// ***************************************************************************
// BamAlignment.cpp (c) 2009 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 21 March 2011 (DB)
+// Last modified: 22 April 2011 (DB)
// ---------------------------------------------------------------------------
// Provides the BamAlignment data structure
// ***************************************************************************
#include <cstdlib>
#include <cstring>
#include <exception>
+#include <iostream>
#include <map>
#include <utility>
using namespace std;
-// internal utility methods
-namespace BamTools {
-namespace Internal {
-
-/*! \fn bool IsValidSize(const string& tag, const string& type)
- \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
-*/
-bool IsValidSize(const string& tag, const string& type) {
- return (tag.size() == Constants::BAM_TAG_TAGSIZE) &&
- (type.size() == Constants::BAM_TAG_TYPESIZE);
-}
-
-/*! \fn bool SkipToNextTag(const char storageType, char* &pTagData, unsigned int& numBytesParsed)
- \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)
-
- \return \c if storageType was a recognized BAM tag type
- \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 SkipToNextTag(const char storageType, char* &pTagData, unsigned int& numBytesParsed) {
-
- switch (storageType) {
-
- case (Constants::BAM_TAG_TYPE_ASCII) :
- case (Constants::BAM_TAG_TYPE_INT8) :
- case (Constants::BAM_TAG_TYPE_UINT8) :
- ++numBytesParsed;
- ++pTagData;
- break;
-
- case (Constants::BAM_TAG_TYPE_INT16) :
- case (Constants::BAM_TAG_TYPE_UINT16) :
- numBytesParsed += 2;
- pTagData += 2;
- break;
-
- case (Constants::BAM_TAG_TYPE_FLOAT) :
- case (Constants::BAM_TAG_TYPE_INT32) :
- case (Constants::BAM_TAG_TYPE_UINT32) :
- numBytesParsed += 4;
- pTagData += 4;
- break;
-
- case (Constants::BAM_TAG_TYPE_STRING) :
- case (Constants::BAM_TAG_TYPE_HEX) :
- while(*pTagData) {
- ++numBytesParsed;
- ++pTagData;
- }
- // increment for null-terminator
- ++numBytesParsed;
- ++pTagData;
- break;
-
- default:
- // error case
- fprintf(stderr, "BamAlignment ERROR: unknown tag type encountered: [%c]\n", storageType);
- return false;
- }
-
- // return success
- return true;
-}
-
-/*! \fn bool FindTag(const std::string& tag, char* &pTagData, const unsigned int& tagDataLength, unsigned int& numBytesParsed)
- \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
-
- \return \c true if found
-
- \post If \a tag is found, \a pTagData will point to the byte where the tag data begins.
- \a numBytesParsed will correspond to the position in the full TagData string.
-
-*/
-bool FindTag(const std::string& tag,
- char* &pTagData,
- const unsigned int& tagDataLength,
- unsigned int& numBytesParsed)
-{
-
- while ( numBytesParsed < tagDataLength ) {
-
- const char* pTagType = pTagData;
- const char* pTagStorageType = pTagData + 2;
- pTagData += 3;
- numBytesParsed += 3;
-
- // check the current tag, return true on match
- if ( strncmp(pTagType, tag.c_str(), 2) == 0 )
- return true;
-
- // get the storage class and find the next tag
- if ( *pTagStorageType == '\0' ) return false;
- if ( !SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed) ) return false;
- if ( *pTagData == '\0' ) return false;
- }
-
- // checked all tags, none match
- return false;
-}
-
-} // namespace Internal
-} // namespace BamTools
-
/*! \class BamTools::BamAlignment
\brief The main BAM alignment data structure.
\param value string data to store
\return \c true if the \b new tag was added successfully
-
- \sa http://samtools.sourceforge.net/SAM-1.3.pdf
- for more details on reserved tag names, supported tag types, etc.
+ \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) {
if ( SupportData.HasCoreOnly ) return false;
// validate tag/type size & that type is OK for string value
- if ( !Internal::IsValidSize(tag, type) ) return false;
+ 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_HEX
+ )
+ {
return false;
+ }
// localize the tag data
char* pTagData = (char*)TagData.data();
// if tag already exists, return false
// use EditTag explicitly instead
- if ( Internal::FindTag(tag, pTagData, tagDataLength, numBytesParsed) )
+ 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[newTagDataLength];
+ 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;
}
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", or "H")
+ \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 http://samtools.sourceforge.net/SAM-1.3.pdf
- for more details on reserved tag names, supported tag types, etc.
+ \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) {
if ( SupportData.HasCoreOnly ) return false;
// validate tag/type size & that type is OK for uint32_t value
- if ( !Internal::IsValidSize(tag, type) ) return false;
- if ( type.at(0) == Constants::BAM_TAG_TYPE_FLOAT ||
+ 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_HEX ||
+ type.at(0) == Constants::BAM_TAG_TYPE_ARRAY
+ )
+ {
return false;
+ }
// localize the tag data
char* pTagData = (char*)TagData.data();
// if tag already exists, return false
// use EditTag explicitly instead
- if ( Internal::FindTag(tag, pTagData, tagDataLength, numBytesParsed) )
+ if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) )
return false;
// otherwise, convert value to string
// 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[newTagDataLength];
+ char* originalTagData = new char[newTagDataLength];
memcpy(originalTagData, TagData.c_str(), tagDataLength + 1); // '+1' for TagData null-term
// append newTag
// store temp buffer back in TagData
const char* newTagData = (const char*)originalTagData;
TagData.assign(newTagData, newTagDataLength);
+ delete[] originalTagData;
// return success
return true;
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", or "H")
+ \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 http://samtools.sourceforge.net/SAM-1.3.pdf
- for more details on reserved tag names, supported tag types, etc.
+ \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);
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" or "H")
+ \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 http://samtools.sourceforge.net/SAM-1.3.pdf
- for more details on reserved tag names, supported tag types, etc.
+ \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) {
if ( SupportData.HasCoreOnly ) return false;
// validate tag/type size & that type is OK for float value
- if ( !Internal::IsValidSize(tag, type) ) return false;
+ 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_HEX ||
+ type.at(0) == Constants::BAM_TAG_TYPE_ARRAY
+ )
+ {
return false;
+ }
// localize the tag data
char* pTagData = (char*)TagData.data();
// if tag already exists, return false
// use EditTag explicitly instead
- if ( Internal::FindTag(tag, pTagData, tagDataLength, numBytesParsed) )
+ if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) )
return false;
// otherwise, convert value to string
// 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[newTagDataLength];
+ char* originalTagData = new char[newTagDataLength];
memcpy(originalTagData, TagData.c_str(), tagDataLength + 1); // '+1' for TagData null-term
// append newTag
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;
+
+ // 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;
}
switch (op.Type) {
- // for 'M', 'I' - write bases
- case (Constants::BAM_CIGAR_MATCH_CHAR) :
- case (Constants::BAM_CIGAR_INS_CHAR) :
+ // for 'M', 'I', '=', 'X' - write bases
+ case (Constants::BAM_CIGAR_MATCH_CHAR) :
+ case (Constants::BAM_CIGAR_INS_CHAR) :
+ case (Constants::BAM_CIGAR_SEQMATCH_CHAR) :
+ case (Constants::BAM_CIGAR_MISMATCH_CHAR) :
AlignedBases.append(QueryBases.substr(k, op.Length));
// fall through
// shouldn't get here
default:
- fprintf(stderr, "BamAlignment ERROR: invalid CIGAR operation type: %c\n", op.Type);
+ cerr << "BamAlignment ERROR: invalid CIGAR operation type: "
+ << op.Type << endl;
exit(1);
}
}
case(Constants::BAM_TAG_TYPE_ASCII) :
case(Constants::BAM_TAG_TYPE_INT8) :
case(Constants::BAM_TAG_TYPE_UINT8) :
+ // no endian swapping necessary for single-byte data
++i;
break;
case(Constants::BAM_TAG_TYPE_HEX) :
case(Constants::BAM_TAG_TYPE_STRING) :
// no endian swapping necessary for hex-string/string data
- while (tagData[i]) { ++i; }
+ while ( tagData[i] )
+ ++i;
// increment one more for null terminator
++i;
break;
+ case(Constants::BAM_TAG_TYPE_ARRAY) :
+
+ {
+ // read array type
+ const char arrayType = tagData[i];
+ ++i;
+
+ // swap endian-ness of number of elements in place, then retrieve for loop
+ BamTools::SwapEndian_32p(&tagData[i]);
+ int32_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 ) {
+ switch (arrayType) {
+ case (Constants::BAM_TAG_TYPE_INT8) :
+ case (Constants::BAM_TAG_TYPE_UINT8) :
+ // no endian-swapping necessary
+ ++i;
+ break;
+ case (Constants::BAM_TAG_TYPE_INT16) :
+ case (Constants::BAM_TAG_TYPE_UINT16) :
+ BamTools::SwapEndian_16p(&tagData[i]);
+ i += sizeof(uint16_t);
+ break;
+ case (Constants::BAM_TAG_TYPE_FLOAT) :
+ case (Constants::BAM_TAG_TYPE_INT32) :
+ case (Constants::BAM_TAG_TYPE_UINT32) :
+ BamTools::SwapEndian_32p(&tagData[i]);
+ i += sizeof(uint32_t);
+ break;
+ default:
+ // error case
+ cerr << "BamAlignment ERROR: unknown binary array type encountered: "
+ << arrayType << endl;
+ return false;
+ }
+ }
+
+ break;
+ }
+
// shouldn't get here
default :
- fprintf(stderr, "BamAlignment ERROR: invalid tag value type: %c\n", type);
+ cerr << "BamAlignment ERROR: invalid tag value type: "
+ << type << endl;
exit(1);
}
}
\return \c true if the tag was modified/created successfully
\sa BamAlignment::RemoveTag()
- \sa http://samtools.sourceforge.net/SAM-1.3.pdf
- for more details on reserved tag names, supported tag types, etc.
+ \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) {
if ( SupportData.HasCoreOnly ) return false;
// validate tag/type size & that type is OK for string value
- if ( !Internal::IsValidSize(tag, type) ) return false;
+ 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;
unsigned int newTagDataLength = 0;
unsigned int numBytesParsed = 0;
- // if tag found, store data in readGroup, return success
- if ( Internal::FindTag(tag, pTagData, originalTagDataLength, numBytesParsed) ) {
+ // if tag found
+ if ( FindTag(tag, pTagData, originalTagDataLength, numBytesParsed) ) {
// make sure array is more than big enough
- char newTagData[originalTagDataLength + value.size()];
+ 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
+ // 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 ( !Internal::SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed) )
+ if ( !SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed) )
return true;
// copy everything from current tag (the next one after tag for removal) to end
// save new tag data
TagData.assign(newTagData, endTagOffset + endTagDataLength);
+
+ delete[] newTagData;
+
return true;
}
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", or "H")
+ \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 http://samtools.sourceforge.net/SAM-1.3.pdf
- for more details on reserved tag names, supported tag types, etc.
+ \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) {
if ( SupportData.HasCoreOnly ) return false;
// validate tag/type size & that type is OK for uint32_t value
- if ( !Internal::IsValidSize(tag, type) ) return false;
- if ( type.at(0) == Constants::BAM_TAG_TYPE_FLOAT ||
+ 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_HEX ||
+ type.at(0) == Constants::BAM_TAG_TYPE_ARRAY
+ )
+ {
return false;
+ }
// localize the tag data
char* pOriginalTagData = (char*)TagData.data();
unsigned int newTagDataLength = 0;
unsigned int numBytesParsed = 0;
- // if tag found, store data in readGroup, return success
- if ( Internal::FindTag(tag, pTagData, originalTagDataLength, numBytesParsed) ) {
+ // if tag found
+ if ( FindTag(tag, pTagData, originalTagDataLength, numBytesParsed) ) {
// make sure array is more than big enough
- char newTagData[originalTagDataLength + sizeof(value)];
+ 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
+ // 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 ( !Internal::SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed) )
+ if ( !SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed) )
return true;
// copy everything from current tag (the next one after tag for removal) to end
// save new tag data
TagData.assign(newTagData, endTagOffset + endTagDataLength);
+
+ delete[] newTagData;
+
return true;
}
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", or "H")
+ \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 http://samtools.sourceforge.net/SAM-1.3.pdf
- for more details on reserved tag names, supported tag types, etc.
+ \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);
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" or "H")
+ \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 http://samtools.sourceforge.net/SAM-1.3.pdf
- for more details on reserved tag names, supported tag types, etc.
+ \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) {
if ( SupportData.HasCoreOnly ) return false;
// validate tag/type size & that type is OK for float value
- if ( !Internal::IsValidSize(tag, type) ) return false;
+ 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_HEX ||
+ type.at(0) == Constants::BAM_TAG_TYPE_ARRAY
+ )
+ {
return false;
+ }
// localize the tag data
char* pOriginalTagData = (char*)TagData.data();
unsigned int newTagDataLength = 0;
unsigned int numBytesParsed = 0;
- // if tag found, store data in readGroup, return success
- if ( Internal::FindTag(tag, pTagData, originalTagDataLength, numBytesParsed) ) {
+ // if tag found
+ if ( FindTag(tag, pTagData, originalTagDataLength, numBytesParsed) ) {
// make sure array is more than big enough
- char newTagData[originalTagDataLength + sizeof(value)];
+ 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
+ // 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 ( !Internal::SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed) )
+ if ( !SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed) )
return true;
// copy everything from current tag (the next one after tag for removal) to end
// save new tag data
TagData.assign(newTagData, endTagOffset + endTagDataLength);
+
+ delete[] newTagData;
+
return true;
}
-
- // tag not found, attempt AddTag
- else return AddTag(tag, type, value);
+
+ // 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;
+
+ // 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<float>& 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<float>& 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 BamAlignment::FindTag(const std::string& tag, char*& pTagData, const unsigned int& tagDataLength, unsigned int& numBytesParsed)
+ \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
+
+ \return \c true if found
+
+ \post If \a tag is found, \a pTagData will point to the byte where the tag data begins.
+ \a numBytesParsed will correspond to the position in the full TagData string.
+
+*/
+bool BamAlignment::FindTag(const std::string& tag,
+ char*& pTagData,
+ const unsigned int& tagDataLength,
+ unsigned int& numBytesParsed) const
+{
+
+ while ( numBytesParsed < tagDataLength ) {
+
+ const char* pTagType = pTagData;
+ const char* pTagStorageType = pTagData + 2;
+ pTagData += 3;
+ numBytesParsed += 3;
+
+ // check the current tag, return true on match
+ if ( strncmp(pTagType, tag.c_str(), 2) == 0 )
+ return true;
+
+ // get the storage class and find the next tag
+ if ( *pTagStorageType == '\0' ) return false;
+ if ( !SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed) ) return false;
+ if ( *pTagData == '\0' ) return false;
+ }
+
+ // checked all tags, none match
+ return false;
}
/*! \fn bool BamAlignment::GetEditDistance(uint32_t& editDistance) const
const unsigned int tagDataLength = TagData.size();
unsigned int numBytesParsed = 0;
- // if tag found, store data in readGroup, return success
- if ( Internal::FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {
+ // if tag found
+ if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {
const unsigned int dataLength = strlen(pTagData);
destination.clear();
destination.resize(dataLength);
const unsigned int tagDataLength = TagData.size();
unsigned int numBytesParsed = 0;
- // if tag found, determine data byte-length, store data in readGroup, return success
- if ( Internal::FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {
+ // if tag found
+ if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {
// determine data byte-length
const char type = *(pTagData - 1);
case (Constants::BAM_TAG_TYPE_FLOAT) :
case (Constants::BAM_TAG_TYPE_STRING) :
case (Constants::BAM_TAG_TYPE_HEX) :
- fprintf(stderr, "BamAlignment ERROR: cannot store tag of type %c in integer destination\n", type);
+ 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:
- fprintf(stderr, "BamAlignment ERROR: unknown tag type encountered: [%c]\n", type);
+ cerr << "BamAlignment ERROR: unknown tag type encountered: "
+ << type << endl;
return false;
}
const unsigned int tagDataLength = TagData.size();
unsigned int numBytesParsed = 0;
- // if tag found, determine data byte-length, store data in readGroup, return success
- if ( Internal::FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {
+ // if tag found
+ if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {
// determine data byte-length
const char type = *(pTagData - 1);
// unsupported type (var-length strings)
case (Constants::BAM_TAG_TYPE_STRING) :
case (Constants::BAM_TAG_TYPE_HEX) :
- fprintf(stderr, "BamAlignment ERROR: cannot store tag of type %c in float destination\n", type);
+ 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:
- fprintf(stderr, "BamAlignment ERROR: unknown tag type encountered: [%c]\n", type);
+ cerr << "BamAlignment ERROR: unknown tag type encountered: "
+ << type << endl;
return false;
}
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 ( !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) :
+ 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;
+
+ // 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
+ 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 type destination for the retrieved (1-character) tag type
\return \c true if found
-
- \sa http://samtools.sourceforge.net/SAM-1.3.pdf
- for more details on reserved tag names, supported tag types, etc.
+ \sa \samSpecURL for more details on reserved tag names, supported tag types, etc.
*/
bool BamAlignment::GetTagType(const std::string& tag, char& type) const {
unsigned int numBytesParsed = 0;
// lookup tag
- if ( Internal::FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {
+ if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {
// retrieve tag type code
type = *(pTagData - 1);
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:
- fprintf(stderr, "BamAlignment ERROR: unknown tag type encountered: [%c]\n", type);
+ cerr << "BamAlignment ERROR: unknown tag type encountered: "
+ << type << endl;
return false;
}
}
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
+ \return \c true if alignment has a record for tag
+*/
+bool BamAlignment::HasTag(const std::string& tag) const {
+
+ // return false if no tag data present
+ if ( SupportData.HasCoreOnly || TagData.empty() )
+ return false;
+
+ // localize the tag data for lookup
+ char* pTagData = (char*)TagData.data();
+ const unsigned int tagDataLength = TagData.size();
+ unsigned int numBytesParsed = 0;
+
+ // if result of tag lookup
+ return FindTag(tag, pTagData, tagDataLength, numBytesParsed);
+}
+
/*! \fn bool BamAlignment::IsDuplicate(void) const
\return \c true if this read is a PCR duplicate
*/
return ( (AlignmentFlag & Constants::BAM_ALIGNMENT_READ_2) != 0 );
}
+/*! \fn bool BamAlignment::IsValidSize(const string& tag, const 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
+*/
+bool BamAlignment::IsValidSize(const string& tag, const string& type) const {
+ return (tag.size() == Constants::BAM_TAG_TAGSIZE) &&
+ (type.size() == Constants::BAM_TAG_TYPESIZE);
+}
+
/*! \fn bool BamAlignment::RemoveTag(const std::string& tag)
\brief Removes field from BAM tags.
*/
bool BamAlignment::RemoveTag(const std::string& tag) {
- // BamAlignments fetched using BamReader::GetNextAlignmentCore() are not allowed
- // also, return false if no data present to remove
+ // skip if no tag data available
if ( SupportData.HasCoreOnly || TagData.empty() )
return false;
unsigned int newTagDataLength = 0;
unsigned int numBytesParsed = 0;
- // if tag found, store data in readGroup, return success
- if ( Internal::FindTag(tag, pTagData, originalTagDataLength, numBytesParsed) ) {
+ // if tag found
+ if ( FindTag(tag, pTagData, originalTagDataLength, numBytesParsed) ) {
- char newTagData[originalTagDataLength];
+ char* newTagData = new char[originalTagDataLength];
// copy original tag data up til desired tag
pTagData -= 3;
const char* pTagStorageType = pTagData + 2;
pTagData += 3;
numBytesParsed += 3;
- if ( !Internal::SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed) )
+ if ( !SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed) )
return true;
// copy everything from current tag (the next one after tag for removal) to end
// save new tag data
TagData.assign(newTagData, beginningTagDataLength + endTagDataLength);
+
+ delete[] newTagData;
+
return true;
}
void BamAlignment::SetIsUnmapped(bool ok) {
SetIsMapped(!ok);
}
+
+/*! \fn bool BamAlignment::SkipToNextTag(const char storageType, char*& pTagData, unsigned int& numBytesParsed)
+ \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)
+
+ \return \c if storageType was a recognized BAM tag type
+ \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,
+ char*& pTagData,
+ unsigned int& numBytesParsed) const
+{
+ switch (storageType) {
+
+ case (Constants::BAM_TAG_TYPE_ASCII) :
+ case (Constants::BAM_TAG_TYPE_INT8) :
+ case (Constants::BAM_TAG_TYPE_UINT8) :
+ ++numBytesParsed;
+ ++pTagData;
+ break;
+
+ case (Constants::BAM_TAG_TYPE_INT16) :
+ case (Constants::BAM_TAG_TYPE_UINT16) :
+ numBytesParsed += sizeof(uint16_t);
+ pTagData += sizeof(uint16_t);
+ break;
+
+ case (Constants::BAM_TAG_TYPE_FLOAT) :
+ case (Constants::BAM_TAG_TYPE_INT32) :
+ case (Constants::BAM_TAG_TYPE_UINT32) :
+ numBytesParsed += sizeof(uint32_t);
+ pTagData += sizeof(uint32_t);
+ break;
+
+ case (Constants::BAM_TAG_TYPE_STRING) :
+ case (Constants::BAM_TAG_TYPE_HEX) :
+ while( *pTagData ) {
+ ++numBytesParsed;
+ ++pTagData;
+ }
+ // increment for null-terminator
+ ++numBytesParsed;
+ ++pTagData;
+ break;
+
+ case (Constants::BAM_TAG_TYPE_ARRAY) :
+
+ {
+ // read array type
+ const char arrayType = *pTagData;
+ ++numBytesParsed;
+ ++pTagData;
+
+ // read number of elements
+ int32_t numElements;
+ memcpy(&numElements, pTagData, sizeof(uint32_t)); // already endian-swapped if necessary
+ numBytesParsed += sizeof(uint32_t);
+ pTagData += sizeof(uint32_t);
+
+ // calculate number of bytes to skip
+ int bytesToSkip = 0;
+ switch (arrayType) {
+ case (Constants::BAM_TAG_TYPE_INT8) :
+ case (Constants::BAM_TAG_TYPE_UINT8) :
+ bytesToSkip = numElements;
+ break;
+ case (Constants::BAM_TAG_TYPE_INT16) :
+ case (Constants::BAM_TAG_TYPE_UINT16) :
+ bytesToSkip = numElements*sizeof(uint16_t);
+ break;
+ case (Constants::BAM_TAG_TYPE_FLOAT) :
+ case (Constants::BAM_TAG_TYPE_INT32) :
+ case (Constants::BAM_TAG_TYPE_UINT32) :
+ bytesToSkip = numElements*sizeof(uint32_t);
+ break;
+ default:
+ cerr << "BamAlignment ERROR: unknown binary array type encountered: "
+ << arrayType << endl;
+ return false;
+ }
+
+ // skip binary array contents
+ numBytesParsed += bytesToSkip;
+ pTagData += bytesToSkip;
+ break;
+ }
+
+ default:
+ cerr << "BamAlignment ERROR: unknown tag type encountered"
+ << storageType << endl;
+ return false;
+ }
+
+ // return success
+ return true;
+}
projects / bamtools.git / blobdiff