// Hit needs to be from the collapsed (non_redundant) list to match indexing
double BiasCorrectionHelper::get_cond_prob(const MateHit& hit)
{
shared_ptr<ReadGroupProperties const> rgp = hit.read_group_props();
int i = get_index(rgp);
int start;
int end;
int frag_len;
int trans_len = _transcript->length();
_transcript->map_frag(hit, start, end, frag_len);
shared_ptr<const EmpDist> fld = rgp->frag_len_dist();
double cond_prob = 1.0;
cond_prob *= _start_biases[i][start];
cond_prob *= _end_biases[i][end];
double frag_prob = (bias_mode == POS || bias_mode == POS_VLMM || bias_mode == POS_SITE) ? fld->npdf(frag_len, trans_len-start) : fld->pdf(frag_len);
cond_prob *= frag_prob;
if (cond_prob==0.0)
return 0.0;
if (hit.is_pair() || hit.read_group_props()->complete_fragments())
{
if (frag_len >= (int)_tot_biases_for_len[i].size())
cond_prob = 0.0;
else
cond_prob /= _tot_biases_for_len[i][frag_len];
}
else if (start!=trans_len && end==trans_len) // The hit is a singleton at the start of a fragment
cond_prob /= _start_biases_for_len[i][frag_len];
else if (start==trans_len && end!=trans_len) // The hit is a singleton at the end of a fragment
cond_prob /= _end_biases_for_len[i][frag_len];
else if (frag_len==trans_len) // We don't actually know where we start or end and can't subtract off the frag_len or we'll get inf
cond_prob /= trans_len;
else
{
if (trans_len < frag_len)
{
cond_prob = 0;
}
else
{
// Single-end read w/ library type FF or RR
cond_prob /= trans_len-frag_len;
}
}
if (cond_prob > 0 && hit.collapse_mass() > 0)
{
_rg_masses[i] += hit.collapse_mass();
_mapped = true;
}
#if DEBUG
if (isinf(cond_prob))
{
double cond_prob = 1.0;
cond_prob *= _start_biases[i][start];
cond_prob *= _end_biases[i][end];
double frag_prob = (bias_mode == POS || bias_mode == POS_VLMM || bias_mode == POS_SITE) ? fld->npdf(frag_len, trans_len-start) : fld->pdf(frag_len);
cond_prob *= frag_prob;
if (cond_prob==0.0)
return 0.0;
if (hit.is_pair())
{
if (frag_len >= _tot_biases_for_len[i].size())
cond_prob = 0.0;
else
cond_prob /= _tot_biases_for_len[i][frag_len];
}
else if (start!=trans_len && end==trans_len) // The hit is a singleton at the start of a fragment
cond_prob /= _start_biases_for_len[i][frag_len];
else if (start==trans_len && end!=trans_len) // The hit is a singleton at the end of a fragment
cond_prob /= _end_biases_for_len[i][frag_len];
else if (frag_len==trans_len) // We don't actually know where we start or end and can't subtract off the frag_len or we'll get inf
cond_prob /= trans_len;
else
{
if (trans_len < frag_len)
{
cond_prob = 0;
}
else
{
// Single-end read w/ library type FF or RR
cond_prob /= trans_len-frag_len;
}
}
}
#endif
assert(!isinf(cond_prob));
assert(!isnan(cond_prob));
if (isinf(cond_prob) || isnan(cond_prob))
cond_prob = 0.0;
return cond_prob;
}
// Places multi-reads to the right of reads they match
bool mate_hit_lt(const MateHit& lhs, const MateHit& rhs)
{
if (lhs.left() != rhs.left())
return lhs.left() < rhs.left();
if (lhs.right() != rhs.right())
return lhs.right() > rhs.right();
if ((lhs.left_alignment() == NULL) != (rhs.left_alignment() == NULL))
return (lhs.left_alignment() == NULL) < (rhs.left_alignment() == NULL);
if ((lhs.right_alignment() == NULL) != (rhs.right_alignment() == NULL))
return (lhs.right_alignment() == NULL) < (rhs.right_alignment() == NULL);
assert ((lhs.right_alignment() == NULL) == (rhs.right_alignment() == NULL));
assert ((lhs.left_alignment() == NULL) == (rhs.left_alignment() == NULL));
const ReadHit* lhs_l = lhs.left_alignment();
const ReadHit* lhs_r = lhs.right_alignment();
const ReadHit* rhs_l = rhs.left_alignment();
const ReadHit* rhs_r = rhs.right_alignment();
if (lhs_l && rhs_l)
{
if (lhs_l->cigar().size() != rhs_l->cigar().size())
return lhs_l->cigar().size() < rhs_l->cigar().size();
for (size_t i = 0; i < lhs_l->cigar().size(); ++i)
{
if (lhs_l->cigar()[i].opcode != rhs_l->cigar()[i].opcode)
return lhs_l->cigar()[i].opcode < rhs_l->cigar()[i].opcode;
if (lhs_l->cigar()[i].length != rhs_l->cigar()[i].length)
return lhs_l->cigar()[i].length < rhs_l->cigar()[i].length;
}
}
if (lhs_r && rhs_r)
{
if (lhs_r->cigar().size() != rhs_r->cigar().size())
return lhs_r->cigar().size() < rhs_r->cigar().size();
for (size_t i = 0; i < lhs_r->cigar().size(); ++i)
{
if (lhs_r->cigar()[i].opcode != rhs_r->cigar()[i].opcode)
return lhs_r->cigar()[i].opcode < rhs_r->cigar()[i].opcode;
if (lhs_r->cigar()[i].length != rhs_r->cigar()[i].length)
return lhs_r->cigar()[i].length < rhs_r->cigar()[i].length;
}
}
if (lhs.is_multi() != rhs.is_multi())
{
return rhs.is_multi();
}
return false;
}
bool has_no_collapse_mass(const MateHit& hit)
{
return hit.collapse_mass() == 0;
}
// Does NOT care about the read group this hit came from.
bool hits_equals(const MateHit& lhs, const MateHit& rhs)
{
if (lhs.ref_id() != rhs.ref_id())
return false;
if ((lhs.left_alignment() == NULL) != (rhs.left_alignment() == NULL))
return false;
if ((lhs.right_alignment() == NULL) != (rhs.right_alignment() == NULL))
return false;
if (lhs.left_alignment())
{
if (!(hits_eq_mod_id(*lhs.left_alignment(),*(rhs.left_alignment()))))
return false;
}
if (lhs.right_alignment())
{
if (!(hits_eq_mod_id(*lhs.right_alignment(),*(rhs.right_alignment()))))
return false;
}
return true;
}
// Compares for structural equality, but won't declare multihits equal to one another
// and won't return true for hits from different read groups (e.g. replicate samples)
bool hits_eq_non_multi_non_replicate(const MateHit& lhs, const MateHit& rhs)
{
if ((lhs.is_multi() || rhs.is_multi() || lhs.read_group_props() != rhs.read_group_props()) && lhs.insert_id() != rhs.insert_id())
return false;
return hits_equals(lhs, rhs);
}
// Compares for structural equality, but won't declare multihits equal to one another
bool hits_eq_non_multi(const MateHit& lhs, const MateHit& rhs)
{
if ((lhs.is_multi() || rhs.is_multi() ) && lhs.insert_id() != rhs.insert_id())
return false;
return hits_equals(lhs, rhs);
}
