// Check that all the strings in the vector align to the same coordinates
// of the passed in sequence
bool HapgenUtil::checkAlignmentsAreConsistent(const std::string& refString, const StringVector& queries)
{
if(queries.empty())
return true;
// Perform local alignments of each query to the refString
LocalAlignmentResultVector alignments;
for(size_t i = 0; i < queries.size(); ++i)
alignments.push_back(StdAlnTools::localAlignment(refString, queries[i]));
size_t i = 0;
for(size_t j = 1; j < alignments.size(); ++j)
{
if(alignments[i].targetStartIndex != alignments[j].targetStartIndex ||
alignments[j].targetEndIndex != alignments[j].targetEndIndex)
{
std::cerr << "Warning: inconsistent alignments found for haplotype realignment\n";
std::cerr << "A[" << i << "]: " << alignments[i] << "\n";
std::cerr << "A[" << j << "]: " << alignments[j] << "\n";
return false;
}
}
return true;
}
// Align a bunch of reads locally to a sequence
LocalAlignmentResultVector HapgenUtil::alignReadsLocally(const std::string& target, const SeqItemVector& reads)
{
LocalAlignmentResultVector results;
for(size_t i = 0; i < reads.size(); ++i)
{
LocalAlignmentResult fwdAR = StdAlnTools::localAlignment(target, reads[i].seq.toString());
LocalAlignmentResult rcAR = StdAlnTools::localAlignment(target, reverseComplement(reads[i].seq.toString()));
results.push_back(fwdAR.score > rcAR.score ? fwdAR : rcAR);
}
return results;
}
