unsigned UngappedAligner::alignUngapped(
FragmentMetadata &fragmentMetadata,
Cigar &cigarBuffer,
const flowcell::ReadMetadata &readMetadata,
const matchSelector::FragmentSequencingAdapterClipper &adapterClipper,
const reference::ContigList &contigList,
const isaac::reference::ContigAnnotations &contigAnnotations) const
{
const unsigned cigarOffset = cigarBuffer.size();
// Don't reset alignment to preserve the seed-based anchors.
// fragmentMetadata.resetAlignment();
ISAAC_ASSERT_MSG(!fragmentMetadata.isAligned(), "alignUngapped is expected to be performend on a clean fragment");
fragmentMetadata.resetClipping();
const reference::Contig &contig = contigList[fragmentMetadata.contigId];
const Read &read = fragmentMetadata.getRead();
const bool reverse = fragmentMetadata.reverse;
const std::vector<char> &sequence = read.getStrandSequence(reverse);
const reference::Contig &reference = contig;
std::vector<char>::const_iterator sequenceBegin = sequence.begin();
std::vector<char>::const_iterator sequenceEnd = sequence.end();
adapterClipper.clip(contig, fragmentMetadata, sequenceBegin, sequenceEnd);
clipReadMasking(read, fragmentMetadata, sequenceBegin, sequenceEnd);
clipReference(reference.size(), fragmentMetadata, sequenceBegin, sequenceEnd);
const unsigned firstMappedBaseOffset = std::distance(sequence.begin(), sequenceBegin);
if (firstMappedBaseOffset)
{
cigarBuffer.addOperation(firstMappedBaseOffset, Cigar::SOFT_CLIP);
}
const unsigned mappedBases = std::distance(sequenceBegin, sequenceEnd);
if (mappedBases)
{
const Cigar::OpCode opCode = Cigar::ALIGN;
cigarBuffer.addOperation(mappedBases, opCode);
}
const unsigned clipEndBases = std::distance(sequenceEnd, sequence.end());
if (clipEndBases)
{
cigarBuffer.addOperation(clipEndBases, Cigar::SOFT_CLIP);
}
const unsigned ret = updateFragmentCigar(
readMetadata, contigList, contigAnnotations, fragmentMetadata,
fragmentMetadata.reverse, fragmentMetadata.contigId, fragmentMetadata.position, cigarBuffer, cigarOffset);
if (!ret)
{
fragmentMetadata.setUnaligned();
}
return ret;
}
/**
* \return true, if the clipping changed the alignment position
*/
bool SemialignedEndsClipper::clip(
const std::vector<reference::Contig> &contigList,
FragmentMetadata &fragmentMetadata)
{
if (!fragmentMetadata.isAligned() || fragmentMetadata.gapCount)
{
return false;
}
bool ret = clipLeftSide(contigList, fragmentMetadata);
if (clipRightSide(contigList, fragmentMetadata))
{
ret = true;
}
if (ret)
{
ISAAC_THREAD_CERR_DEV_TRACE(" SemialignedEndsClipper::clip: " << fragmentMetadata);
}
return ret;
}