// BamAlignment.cpp (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/BamAlignment.h>
#include <api/BamConstants.h>
using namespace BamTools;
-
-#include <cctype>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-#include <exception>
-#include <iostream>
-#include <map>
-#include <utility>
using namespace std;
/*! \class BamTools::BamAlignment
// calculate character lengths/offsets
const unsigned int dataLength = SupportData.BlockLength - Constants::BAM_CORE_SIZE;
- const unsigned int seqDataOffset = SupportData.QueryNameLength + (SupportData.NumCigarOperations * 4);
+ const unsigned int seqDataOffset = SupportData.QueryNameLength + (SupportData.NumCigarOperations*4);
const unsigned int qualDataOffset = seqDataOffset + (SupportData.QuerySequenceLength+1)/2;
const unsigned int tagDataOffset = qualDataOffset + SupportData.QuerySequenceLength;
const unsigned int tagDataLength = dataLength - tagDataOffset;
QueryBases.clear();
if ( hasSeqData ) {
QueryBases.reserve(SupportData.QuerySequenceLength);
- for (unsigned int i = 0; i < SupportData.QuerySequenceLength; ++i) {
- char singleBase = Constants::BAM_DNA_LOOKUP[ ( (seqData[(i/2)] >> (4*(1-(i%2)))) & 0xf ) ];
+ for ( size_t i = 0; i < SupportData.QuerySequenceLength; ++i ) {
+ const char singleBase = Constants::BAM_DNA_LOOKUP[ ( (seqData[(i/2)] >> (4*(1-(i%2)))) & 0xf ) ];
QueryBases.append(1, singleBase);
}
}
Qualities.clear();
if ( hasQualData ) {
Qualities.reserve(SupportData.QuerySequenceLength);
- for (unsigned int i = 0; i < SupportData.QuerySequenceLength; ++i) {
- char singleQuality = (char)(qualData[i]+33);
+ for ( size_t i = 0; i < SupportData.QuerySequenceLength; ++i ) {
+ const char singleQuality = static_cast<const char>(qualData[i]+33);
Qualities.append(1, singleQuality);
}
}
for ( ; cigarIter != cigarEnd; ++cigarIter ) {
const CigarOp& op = (*cigarIter);
- switch (op.Type) {
+ switch ( op.Type ) {
// for 'M', 'I', '=', 'X' - write bases
case (Constants::BAM_CIGAR_MATCH_CHAR) :
case (Constants::BAM_CIGAR_HARDCLIP_CHAR) :
break;
- // shouldn't get here
+ // invalid CIGAR op-code
default:
- cerr << "BamAlignment ERROR: invalid CIGAR operation type: "
- << op.Type << endl;
- exit(1);
+ const string message = string("invalid CIGAR operation type: ") + op.Type;
+ SetErrorString("BamAlignment::BuildCharData", message);
+ return false;
}
}
}
TagData.clear();
if ( hasTagData ) {
if ( IsBigEndian ) {
- int i = 0;
- while ( (unsigned int)i < tagDataLength ) {
+ size_t i = 0;
+ while ( i < tagDataLength ) {
i += Constants::BAM_TAG_TAGSIZE; // skip tag chars (e.g. "RG", "NM", etc.)
const char type = tagData[i]; // get tag type at position i
// swap endian-ness of number of elements in place, then retrieve for loop
BamTools::SwapEndian_32p(&tagData[i]);
- int32_t numElements;
+ uint32_t numElements;
memcpy(&numElements, &tagData[i], sizeof(uint32_t));
i += sizeof(uint32_t);
// swap endian-ness of array elements
- for ( int j = 0; j < numElements; ++j ) {
+ for ( size_t j = 0; j < numElements; ++j ) {
switch (arrayType) {
case (Constants::BAM_TAG_TYPE_INT8) :
case (Constants::BAM_TAG_TYPE_UINT8) :
i += sizeof(uint32_t);
break;
default:
- // error case
- cerr << "BamAlignment ERROR: unknown binary array type encountered: "
- << arrayType << endl;
+ const string message = string("invalid binary array type: ") + arrayType;
+ SetErrorString("BamAlignment::BuildCharData", message);
return false;
}
}
break;
}
- // shouldn't get here
+ // invalid tag type-code
default :
- cerr << "BamAlignment ERROR: invalid tag value type: "
- << type << endl;
- exit(1);
+ const string message = string("invalid tag type: ") + type;
+ SetErrorString("BamAlignment::BuildCharData", message);
+ return false;
}
}
}
// store tagData in alignment
TagData.resize(tagDataLength);
- memcpy((char*)TagData.data(), tagData, tagDataLength);
+ memcpy((char*)(TagData.data()), tagData, tagDataLength);
}
// clear the core-only flag
bool BamAlignment::FindTag(const std::string& tag,
char*& pTagData,
const unsigned int& tagDataLength,
- unsigned int& numBytesParsed)
+ unsigned int& numBytesParsed) const
{
while ( numBytesParsed < tagDataLength ) {
*/
int BamAlignment::GetEndPosition(bool usePadded, bool zeroBased) const {
+ // TODO: Come back to this for coordinate issues !!!
+
// initialize alignment end to starting position
int alignEnd = Position;
return alignEnd;
}
+/*! \fn std::string BamAlignment::GetErrorString(void) const
+ \brief Returns a description of the last error that occurred
+
+ This method allows elimnation of STDERR pollution. Developers of client code
+ may choose how the messages are displayed to the user, if at all.
+
+ \return description of last error that occurred
+*/
+std::string BamAlignment::GetErrorString(void) const {
+ return ErrorString;
+}
+
/*! \fn bool BamAlignment::GetReadGroup(std::string& readGroup) const
\brief Retrieves value of read group tag ("RG").
*/
bool BamAlignment::GetTagType(const std::string& tag, char& type) const {
- // make sure tag data exists
- 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;
// if tag not found, return failure
- if ( !FindTag(tag, pTagData, tagDataLength, numBytesParsed) )
+ if ( !FindTag(tag, pTagData, tagDataLength, numBytesParsed) ){
+ // TODO: set error string?
return false;
+ }
// otherwise, retrieve & validate tag type code
type = *(pTagData - 1);
// unknown tag type
default:
- cerr << "BamAlignment ERROR: unknown tag type encountered: "
- << type << endl;
+ const string message = string("invalid tag type: ") + type;
+ SetErrorString("BamAlignment::GetTagType", message);
return false;
}
}
\return \c true if both \a tag and \a type are correct sizes
*/
-bool BamAlignment::IsValidSize(const string& tag, const string& type) {
+bool BamAlignment::IsValidSize(const std::string& tag, const std::string& type) const {
return (tag.size() == Constants::BAM_TAG_TAGSIZE) &&
(type.size() == Constants::BAM_TAG_TYPESIZE);
}
-/*! \fn bool BamAlignment::RemoveTag(const std::string& tag)
+/*! \fn void BamAlignment::RemoveTag(const std::string& tag)
\brief Removes field from BAM tags.
-
- \return \c true if tag was removed successfully (or didn't exist before)
*/
-bool BamAlignment::RemoveTag(const std::string& tag) {
+void BamAlignment::RemoveTag(const std::string& tag) {
// if char data not populated, do that first
if ( SupportData.HasCoreOnly )
// skip if no tags available
if ( TagData.empty() )
- return false;
+ return;
// localize the tag data
char* pOriginalTagData = (char*)TagData.data();
unsigned int newTagDataLength = 0;
unsigned int numBytesParsed = 0;
- // if tag not found, simply return true
+ // skip if tag not found
if ( !FindTag(tag, pTagData, originalTagDataLength, numBytesParsed) )
- return true;
+ return;
// otherwise, remove it
- char* newTagData = new char[originalTagDataLength];
+ RaiiBuffer newTagData(originalTagDataLength);
// copy original tag data up til desired tag
pTagData -= 3;
numBytesParsed -= 3;
const unsigned int beginningTagDataLength = numBytesParsed;
newTagDataLength += beginningTagDataLength;
- memcpy(newTagData, pOriginalTagData, numBytesParsed);
+ memcpy(newTagData.Buffer, pOriginalTagData, numBytesParsed);
// attemp to skip to next tag
const char* pTagStorageType = pTagData + 2;
// squeeze remaining tag data
const unsigned int skippedDataLength = (numBytesParsed - beginningTagDataLength);
const unsigned int endTagDataLength = originalTagDataLength - beginningTagDataLength - skippedDataLength;
- memcpy(newTagData + beginningTagDataLength, pTagData, endTagDataLength );
+ memcpy(newTagData.Buffer + beginningTagDataLength, pTagData, endTagDataLength );
// save modified tag data in alignment
- TagData.assign(newTagData, beginningTagDataLength + endTagDataLength);
+ TagData.assign(newTagData.Buffer, beginningTagDataLength + endTagDataLength);
}
+}
- // clean up & return success
- delete[] newTagData;
- return true;
+/*! \fn void BamAlignment::SetErrorString(const std::string& where, const std::string& what) const
+ \internal
+
+ Sets a formatted error string for this alignment.
+*/
+void BamAlignment::SetErrorString(const std::string& where, const std::string& what) const {
+ static const string SEPARATOR = ": ";
+ ErrorString = where + SEPARATOR + what;
}
/*! \fn void BamAlignment::SetIsDuplicate(bool ok)
*/
bool BamAlignment::SkipToNextTag(const char storageType,
char*& pTagData,
- unsigned int& numBytesParsed)
+ unsigned int& numBytesParsed) const
{
switch (storageType) {
// read number of elements
int32_t numElements;
- memcpy(&numElements, pTagData, sizeof(uint32_t)); // already endian-swapped if necessary
+ memcpy(&numElements, pTagData, sizeof(uint32_t)); // already endian-swapped, if needed
numBytesParsed += sizeof(uint32_t);
pTagData += sizeof(uint32_t);
bytesToSkip = numElements*sizeof(uint32_t);
break;
default:
- cerr << "BamAlignment ERROR: unknown binary array type encountered: "
- << arrayType << endl;
+ const string message = string("invalid binary array type: ") + arrayType;
+ SetErrorString("BamAlignment::SkipToNextTag", message);
return false;
}
}
default:
- cerr << "BamAlignment ERROR: unknown tag type encountered"
- << storageType << endl;
+ const string message = string("invalid tag type: ") + storageType;
+ SetErrorString("BamAlignment::SkipToNextTag", message);
return false;
}
- // return success
+ // if we get here, tag skipped OK - return success
return true;
}
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