void SamWriterPrivate::Write(const BamRecord& record)
{
#if PBBAM_AUTOVALIDATE
Validator::Validate(record);
#endif
const auto rawRecord = internal::BamRecordMemory::GetRawData(record);
// store bin number
// min_shift=14 & n_lvls=5 are SAM/BAM "magic numbers"
rawRecord->core.bin = hts_reg2bin(rawRecord->core.pos,
bam_endpos(rawRecord.get()), 14, 5);
// write record to file
const int ret = sam_write1(file_.get(), header_.get(), rawRecord.get());
if (ret <= 0)
throw std::runtime_error("could not write record");
}
bool BamRecordBuilder::BuildInPlace(BamRecord& record) const
{
// initialize with basic 'core data'
PBBAM_SHARED_PTR<bam1_t> recordRawData = internal::BamRecordMemory::GetRawData(record); /* record.impl_.RawData().get();*/
if (!recordRawData || !recordRawData->data)
throw std::runtime_error("BamRecord memory in invalid state");
recordRawData->core = core_;
// setup variable length data
const std::vector<uint8_t> encodedTags = BamTagCodec::Encode(tags_);
const size_t nameLength = name_.size() + 1;
const size_t numCigarOps = cigar_.size();
const size_t cigarLength = numCigarOps * sizeof(uint32_t);
const size_t seqLength = sequence_.size();
const size_t qualLength = seqLength;
const size_t tagLength = encodedTags.size();
const size_t dataLength = nameLength + cigarLength + seqLength + qualLength + tagLength;
// realloc if necessary
uint8_t* varLengthDataBlock = recordRawData->data;
if (!varLengthDataBlock)
throw std::runtime_error("BamRecord memory in invalid state");
size_t allocatedDataLength = recordRawData->m_data;
if (allocatedDataLength < dataLength) {
allocatedDataLength = dataLength;
kroundup32(allocatedDataLength);
varLengthDataBlock = (uint8_t*)realloc(varLengthDataBlock, allocatedDataLength);
}
recordRawData->data = varLengthDataBlock;
recordRawData->l_data = dataLength;
recordRawData->m_data = allocatedDataLength;
size_t index = 0;
// name
memcpy(&varLengthDataBlock[index], name_.c_str(), nameLength);
index += nameLength;
// cigar
if (cigarLength > 0) {
std::vector<uint32_t> encodedCigar(numCigarOps);
for (size_t i = 0; i < numCigarOps; ++i) {
const CigarOperation& op = cigar_.at(i);
encodedCigar[i] = op.Length() << BAM_CIGAR_SHIFT;
const uint8_t type = static_cast<uint8_t>(op.Type());
if (type >= 8)
throw std::runtime_error("invalid CIGAR op type: " + std::to_string(type));
encodedCigar[i] |= type;
}
memcpy(&varLengthDataBlock[index], &encodedCigar[0], cigarLength);
index += cigarLength;
// update bin after we've calculated cigar info
const int32_t endPosition = bam_cigar2rlen(recordRawData->core.n_cigar, &encodedCigar[0]);
recordRawData->core.bin = hts_reg2bin(core_.pos, endPosition, 14, 5);
}
// seq & qual
if (seqLength > 0) {
uint8_t* s = &varLengthDataBlock[index];
for (size_t i = 0; i < seqLength; ++i)
s[i>>1] |= ( seq_nt16_table[static_cast<int>(sequence_.at(i))] << ((~i&1)<<2) );
index += seqLength;
uint8_t* q = &varLengthDataBlock[index];
if (!qualities_.empty())
memset(q, 0xFF, seqLength);
else {
for (size_t i = 0; i < seqLength; ++i)
q[i] = qualities_.at(i) - 33;
}
index += seqLength;
}
