const unsigned int tagDataOffset = qualDataOffset + bAlignment.SupportData.QuerySequenceLength;
const unsigned int tagDataLength = dataLength - tagDataOffset;
+ // check offsets to see what char data exists
+ const bool hasSeqData = ( seqDataOffset < dataLength );
+ const bool hasQualData = ( qualDataOffset < dataLength );
+ const bool hasTagData = ( tagDataOffset < dataLength );
+
// set up char buffers
const char* allCharData = bAlignment.SupportData.AllCharData.data();
- const char* seqData = ((const char*)allCharData) + seqDataOffset;
- const char* qualData = ((const char*)allCharData) + qualDataOffset;
- char* tagData = ((char*)allCharData) + tagDataOffset;
+ const char* seqData = ( hasSeqData ? (((const char*)allCharData) + seqDataOffset) : (const char*)0 );
+ const char* qualData = ( hasQualData ? (((const char*)allCharData) + qualDataOffset) : (const char*)0 );
+ char* tagData = ( hasTagData ? (((char*)allCharData) + tagDataOffset) : (char*)0 );
// store alignment name (relies on null char in name as terminator)
bAlignment.Name.assign((const char*)(allCharData));
// save query sequence
bAlignment.QueryBases.clear();
- bAlignment.QueryBases.reserve(bAlignment.SupportData.QuerySequenceLength);
- for (unsigned int i = 0; i < bAlignment.SupportData.QuerySequenceLength; ++i) {
- char singleBase = DNA_LOOKUP[ ( (seqData[(i/2)] >> (4*(1-(i%2)))) & 0xf ) ];
- bAlignment.QueryBases.append(1, singleBase);
+ if ( hasSeqData ) {
+ bAlignment.QueryBases.reserve(bAlignment.SupportData.QuerySequenceLength);
+ for (unsigned int i = 0; i < bAlignment.SupportData.QuerySequenceLength; ++i) {
+ char singleBase = DNA_LOOKUP[ ( (seqData[(i/2)] >> (4*(1-(i%2)))) & 0xf ) ];
+ bAlignment.QueryBases.append(1, singleBase);
+ }
}
// save qualities, converting from numeric QV to 'FASTQ-style' ASCII character
bAlignment.Qualities.clear();
- bAlignment.Qualities.reserve(bAlignment.SupportData.QuerySequenceLength);
- for (unsigned int i = 0; i < bAlignment.SupportData.QuerySequenceLength; ++i) {
- char singleQuality = (char)(qualData[i]+33);
- bAlignment.Qualities.append(1, singleQuality);
+ if ( hasQualData ) {
+ bAlignment.Qualities.reserve(bAlignment.SupportData.QuerySequenceLength);
+ for (unsigned int i = 0; i < bAlignment.SupportData.QuerySequenceLength; ++i) {
+ char singleQuality = (char)(qualData[i]+33);
+ bAlignment.Qualities.append(1, singleQuality);
+ }
}
// if QueryBases is empty (and this is a allowed case)
if ( bAlignment.QueryBases.empty() )
- bAlignment.AlignedBases = bAlignment.QueryBases;
+ bAlignment.AlignedBases = bAlignment.QueryBases;
// if QueryBases contains data, then build AlignedBases using CIGAR data
else {
- // resize AlignedBases
- bAlignment.AlignedBases.clear();
- bAlignment.AlignedBases.reserve(bAlignment.SupportData.QuerySequenceLength);
+ // resize AlignedBases
+ bAlignment.AlignedBases.clear();
+ bAlignment.AlignedBases.reserve(bAlignment.SupportData.QuerySequenceLength);
- // iterate over CigarOps
- int k = 0;
- vector<CigarOp>::const_iterator cigarIter = bAlignment.CigarData.begin();
- vector<CigarOp>::const_iterator cigarEnd = bAlignment.CigarData.end();
- for ( ; cigarIter != cigarEnd; ++cigarIter ) {
+ // iterate over CigarOps
+ int k = 0;
+ vector<CigarOp>::const_iterator cigarIter = bAlignment.CigarData.begin();
+ vector<CigarOp>::const_iterator cigarEnd = bAlignment.CigarData.end();
+ for ( ; cigarIter != cigarEnd; ++cigarIter ) {
- const CigarOp& op = (*cigarIter);
- switch(op.Type) {
+ const CigarOp& op = (*cigarIter);
+ switch(op.Type) {
- case ('M') :
- case ('I') :
- bAlignment.AlignedBases.append(bAlignment.QueryBases.substr(k, op.Length)); // for 'M', 'I' - write bases
- // fall through
+ case ('M') :
+ case ('I') :
+ bAlignment.AlignedBases.append(bAlignment.QueryBases.substr(k, op.Length)); // for 'M', 'I' - write bases
+ // fall through
- case ('S') :
- k += op.Length; // for 'S' - soft clip, skip over query bases
- break;
+ case ('S') :
+ k += op.Length; // for 'S' - soft clip, skip over query bases
+ break;
- case ('D') :
- bAlignment.AlignedBases.append(op.Length, '-'); // for 'D' - write gap character
- break;
+ case ('D') :
+ bAlignment.AlignedBases.append(op.Length, '-'); // for 'D' - write gap character
+ break;
- case ('P') :
- bAlignment.AlignedBases.append( op.Length, '*' ); // for 'P' - write padding character
- break;
+ case ('P') :
+ bAlignment.AlignedBases.append( op.Length, '*' ); // for 'P' - write padding character
+ break;
- case ('N') :
- bAlignment.AlignedBases.append( op.Length, 'N' ); // for 'N' - write N's, skip bases in original query sequence
- break;
+ case ('N') :
+ bAlignment.AlignedBases.append( op.Length, 'N' ); // for 'N' - write N's, skip bases in original query sequence
+ break;
- case ('H') :
- break; // for 'H' - hard clip, do nothing to AlignedBases, move to next op
+ case ('H') :
+ break; // for 'H' - hard clip, do nothing to AlignedBases, move to next op
- default:
- fprintf(stderr, "ERROR: Invalid Cigar op type\n"); // shouldn't get here
- exit(1);
- }
- }
+ default:
+ fprintf(stderr, "ERROR: Invalid Cigar op type\n"); // shouldn't get here
+ exit(1);
+ }
+ }
}
- // -----------------------
- // Added: 3-25-2010 DB
- // Fixed: endian-correctness for tag data
- // -----------------------
- if ( IsBigEndian ) {
- int i = 0;
- while ( (unsigned int)i < tagDataLength ) {
-
- i += 2; // skip tag type (e.g. "RG", "NM", etc)
- uint8_t type = toupper(tagData[i]); // lower & upper case letters have same meaning
- ++i; // skip value type
-
- switch (type) {
-
- case('A') :
- case('C') :
- ++i;
- break;
-
- case('S') :
- SwapEndian_16p(&tagData[i]);
- i += sizeof(uint16_t);
- break;
-
- case('F') :
- case('I') :
- SwapEndian_32p(&tagData[i]);
- i += sizeof(uint32_t);
- break;
-
- case('D') :
- SwapEndian_64p(&tagData[i]);
- i += sizeof(uint64_t);
- break;
-
- case('H') :
- case('Z') :
- while (tagData[i]) { ++i; }
- ++i; // increment one more for null terminator
- break;
-
- default :
- fprintf(stderr, "ERROR: Invalid tag value type\n"); // shouldn't get here
- exit(1);
- }
- }
- }
-
- // store TagData
+ // save tag data
bAlignment.TagData.clear();
- bAlignment.TagData.resize(tagDataLength);
- memcpy((char*)bAlignment.TagData.data(), tagData, tagDataLength);
+ if ( hasTagData ) {
+ if ( IsBigEndian ) {
+ int i = 0;
+ while ( (unsigned int)i < tagDataLength ) {
+
+ i += 2; // skip tag type (e.g. "RG", "NM", etc)
+ uint8_t type = toupper(tagData[i]); // lower & upper case letters have same meaning
+ ++i; // skip value type
+
+ switch (type) {
+
+ case('A') :
+ case('C') :
+ ++i;
+ break;
+
+ case('S') :
+ SwapEndian_16p(&tagData[i]);
+ i += sizeof(uint16_t);
+ break;
+
+ case('F') :
+ case('I') :
+ SwapEndian_32p(&tagData[i]);
+ i += sizeof(uint32_t);
+ break;
+
+ case('D') :
+ SwapEndian_64p(&tagData[i]);
+ i += sizeof(uint64_t);
+ break;
+
+ case('H') :
+ case('Z') :
+ while (tagData[i]) { ++i; }
+ ++i; // increment one more for null terminator
+ break;
+
+ default :
+ fprintf(stderr, "ERROR: Invalid tag value type\n"); // shouldn't get here
+ exit(1);
+ }
+ }
+ }
+
+ // store tagData in alignment
+ bAlignment.TagData.resize(tagDataLength);
+ memcpy((char*)bAlignment.TagData.data(), tagData, tagDataLength);
+ }
// clear the core-only flag
bAlignment.SupportData.HasCoreOnly = false;
projects / bamtools.git / commitdiff