void junctions_from_alignment(const BowtieHit& spliced_alignment,
JunctionSet& junctions)
{
vector<pair<Junction, JunctionStats> > juncs;
junctions_from_spliced_hit(spliced_alignment, juncs);
for (size_t i = 0; i < juncs.size(); ++i)
{
pair<Junction, JunctionStats>& junc = juncs[i];
JunctionSet::iterator itr = junctions.find(junc.first);
if (itr != junctions.end())
{
JunctionStats& j = itr->second;
j.left_extent = max(j.left_extent, junc.second.left_extent);
j.right_extent = max(j.right_extent, junc.second.right_extent);
j.min_splice_mms = min(j.min_splice_mms, junc.second.min_splice_mms);
j.supporting_hits++;
}
else
{
assert(junc.first.refid != 0xFFFFFFFF);
junctions[junc.first] = junc.second;
}
}
}
/**
* Parse the cigar string of a BowtieHit in order to determine the alignment status.
*/
AlignStatus::AlignStatus(const BowtieHit& bh, const JunctionSet& gtf_junctions)
{
const vector<CigarOp>& cigar = bh.cigar();
_aligned = cigar.size() > 0;
_indelFreeAlignment = true;
_unannotatedSpliceFreeAlignment = true;
_edit_dist = bh.edit_dist();
int j = bh.left();
for (size_t c = 0 ; c < cigar.size(); ++c)
{
Junction junc;
switch(cigar[c].opcode)
{
case REF_SKIP:
junc.refid = bh.ref_id();
junc.left = j;
junc.right = junc.left + cigar[c].length;
junc.antisense = bh.antisense_splice();
j += cigar[c].length;
if (gtf_junctions.find(junc) == gtf_junctions.end())
_unannotatedSpliceFreeAlignment = false;
break;
case MATCH:
j += cigar[c].length;
break;
case DEL:
j += cigar[c].length;
_indelFreeAlignment = false;
break;
case INS:
_indelFreeAlignment = false;
break;
default:
break;
}
}
}