// BamAlignment.h (c) 2009 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 4 October 2011 (DB)
+// Last modified: 7 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>
public:
// 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);
+ 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);
+ 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;
+ 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)
// legacy methods (consider deprecated, but still available)
bool GetEditDistance(uint32_t& editDistance) const; // retrieves value of "NM" tag
bool GetReadGroup(std::string& readGroup) const; // retrieves value of "RG" tag
-
+
// returns true if alignment has a record for this tag name
bool HasTag(const std::string& tag) const;
// removes a tag
- bool RemoveTag(const std::string& tag);
+ void RemoveTag(const std::string& tag);
// additional methods
public:
// calculates alignment end position
int GetEndPosition(bool usePadded = false, bool zeroBased = true) const;
+ // returns a description of the last error that occurred
+ std::string GetErrorString(void) const;
+
// public data fields
public:
std::string Name; // read name
//! \cond
// internal utility methods
private:
- 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,
+ 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;
+ void SetErrorString(const std::string& where,
+ const std::string& what) const;
+ bool SkipToNextTag(const char storageType,
char*& pTagData,
- unsigned int& numBytesParsed);
+ unsigned int& numBytesParsed) const;
// internal data
private:
BamAlignmentSupportData SupportData;
friend class Internal::BamReaderPrivate;
friend class Internal::BamWriterPrivate;
+
+ mutable std::string ErrorString; // mutable to allow updates even in logically const methods
//! \endcond
};
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)) )
+ // check tag/type size
+ if ( !IsValidSize(tag, type) ) {
+ // TODO: set error string?
+ return false;
+ }
+
+ // check that storage type code is OK for T
+ if ( !TagTypeHelper<T>::CanConvertTo(type.at(0)) ) {
+ // TODO: set error string?
return false;
+ }
// localize the tag data
char* pTagData = (char*)TagData.data();
// if tag already exists, return false
// use EditTag explicitly instead
- if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) )
+ if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {
+ // TODO: set error string?
return false;
+ }
// otherwise, convert value to string
union { T value; char valueBuffer[sizeof(T)]; } un;
// 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
+ const size_t newTagDataLength = tagDataLength + newTag.size() + sizeof(T); // leave room for new T
+ RaiiBuffer originalTagData(newTagDataLength);
+ memcpy(originalTagData.Buffer, 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));
+ strcat(originalTagData.Buffer + tagDataLength, newTag.data());
+ memcpy(originalTagData.Buffer + tagDataLength + newTag.size(), un.valueBuffer, sizeof(T));
// store temp buffer back in TagData
- const char* newTagData = (const char*)originalTagData;
+ const char* newTagData = (const char*)originalTagData.Buffer;
TagData.assign(newTagData, newTagDataLength);
-
- // clean up & return success
- delete[] originalTagData;
return true;
}
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)) )
+ // check tag/type size
+ if ( !IsValidSize(tag, type) ) {
+ // TODO: set error string?
+ return false;
+ }
+
+ // check that storage type code is OK for string
+ if ( !TagTypeHelper<std::string>::CanConvertTo(type.at(0)) ) {
+ // TODO: set error string?
return false;
+ }
// localize the tag data
char* pTagData = (char*)TagData.data();
// if tag already exists, return false
// use EditTag explicitly instead
- if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) )
+ if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {
+ // TODO: set error string?
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
+ const size_t newTagDataLength = tagDataLength + newTag.size() + 1; // leave room for null-term
+ RaiiBuffer originalTagData(newTagDataLength);
+ memcpy(originalTagData.Buffer, 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
+ // append newTag (removes original null-term, then appends newTag + null-term)
+ strcat(originalTagData.Buffer + tagDataLength, newTag.data());
// store temp buffer back in TagData
- const char* newTagData = (const char*)originalTagData;
+ const char* newTagData = (const char*)originalTagData.Buffer;
TagData.assign(newTagData, newTagDataLength);
-
- // clean up & return success
- delete[] originalTagData;
return true;
}
// if tag already exists, return false
// use EditTag explicitly instead
- if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) )
+ if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {
+ // TODO: set error string?
return false;
+ }
// build new tag's base information
char newTagBase[Constants::BAM_TAG_ARRAYBASE_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
+ const size_t newTagDataLength = tagDataLength +
+ Constants::BAM_TAG_ARRAYBASE_SIZE +
+ numElements*sizeof(T);
+ RaiiBuffer originalTagData(newTagDataLength);
+ memcpy(originalTagData.Buffer, TagData.c_str(), tagDataLength+1); // '+1' for TagData's null-term
// write newTagBase (removes old null term)
- strcat(originalTagData + tagDataLength, (const char*)newTagBase);
+ strcat(originalTagData.Buffer + 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));
+ memcpy(originalTagData.Buffer + elementsBeginOffset + i*sizeof(T), &value, sizeof(T));
}
// store temp buffer back in TagData
- const char* newTagData = (const char*)originalTagData;
+ const char* newTagData = (const char*)originalTagData.Buffer;
TagData.assign(newTagData, newTagDataLength);
-
- // cleanup & return success
- delete[] originalTagData;
return true;
}
inline bool BamAlignment::GetTag(const std::string& tag,
T& destination) const
{
- // skip if core-only or no tags present
- if ( SupportData.HasCoreOnly || TagData.empty() )
+ // skip if alignment is core-only
+ if ( SupportData.HasCoreOnly ) {
+ // TODO: set error string?
return false;
+ }
+
+ // skip if no tags present
+ if ( TagData.empty() ) {
+ // TODO: set error string?
+ return false;
+ }
// localize the tag data
char* pTagData = (char*)TagData.data();
unsigned int numBytesParsed = 0;
// return failure if tag not found
- if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) )
+ if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {
+ // TODO: set error string?
return false;
+ }
- // otherwise try to copy data into destination
+ // fetch data type
const char type = *(pTagData - 1);
- if ( !TagTypeHelper<T>::CanConvertFrom(type) )
+ if ( !TagTypeHelper<T>::CanConvertFrom(type) ) {
+ // TODO: set error string ?
return false;
+ }
+
+ // determine data length
int destinationLength = 0;
switch ( type ) {
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;
+ SetErrorString("BamAlignment::GetTag",
+ "cannot store variable length tag data into a numeric destination");
return false;
// unrecognized tag type
default:
- std::cerr << "BamAlignment ERROR: unknown tag type encountered: "
- << type << std::endl;
+ const std::string message = std::string("invalid tag type: ") + type;
+ SetErrorString("BamAlignment::GetTag", message);
return false;
}
- // store in destination
+ // store data in destination
destination = 0;
memcpy(&destination, pTagData, destinationLength);
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() )
+ // skip if alignment is core-only
+ if ( SupportData.HasCoreOnly ) {
+ // TODO: set error string?
return false;
+ }
+
+ // skip if no tags present
+ if ( TagData.empty() ) {
+ // TODO: set error string?
+ return false;
+ }
// localize the tag data
char* pTagData = (char*)TagData.data();
unsigned int numBytesParsed = 0;
// return failure if tag not found
- if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) )
+ if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {
+ // TODO: set error string?
return false;
+ }
// otherwise copy data into destination
const unsigned int dataLength = strlen(pTagData);
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() )
+ // skip if alignment is core-only
+ if ( SupportData.HasCoreOnly ) {
+ // TODO: set error string?
return false;
+ }
+
+ // skip if no tags present
+ if ( TagData.empty() ) {
+ // TODO: set error string?
+ return false;
+ }
// localize the tag data
char* pTagData = (char*)TagData.data();
unsigned int numBytesParsed = 0;
// return false if tag not found
- if ( !FindTag(tag, pTagData, tagDataLength, numBytesParsed) )
+ if ( !FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {
+ // TODO: set error string?
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;
+ SetErrorString("BamAlignment::GetTag", "cannot store a non-array tag in array destination");
return false;
}
- // calculate length of each element in tag's array
+ // fetch element type
const char elementType = *pTagData;
- if ( !TagTypeHelper<T>::CanConvertFrom(elementType) )
+ if ( !TagTypeHelper<T>::CanConvertFrom(elementType) ) {
+ // TODO: set error string ?
return false;
+ }
++pTagData;
+
+ // calculate length of each element in tag's array
int elementLength = 0;
switch ( elementType ) {
case (Constants::BAM_TAG_TYPE_ASCII) :
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;
+ SetErrorString("BamAlignment::GetTag",
+ "invalid array data, variable-length elements are not allowed");
return false;
// unknown tag type
default:
- std::cerr << "BamAlignment ERROR: unknown element type encountered: "
- << elementType << std::endl;
+ const std::string message = std::string("invalid array element type: ") + elementType;
+ SetErrorString("BamAlignment::GetTag", message);
return false;
}
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