tag, const std::string& type, const std::string& value);
- bool AddTag(const std::string& tag, const std::string& type, const uint32_t& value);
- bool AddTag(const std::string& tag, const std::string& type, const int32_t& value);
- bool AddTag(const std::string& tag, const std::string& type, const float& value);
-
- // adds a "binary array" tag
- bool AddTag(const std::string& tag, const std::vector<uint8_t>& values);
- bool AddTag(const std::string& tag, const std::vector<int8_t>& values);
- bool AddTag(const std::string& tag, const std::vector<uint16_t>& values);
- bool AddTag(const std::string& tag, const std::vector<int16_t>& values);
- bool AddTag(const std::string& tag, const std::vector<uint32_t>& values);
- bool AddTag(const std::string& tag, const std::vector<int32_t>& values);
- bool AddTag(const std::string& tag, const std::vector<float>& values);
-
- // edits a tag
- bool EditTag(const std::string& tag, const std::string& type, const std::string& value);
- bool EditTag(const std::string& tag, const std::string& type, const uint32_t& value);
- bool EditTag(const std::string& tag, const std::string& type, const int32_t& value);
- bool EditTag(const std::string& tag, const std::string& type, const float& value);
-
- // edits a "binary array" tag
- bool EditTag(const std::string& tag, const std::vector<uint8_t>& values);
- bool EditTag(const std::string& tag, const std::vector<int8_t>& values);
- bool EditTag(const std::string& tag, const std::vector<uint16_t>& values);
- bool EditTag(const std::string& tag, const std::vector<int16_t>& values);
- bool EditTag(const std::string& tag, const std::vector<uint32_t>& values);
- bool EditTag(const std::string& tag, const std::vector<int32_t>& values);
- bool EditTag(const std::string& tag, const std::vector<float>& values);
-
- // retrieves data for a tag
- bool GetTag(const std::string& tag, std::string& destination) const;
- bool GetTag(const std::string& tag, uint32_t& destination) const;
- bool GetTag(const std::string& tag, int32_t& destination) const;
- bool GetTag(const std::string& tag, float& destination) const;
-
- // retrieves data for a "binary array" tag
- bool GetTag(const std::string& tag, std::vector<uint32_t>& destination) const;
- bool GetTag(const std::string& tag, std::vector<int32_t>& destination) const;
- bool GetTag(const std::string& tag, std::vector<float>& destination) const;
-
- // retrieves the BAM tag-type character for a tag
+ // add a new tag
+ template<typename T> bool AddTag(const std::string& tag,
+ const std::string& type,
+ const T& value);
+ template<typename T> bool AddTag(const std::string& tag,
+ const std::vector<T>& values);
+
+ // edit (or append) tag
+ template<typename T> bool EditTag(const std::string& tag,
+ const std::string& type,
+ const T& value);
+ template<typename T> bool EditTag(const std::string& tag,
+ const std::vector<T>& values);
+
+ // retrieves tag data
+ template<typename T> bool GetTag(const std::string& tag,
+ T& destination) const;
+ template<typename T> bool GetTag(const std::string& tag,
+ std::vector<T>& destination) const;
+
+ // retrieves the BAM type-code for requested tag
+ // (returns whether or not tag exists, and type-code is valid)
bool GetTagType(const std::string& tag, char& type) const;
// legacy methods (consider deprecated, but still available)
public:
// populates alignment string fields
bool BuildCharData(void);
+
// calculates alignment end position
int GetEndPosition(bool usePadded = false, bool zeroBased = true) const;
//! \cond
// internal utility methods
private:
- bool FindTag(const std::string& tag,
- char*& pTagData,
- const unsigned int& tagDataLength,
- unsigned int& numBytesParsed) const;
- bool IsValidSize(const std::string& tag,
- const std::string& type) const;
- bool SkipToNextTag(const char storageType,
+ static bool FindTag(const std::string& tag,
+ char*& pTagData,
+ const unsigned int& tagDataLength,
+ unsigned int& numBytesParsed);
+ static bool IsValidSize(const std::string& tag,
+ const std::string& type);
+ static bool SkipToNextTag(const char storageType,
char*& pTagData,
- unsigned int& numBytesParsed) const;
+ unsigned int& numBytesParsed);
// internal data
private:
//! \endcond
};
+// ---------------------------------------------------------
+// BamAlignment tag access methods
+
+template<typename T>
+inline bool BamAlignment::AddTag(const std::string& tag,
+ const std::string& type,
+ const T& value)
+{
+ // if char data not populated, do that first
+ if ( SupportData.HasCoreOnly )
+ BuildCharData();
+
+ // validate tag/type size & that storage type code is OK for T
+ if ( !IsValidSize(tag, type) ) return false;
+ if ( !TagTypeHelper<T>::CanConvertTo(type.at(0)) )
+ 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 { T value; char valueBuffer[sizeof(T)]; } un;
+ un.value = value;
+
+ // copy original tag data to temp buffer
+ const std::string newTag = tag + type;
+ const int newTagDataLength = tagDataLength + newTag.size() + sizeof(T); // leave room for new T
+ 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(T));
+
+ // store temp buffer back in TagData
+ const char* newTagData = (const char*)originalTagData;
+ TagData.assign(newTagData, newTagDataLength);
+
+ // clean up & return success
+ delete[] originalTagData;
+ return true;
+}
+
+template<>
+inline bool BamAlignment::AddTag<std::string>(const std::string& tag,
+ const std::string& type,
+ const std::string& value)
+{
+ // if char data not populated, do that first
+ if ( SupportData.HasCoreOnly )
+ BuildCharData();
+
+ // validate tag/type size & that storage type code is OK for string
+ if ( !IsValidSize(tag, type) ) return false;
+ if ( !TagTypeHelper<std::string>::CanConvertTo(type.at(0)) )
+ 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
+ const std::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);
+
+ // clean up & return success
+ delete[] originalTagData;
+ return true;
+}
+
+template<typename T>
+inline bool BamAlignment::AddTag(const std::string& tag,
+ const std::vector<T>& values)
+{
+ // if char data not populated, do that first
+ if ( SupportData.HasCoreOnly )
+ BuildCharData();
+
+ // check for valid tag name 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] = TagTypeHelper<T>::TypeCode();
+
+ // 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(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 T& value = values.at(i);
+ memcpy(originalTagData + elementsBeginOffset + i*sizeof(T), &value, sizeof(T));
+ }
+
+ // store temp buffer back in TagData
+ const char* newTagData = (const char*)originalTagData;
+ TagData.assign(newTagData, newTagDataLength);
+
+ // cleanup & return success
+ delete[] originalTagData;
+ return true;
+}
+
+template<typename T>
+inline bool BamAlignment::EditTag(const std::string& tag,
+ const std::string& type,
+ const T& value)
+{
+ // if char data not populated, do that first
+ if ( SupportData.HasCoreOnly )
+ BuildCharData();
+
+ // remove existing tag if present, then append tag with new value
+ if ( HasTag(tag) )
+ RemoveTag(tag);
+ return AddTag(tag, type, value);
+}
+
+template<typename T>
+inline bool BamAlignment::EditTag(const std::string& tag,
+ const std::vector<T>& values)
+{
+ // if char data not populated, do that first
+ if ( SupportData.HasCoreOnly )
+ BuildCharData();
+
+ // remove existing tag if present, then append tag with new values
+ if ( HasTag(tag) )
+ RemoveTag(tag);
+ return AddTag(tag, values);
+}
+
+template<typename T>
+inline bool BamAlignment::GetTag(const std::string& tag,
+ T& destination) const
+{
+ // skip if core-only or no tags present
+ 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 failure if tag not found
+ if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) )
+ return false;
+
+ // otherwise try to copy data into destination
+ const char type = *(pTagData - 1);
+ if ( !TagTypeHelper<T>::CanConvertFrom(type) )
+ return false;
+ 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) :
+ case (Constants::BAM_TAG_TYPE_FLOAT) :
+ destinationLength = 4;
+ break;
+
+ // var-length types not supported for numeric destination
+ case (Constants::BAM_TAG_TYPE_STRING) :
+ case (Constants::BAM_TAG_TYPE_HEX) :
+ case (Constants::BAM_TAG_TYPE_ARRAY) :
+ std::cerr << "BamAlignment ERROR: cannot store tag of type " << type
+ << " in integer destination" << std::endl;
+ return false;
+
+ // unrecognized tag type
+ default:
+ std::cerr << "BamAlignment ERROR: unknown tag type encountered: "
+ << type << std::endl;
+ return false;
+ }
+
+ // store in destination
+ destination = 0;
+ memcpy(&destination, pTagData, destinationLength);
+
+ // return success
+ return true;
+}
+
+template<>
+inline bool BamAlignment::GetTag<std::string>(const std::string& tag,
+ std::string& destination) const
+{
+ // skip if core-only or no tags present
+ 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 failure if tag not found
+ if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) )
+ return false;
+
+ // otherwise copy data into destination
+ const unsigned int dataLength = strlen(pTagData);
+ destination.clear();
+ destination.resize(dataLength);
+ memcpy( (char*)destination.data(), pTagData, dataLength );
+
+ // return success
+ return true;
+}
+
+// retrieves "binary-array" tag data
+template<typename T>
+inline bool BamAlignment::GetTag(const std::string& tag,
+ std::vector<T>& destination) const
+{
+ // skip if core-only or no tags present
+ 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 ) {
+ std::cerr << "BamAlignment ERROR: Cannot store non-array data from tag: "
+ << tag << " in array destination" << std::endl;
+ return false;
+ }
+
+ // calculate length of each element in tag's array
+ const char elementType = *pTagData;
+ if ( !TagTypeHelper<T>::CanConvertFrom(elementType) )
+ return false;
+ ++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) :
+ case (Constants::BAM_TAG_TYPE_FLOAT) :
+ elementLength = sizeof(uint32_t);
+ break;
+
+ // var-length types not supported for numeric destination
+ case (Constants::BAM_TAG_TYPE_STRING) :
+ case (Constants::BAM_TAG_TYPE_HEX) :
+ case (Constants::BAM_TAG_TYPE_ARRAY) :
+ std::cerr << "BamAlignment ERROR: array element type: " << elementType
+ << " cannot be stored in integer value" << std::endl;
+ return false;
+
+ // unknown tag type
+ default:
+ std::cerr << "BamAlignment ERROR: unknown element type encountered: "
+ << elementType << std::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
+ T value;
+ for ( int i = 0 ; i < numElements; ++i ) {
+ memcpy(&value, pTagData, sizeof(T));
+ pTagData += sizeof(T);
+ destination.push_back(value);
+ }
+
+ // return success
+ return true;
+}
+
typedef std::vector<BamAlignment> BamAlignmentVector;
} // namespace BamTools
projects / bamtools.git / commitdiff