void
apath_append(
path_t& apath,
const align_t seg_type,
const unsigned length)
{
if (apath.size() && apath.back().type == seg_type)
{
apath.back().length += length;
}
else
{
apath.emplace_back(seg_type,length);
}
}
void
export_md_to_apath(const char* md,
const bool is_fwd_strand,
path_t& apath,
const bool is_edge_deletion_error)
{
// to make best use of previous code, we parse the MD in the
// alignment direction and then orient apath to the forward strand
// as a second step if required
//
assert(NULL != md);
apath.clear();
export_md_to_apath_impl(md,apath);
unsigned as(apath.size());
if ( ((as>0) and (apath.front().type == DELETE)) or
((as>1) and (apath.back().type == DELETE)) )
{
std::ostringstream oss;
if (is_edge_deletion_error)
{
oss << "ERROR: ";
}
else
{
oss << "WARNING: ";
}
oss << "alignment path: " << apath_to_cigar(apath) << " contains meaningless edge deletion.\n";
if (is_edge_deletion_error)
{
throw blt_exception(oss.str().c_str());
}
else
{
log_os << oss.str();
path_t apath2;
for (unsigned i(0); i<as; ++i)
{
if (((i==0) or ((i+1)==as)) and
apath[i].type == DELETE) continue;
apath2.push_back(apath[i]);
}
apath=apath2;
as=apath.size();
}
}
if ( (not is_fwd_strand) and (as>1) )
{
std::reverse(apath.begin(),apath.end());
}
}
