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bind_oligo.cpp
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bind_oligo.cpp
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#ifdef USE_MPI
#include <mpi.h>
#endif // USE_MPI
#include "tntblast.h"
#include <sstream>
using namespace std;
#ifdef PROFILE
extern unsigned int num_plus_tm_eval;
extern unsigned int num_minus_tm_eval;
#endif // PROFILE
struct sort_by_delta
{
inline bool operator()(const pair<unsigned int, unsigned int> &m_a,
const pair<unsigned int, unsigned int> &m_b) const
{
return ( int(m_a.first) - int(m_a.second) ) < ( int(m_b.first) - int(m_b.second) );
};
};
struct unique_by_delta
{
inline bool operator()(const pair<unsigned int, unsigned int> &m_a,
const pair<unsigned int, unsigned int> &m_b) const
{
return ( int(m_a.first) - int(m_a.second) ) == ( int(m_b.first) - int(m_b.second) );
};
};
struct sort_by_hash_match
{
inline bool operator()(const oligo_info &m_a, const oligo_info &m_b) const
{
return ( int(m_a.query_loc) - int(m_a.target_loc) ) < ( int(m_b.query_loc) - int(m_b.target_loc) );
};
};
struct unique_by_hash_match
{
inline bool operator()(const oligo_info &m_a, const oligo_info &m_b) const
{
return ( ( int(m_a.query_loc) - int(m_a.target_loc) ) == ( int(m_b.query_loc) - int(m_b.target_loc) ) );
};
};
struct sort_by_bound_match
{
inline bool operator()(const oligo_info &m_a, const oligo_info &m_b) const
{
if(m_a.loc_5 != m_b.loc_5){
return (m_a.loc_5 < m_b.loc_5);
}
if(m_a.loc_3 != m_b.loc_3){
return (m_a.loc_3 < m_b.loc_3);
}
// If we get here, then the same target range was found
if(m_a.tm == m_b.tm){
// Due to boundary effects (i.e. how much sequence did we push into the
// comparison buffer) it is possible to get the same alignments but with differing
// numbers of mismatches. Always take the alignment with the *highest* number of mismatches
// (since lower mismatch counts are an artifact!). I wish there were a more elegant way
// to handle this!
if(m_a.num_mm == m_b.num_mm){
// Choose the *longest* (most informative) alignment to preferentially to make sure that we show
// any dangling ends to the user
return ( m_a.alignment.size() > m_b.alignment.size() );
}
return (m_a.num_mm > m_b.num_mm);
}
// Reverse the tm comparison to sort by descending tm
return (m_a.tm > m_b.tm);
};
};
void match_oligo_to_minus_strand(list<oligo_info> &info_list,
DNAHash &m_hash, const string &m_oligo, const unsigned char &m_mask)
{
list<oligo_info> hit_list;
const unsigned char local_mask = m_mask | oligo_info::MINUS_STRAND;
// Iterate over all possible word arrangements within this fragment of window bases. Note that the prefix iterator
// increment (i.e. ++hash_iter) is more efficient than the postfix interator increment (i.e. hash_iter++) since the
// latter requires an addition iterator copy operation.
for(DNAHash::iterator hash_iter = m_hash.find(m_oligo);hash_iter != m_hash.end();++hash_iter){
hit_list.push_back( oligo_info(hash_iter.offset(), *hash_iter, local_mask) );
}
hit_list.sort( sort_by_hash_match() );
hit_list.unique( unique_by_hash_match() );
info_list.merge(hit_list);
}
void match_oligo_to_plus_strand(list<oligo_info> &info_list,
DNAHash &m_hash, const string &m_oligo, const unsigned char &m_mask)
{
list<oligo_info> hit_list;
const unsigned char local_mask = m_mask | oligo_info::PLUS_STRAND;
// Iterate over all possible word arrangements within this fragment of window bases. Note that the prefix iterator
// increment (i.e. ++hash_iter) is more efficient than the postfix interator increment (i.e. hash_iter++) since the
// latter requires an addition iterator copy operation.
for(DNAHash::iterator hash_iter = m_hash.find_complement(m_oligo);hash_iter != m_hash.end();++hash_iter){
hit_list.push_back( oligo_info(hash_iter.offset(), *hash_iter, local_mask) );
}
hit_list.sort( sort_by_hash_match() );
hit_list.unique( unique_by_hash_match() );
info_list.merge(hit_list);
}
void bind_oligo_to_minus_strand(list<oligo_info> &info_list,
DNAHash &m_hash, SEQPTR m_seq,
const string &m_oligo,
NucCruc &m_melt, unordered_map<BindCacheKey, BindCacheValue> &m_melt_cache,
const float &m_min_oligo_tm, const float &m_max_oligo_tm,
const float &m_min_oligo_dg, const float &m_max_oligo_dg,
const unsigned int &m_clamp_5,
const unsigned int &m_clamp_3,
const unsigned int &m_max_gap,
const unsigned int &m_max_mismatch)
{
const unsigned int window = m_melt.size_query();
// How many target bases should we add to both the 5' and 3' tails of the target sequence?
const unsigned int flanking_bases_5 = NUM_FLANK_BASE;
const unsigned int flanking_bases_3 = NUM_FLANK_BASE;
const unsigned int target_length = window + flanking_bases_5 + flanking_bases_3;
list<oligo_info> hit_list;
// Find a unique list of all valid match seeds between the query (i.e. m_oligo_seq) and
// target (i.e. m_background_seq) sequences.
list< pair<unsigned int, unsigned int> > match_seed; // query, target
// Iterate over all possible word arrangements within this fragment of window bases. Note that the prefix iterator
// increment (i.e. ++hash_iter) is more efficient than the postfix interator increment (i.e. hash_iter++) since the
// latter requires an additional iterator copy operation.
for(DNAHash::iterator hash_iter = m_hash.find(m_oligo);hash_iter != m_hash.end();++hash_iter){
match_seed.push_back( make_pair(hash_iter.offset(), *hash_iter) );
}
match_seed.sort( sort_by_delta() );
match_seed.unique( unique_by_delta() );
// Iterate over *unique* word arrangements within this fragment of window bases
for(list< pair<unsigned int, unsigned int> >::const_iterator match_iter = match_seed.begin();match_iter != match_seed.end();
++match_iter){
// The desired target offset (if we can get it)
unsigned int target_start = max( int(match_iter->second) - int(match_iter->first /* query offset */ + flanking_bases_5),
0);
unsigned int target_stop = min( target_start + target_length, SEQ_SIZE(m_seq) );
// Is there a result already in the cache?
BindCacheKey key(m_oligo, target_start, target_stop);
unordered_map<BindCacheKey, BindCacheValue>::const_iterator cache_iter = m_melt_cache.find(key);
if( cache_iter == m_melt_cache.end() ){ // Cache miss
// Clear the target buffer to make room for the bases we're about to add
m_melt.clear_target();
// The first valid base of the target
SEQPTR seq_ptr = SEQ_START(m_seq) + target_start;
// Attempt to extract target_length bases from the start
for(unsigned int i = target_start;i < target_stop;i++, seq_ptr++){
// Bind to the plus strand
switch(*seq_ptr){
case DB_A:
m_melt.push_front_target(BASE::T);
break;
case DB_T:
m_melt.push_front_target(BASE::A);
break;
case DB_C:
m_melt.push_front_target(BASE::G);
break;
case DB_G:
m_melt.push_front_target(BASE::C);
break;
case DB_I:
m_melt.push_front_target(BASE::I);
break;
// IUPAC degenerate bases
case DB_M: // A or C
m_melt.push_front_target(BASE::K);
break;
case DB_R: // G or A
m_melt.push_front_target(BASE::Y);
break;
case DB_S: // G or C
m_melt.push_front_target(BASE::S);
break;
case DB_V: // G or C or A
m_melt.push_front_target(BASE::B);
break;
case DB_W: // A or T
m_melt.push_front_target(BASE::W);
break;
case DB_Y: // T or C
m_melt.push_front_target(BASE::R);
break;
case DB_H: // A or C or T
m_melt.push_front_target(BASE::D);
break;
case DB_K: // G or T
m_melt.push_front_target(BASE::M);
break;
case DB_D: // G or A or T
m_melt.push_front_target(BASE::H);
break;
case DB_B: // G or T or C
m_melt.push_front_target(BASE::V);
break;
case DB_N: // A or T or G or C
m_melt.push_front_target(BASE::N);
break;
default:
// Are we closer to the start or the end?
if( (i - target_start) > (target_stop - (i + 1) ) ){
// Closer to the end
target_stop = i;
}
else{
// Closer to the start
m_melt.clear_target();
target_start = i + 1;
}
break;
};
}
#ifdef PROFILE
num_minus_tm_eval ++;
#endif // PROFILE
const float tm = m_melt.approximate_tm_heterodimer();
if( (tm < m_min_oligo_tm) || (tm > m_max_oligo_tm) ){
// Add this partial result to the cache
m_melt_cache[key] = BindCacheValue(tm, 0.0 /*dg*/, 0.0 /*dH*/, 0.0 /*dS*/,
0 /*anchor_5*/, 0 /*anchor_3*/, 0 /*target_5*/, 0 /*target_3*/,
0 /*num_mismatch*/, 0 /*num_gap*/, 0.0 /*fraction_real_base_pairs*/, string() /*align*/);
continue;
}
const float dg = m_melt.delta_G();
if( (dg < m_min_oligo_dg) || (dg > m_max_oligo_dg) ){
// Add this partial result to the cache
m_melt_cache[key] = BindCacheValue(tm, dg, 0.0f /*dH*/, 0.0f /*dS*/,
0 /*anchor_5*/, 0 /*anchor_3*/, 0 /*target_5*/, 0 /*target_3*/,
0 /*num_mismatch*/, 0 /*num_gap*/, 0.0f /*fraction_real_base_pairs*/, string() /*align*/);
continue;
}
const unsigned int anchor_5 = m_melt.anchor5_query();
if(anchor_5 < m_clamp_5){
// Add this partial result to the cache
m_melt_cache[key] = BindCacheValue(tm, dg, 0.0f /*dH*/, 0.0f /*dS*/,
anchor_5, 0 /*anchor_3*/, 0 /*target_5*/, 0 /*target_3*/,
0 /*num_mismatch*/, 0 /*num_gap*/, 0.0f /*fraction_real_base_pairs*/, string() /*align*/);
continue;
}
const unsigned int anchor_3 = m_melt.anchor3_query();
if(anchor_3 < m_clamp_3){
// Add this partial result to the cache
m_melt_cache[key] = BindCacheValue(tm, dg, 0.0f /*dH*/, 0.0f /*dS*/,
anchor_5, anchor_3, 0 /*target_5*/, 0 /*target_3*/,
0 /*num_mismatch*/, 0 /*num_gap*/, 0.0f /*fraction_real_base_pairs*/, string() /*align*/);
continue;
}
const unsigned int num_mismatch = m_melt.num_mismatch();
if(num_mismatch > m_max_mismatch){
// Add this partial result to the cache
m_melt_cache[key] = BindCacheValue(tm, dg, 0.0f /*dH*/, 0.0f /*dS*/,
anchor_5, anchor_3, 0 /*target_5*/, 0 /*target_3*/,
num_mismatch, 0 /*num_gap*/, 0.0f /*fraction_real_base_pairs*/, string() /*align*/);
continue;
}
const unsigned int num_gap = m_melt.num_gap();
if(num_gap > m_max_gap){
// Add this partial result to the cache
m_melt_cache[key] = BindCacheValue(tm, dg, 0.0f /*dH*/, 0.0f /*dS*/,
anchor_5, anchor_3, 0 /*target_5*/, 0 /*target_3*/,
num_mismatch, num_gap, 0.0f /*fraction_real_base_pairs*/, string() /*align*/);
continue;
}
// How many "real" (non-degenerate, non-virtual) bases make up the target sequence?
// Since degenerate bases get turned into 'N' by the hash function, we can
// end up with spurious matches to poly-N sequences. Require that at least
// half of the query can be aligned to real (ATGCI) bases
const float fraction_real_base_pairs = m_melt.fraction_aligned_real_base_pairs();
if(fraction_real_base_pairs < 0.5f){
// Add this partial result to the cache
m_melt_cache[key] = BindCacheValue(tm, dg, 0.0f /*dH*/, 0.0f /*dS*/,
anchor_5, anchor_3, 0 /*target_5*/, 0 /*target_3*/,
num_mismatch, num_gap, fraction_real_base_pairs, string() /*align*/);
continue;
}
pair<unsigned int, unsigned int> query_range;
pair<unsigned int, unsigned int> target_range;
m_melt.alignment_range(query_range, target_range);
unsigned int target_5 = target_start;
unsigned int target_3 = target_5;
target_5 += target_stop - target_start - 1 - (int)target_range.second;
target_3 += target_stop - target_start - 1 - (int)target_range.first;
// Adjust the extent of the binding region to incorporate
// unbound, non-virtual query bases
target_5 -= (int)query_range.first;
target_3 += (int)(window - 1) - (int)query_range.second;
// Save the alignment
stringstream ss_align;
ss_align << m_melt;
const string align = ss_align.str();
hit_list.push_back(oligo_info( target_5, target_3, tm,
m_melt.delta_H(), m_melt.delta_S(), anchor_5, anchor_3,
num_mismatch, num_gap, align) );
// Add this result to the cache
m_melt_cache[key] = BindCacheValue(tm, dg, m_melt.delta_H(), m_melt.delta_S(),
anchor_5, anchor_3, target_5, target_3,
num_mismatch, num_gap, fraction_real_base_pairs, align);
}
else{ // Cache hit
if( (cache_iter->second.tm < m_min_oligo_tm) || (cache_iter->second.tm > m_max_oligo_tm) ){
continue;
}
if( (cache_iter->second.dg < m_min_oligo_dg) || (cache_iter->second.dg > m_max_oligo_dg) ){
continue;
}
if(cache_iter->second.anchor_5 < m_clamp_5){
continue;
}
if(cache_iter->second.num_mismatch > m_max_mismatch){
continue;
}
if(cache_iter->second.num_gap > m_max_gap){
continue;
}
if(cache_iter->second.fraction_real_base_pairs < 0.5f){
continue;
}
hit_list.push_back(oligo_info( cache_iter->second.target_5, cache_iter->second.target_3,
cache_iter->second.tm,
cache_iter->second.dH, cache_iter->second.dS,
cache_iter->second.anchor_5, cache_iter->second.anchor_3,
cache_iter->second.num_mismatch, cache_iter->second.num_gap, cache_iter->second.seq_align) );
}
}
info_list.clear();
if(hit_list.empty() == true){
return;
}
// Oligos can appear multiple times in the info_list list (but with the same
// target start and stop range). Remove these duplicate entries.
hit_list.sort();
// Only return unique oligos. Take the highest tm oligo out of every set of oligos that
// matches a particular target range.
info_list.push_back( hit_list.front() );
hit_list.pop_front();
while(hit_list.empty() == false){
if( info_list.back() != hit_list.front() ){
info_list.push_back( hit_list.front() );
}
hit_list.pop_front();
}
}
void bind_oligo_to_minus_strand(list<oligo_info> &info_list,
const unsigned char &m_oligo_mask, SEQPTR m_seq,
const string &m_oligo,
NucCruc &m_melt, unordered_map<BindCacheKey, BindCacheValue> &m_melt_cache,
const float &m_min_oligo_tm, const float &m_max_oligo_tm,
const float &m_min_oligo_dg, const float &m_max_oligo_dg,
const unsigned int &m_clamp_5,
const unsigned int &m_clamp_3,
const unsigned int &m_max_gap,
const unsigned int &m_max_mismatch)
{
const unsigned int window = m_melt.size_query();
// How many target bases should we add to both the 5' and 3' tails of the target sequence?
const unsigned int flanking_bases_5 = NUM_FLANK_BASE;
const unsigned int flanking_bases_3 = NUM_FLANK_BASE;
const unsigned int target_length = window + flanking_bases_5 + flanking_bases_3;
// Extract the target oligos into a separate list
list<oligo_info> curr_oligo;
list<oligo_info>::iterator info_iter = info_list.begin();
const char strand_and_oligo_mask = m_oligo_mask | oligo_info::MINUS_STRAND;
while( info_iter != info_list.end() ){
//if( !(info_iter->mask & m_oligo_mask) || !(info_iter->mask & oligo_info::MINUS_STRAND) ){
if( (info_iter->mask & strand_and_oligo_mask) != strand_and_oligo_mask ){
++info_iter;
continue;
}
// Add this element to the curr_oligo list and erase it from the info list
list<oligo_info>::iterator tmp_iter = info_iter;
++info_iter;
curr_oligo.push_front(*tmp_iter);
info_list.erase(tmp_iter);
list<oligo_info>::iterator match_iter = curr_oligo.begin();
// The desired target offset (if we can get it)
unsigned int target_start = max( int(match_iter->target_loc) - int(match_iter->query_loc /* query offset */ + flanking_bases_5),
0);
unsigned int target_stop = min( target_start + target_length, SEQ_SIZE(m_seq) );
// Is there a result already in the cache?
BindCacheKey key(m_oligo, target_start, target_stop);
unordered_map<BindCacheKey, BindCacheValue>::const_iterator cache_iter = m_melt_cache.find(key);
if( cache_iter == m_melt_cache.end() ){ // Cache miss
// Clear the target buffer to make room for the bases we're about to add
m_melt.clear_target();
// The first valid base of the target
SEQPTR seq_ptr = SEQ_START(m_seq) + target_start;
// Attempt to extract target_length bases from the start
for(unsigned int i = target_start;i < target_stop;i++, seq_ptr++){
// Bind to the minus strand
switch(*seq_ptr){
case DB_A:
m_melt.push_front_target(BASE::T);
break;
case DB_T:
m_melt.push_front_target(BASE::A);
break;
case DB_C:
m_melt.push_front_target(BASE::G);
break;
case DB_G:
m_melt.push_front_target(BASE::C);
break;
case DB_I:
m_melt.push_front_target(BASE::I);
break;
// IUPAC degenerate bases
case DB_M: // A or C
m_melt.push_front_target(BASE::K);
break;
case DB_R: // G or A
m_melt.push_front_target(BASE::Y);
break;
case DB_S: // G or C
m_melt.push_front_target(BASE::S);
break;
case DB_V: // G or C or A
m_melt.push_front_target(BASE::B);
break;
case DB_W: // A or T
m_melt.push_front_target(BASE::W);
break;
case DB_Y: // T or C
m_melt.push_front_target(BASE::R);
break;
case DB_H: // A or C or T
m_melt.push_front_target(BASE::D);
break;
case DB_K: // G or T
m_melt.push_front_target(BASE::M);
break;
case DB_D: // G or A or T
m_melt.push_front_target(BASE::H);
break;
case DB_B: // G or T or C
m_melt.push_front_target(BASE::V);
break;
case DB_N: // A or T or G or C
m_melt.push_front_target(BASE::N);
break;
default:
// Are we closer to the start or the end?
if( (i - target_start) > (target_stop - (i + 1) ) ){
// Closer to the end
target_stop = i;
}
else{
// Closer to the start
m_melt.clear_target();
target_start = i + 1;
}
break;
};
}
#ifdef PROFILE
num_minus_tm_eval ++;
#endif // PROFILE
const float tm = m_melt.approximate_tm_heterodimer();
if( (tm < m_min_oligo_tm) || (tm > m_max_oligo_tm) ){
curr_oligo.pop_front();
// Add this partial result to the cache
m_melt_cache[key] = BindCacheValue(tm, 0.0f /*dg*/, 0.0f /*dH*/, 0.0f /*dS*/,
0 /*anchor_5*/, 0 /*anchor_3*/, 0 /*target_5*/, 0 /*target_3*/,
0 /*num_mismatch*/, 0 /*num_gap*/, 0.0f /*fraction_real_base_pairs*/, string() /*align*/);
continue;
}
const float dg = m_melt.delta_G();
if( (dg < m_min_oligo_dg) || (dg > m_max_oligo_dg) ){
curr_oligo.pop_front();
// Add this partial result to the cache
m_melt_cache[key] = BindCacheValue(tm, dg, 0.0f /*dH*/, 0.0f /*dS*/,
0 /*anchor_5*/, 0 /*anchor_3*/, 0 /*target_5*/, 0 /*target_3*/,
0 /*num_mismatch*/, 0 /*num_gap*/, 0.0f /*fraction_real_base_pairs*/, string() /*align*/);
continue;
}
const unsigned int anchor_5 = m_melt.anchor5_query();
if(anchor_5 < m_clamp_5){
curr_oligo.pop_front();
// Add this partial result to the cache
m_melt_cache[key] = BindCacheValue(tm, dg, 0.0f /*dH*/, 0.0f /*dS*/,
anchor_5, 0 /*anchor_3*/, 0 /*target_5*/, 0 /*target_3*/,
0 /*num_mismatch*/, 0 /*num_gap*/, 0.0f /*fraction_real_base_pairs*/, string() /*align*/);
continue;
}
const unsigned int anchor_3 = m_melt.anchor3_query();
if(anchor_3 < m_clamp_3){
curr_oligo.pop_front();
// Add this partial result to the cache
m_melt_cache[key] = BindCacheValue(tm, dg, 0.0f /*dH*/, 0.0f /*dS*/,
anchor_5, anchor_3, 0 /*target_5*/, 0 /*target_3*/,
0 /*num_mismatch*/, 0 /*num_gap*/, 0.0f /*fraction_real_base_pairs*/, string() /*align*/);
continue;
}
const unsigned int num_mismatch = m_melt.num_mismatch();
if(num_mismatch > m_max_mismatch){
curr_oligo.pop_front();
// Add this partial result to the cache
m_melt_cache[key] = BindCacheValue(tm, dg, 0.0f /*dH*/, 0.0f /*dS*/,
anchor_5, anchor_3, 0 /*target_5*/, 0 /*target_3*/,
num_mismatch, 0 /*num_gap*/, 0.0f /*fraction_real_base_pairs*/, string() /*align*/);
continue;
}
const unsigned int num_gap = m_melt.num_gap();
if(num_gap > m_max_gap){
curr_oligo.pop_front();
// Add this partial result to the cache
m_melt_cache[key] = BindCacheValue(tm, dg, 0.0f /*dH*/, 0.0f /*dS*/,
anchor_5, anchor_3, 0 /*target_5*/, 0 /*target_3*/,
num_mismatch, num_gap, 0.0f /*fraction_real_base_pairs*/, string() /*align*/);
continue;
}
// How many "real" (non-degenerate, non-virtual) bases make up the target sequence?
// Since degenerate bases get turned into 'N' by the hash function, we can
// end up with spurious matches to poly-N sequences. Require that at least
// half of the query can be aligned to real (ATGCI) bases
const float fraction_real_base_pairs = m_melt.fraction_aligned_real_base_pairs();
if(fraction_real_base_pairs < 0.5f){
curr_oligo.pop_front();
// Add this partial result to the cache
m_melt_cache[key] = BindCacheValue(tm, dg, 0.0f /*dH*/, 0.0f /*dS*/,
anchor_5, anchor_3, 0 /*target_5*/, 0 /*target_3*/,
num_mismatch, num_gap, fraction_real_base_pairs, string() /*align*/);
continue;
}
pair<unsigned int, unsigned int> query_range;
pair<unsigned int, unsigned int> target_range;
m_melt.alignment_range(query_range, target_range);
int target_5 = target_start;
int target_3 = target_5;
target_5 += target_stop - target_start - 1 - (int)target_range.second;
target_3 += target_stop - target_start - 1 - (int)target_range.first;
// Adjust the extent of the binding region to incorporate
// unbound, non-virtual query bases
target_5 -= (int)query_range.first;
target_3 += (int)(window - 1) - (int)query_range.second;
// Save the alignment
stringstream ss_align;
ss_align << m_melt;
const string align = ss_align.str();
match_iter->loc_5 = target_5;
match_iter->loc_3 = target_3;
match_iter->tm = tm;
match_iter->dH = m_melt.delta_H();
match_iter->dS = m_melt.delta_S();
match_iter->anchor_5 = anchor_5;
match_iter->anchor_3 = anchor_3;
match_iter->num_mm = num_mismatch;
match_iter->num_gap = num_gap;
match_iter->alignment = align;
// Add this result to the cache
m_melt_cache[key] = BindCacheValue(tm, dg, m_melt.delta_H(), m_melt.delta_S(),
anchor_5, anchor_3, target_5, target_3,
num_mismatch, num_gap, fraction_real_base_pairs, align);
}
else{ // Cache hit
if( (cache_iter->second.tm < m_min_oligo_tm) || (cache_iter->second.tm > m_max_oligo_tm) ){
curr_oligo.pop_front();
continue;
}
if( (cache_iter->second.dg < m_min_oligo_dg) || (cache_iter->second.dg > m_max_oligo_dg) ){
curr_oligo.pop_front();
continue;
}
if(cache_iter->second.anchor_5 < m_clamp_5){
curr_oligo.pop_front();
continue;
}
if(cache_iter->second.num_mismatch > m_max_mismatch){
curr_oligo.pop_front();
continue;
}
if(cache_iter->second.num_gap > m_max_gap){
curr_oligo.pop_front();
continue;
}
if(cache_iter->second.fraction_real_base_pairs < 0.5f){
curr_oligo.pop_front();
continue;
}
match_iter->loc_5 = cache_iter->second.target_5;
match_iter->loc_3 = cache_iter->second.target_3;
match_iter->tm = cache_iter->second.tm;
match_iter->dH =cache_iter->second.dH;
match_iter->dS = cache_iter->second.dS;
match_iter->anchor_5 = cache_iter->second.anchor_5;
match_iter->anchor_3 = cache_iter->second.anchor_3;
match_iter->num_mm = cache_iter->second.num_mismatch;
match_iter->num_gap = cache_iter->second.num_gap;
match_iter->alignment = cache_iter->second.seq_align;
}
}
if( curr_oligo.empty() ){
return;
}
// Oligos can appear multiple times in the info_list list (but with the same
// target start and stop range). Remove these duplicate entries.
curr_oligo.sort( sort_by_bound_match() );
// Only return unique oligos. Take the highest tm oligo out of every set of oligos that
// matches a particular target range.
info_list.push_back( curr_oligo.front() );
curr_oligo.pop_front();
while( !curr_oligo.empty() ){
if( info_list.back() != curr_oligo.front() ){
info_list.push_back( curr_oligo.front() );
}
curr_oligo.pop_front();
}
}
void bind_oligo_to_plus_strand(list<oligo_info> &info_list,
DNAHash &m_hash, SEQPTR m_seq,
const string &m_oligo,
NucCruc &m_melt, unordered_map<BindCacheKey, BindCacheValue> &m_melt_cache,
const float &m_min_oligo_tm, const float &m_max_oligo_tm,
const float &m_min_oligo_dg, const float &m_max_oligo_dg,
const unsigned int &m_clamp_5,
const unsigned int &m_clamp_3,
const unsigned int &m_max_gap,
const unsigned int &m_max_mismatch)
{
const unsigned int window = m_melt.size_query();
// How many target bases should we add to both the 5' and 3' tails of the target sequence?
const unsigned int flanking_bases_5 = NUM_FLANK_BASE;
const unsigned int flanking_bases_3 = NUM_FLANK_BASE;
const unsigned int target_length = window + flanking_bases_5 + flanking_bases_3;
// Find a unique list of all valid match seeds between the query (i.e. m_oligo_seq) and
// target (i.e. m_background_seq) sequences.
list< pair<unsigned int, unsigned int> > match_seed; // query, target
// Iterate over all possible word arrangements within this fragment of window bases. Note that the prefix iterator
// increment (i.e. ++hash_iter) is more efficient than the postfix interator increment (i.e. hash_iter++) since the
// latter requires an addition iterator copy operation.
for(DNAHash::iterator hash_iter = m_hash.find_complement(m_oligo);hash_iter != m_hash.end();++hash_iter){
match_seed.push_back( make_pair(hash_iter.offset(), *hash_iter) );
}
match_seed.sort( sort_by_delta() );
match_seed.unique( unique_by_delta() );
list<oligo_info> hit_list;
// Iterate over *unique* word arrangements within this fragment of window bases
for(list< pair<unsigned int, unsigned int> >::const_iterator match_iter = match_seed.begin();match_iter != match_seed.end();
++match_iter){
// The desired target offset (if we can get it)
unsigned int target_start = max( int(match_iter->second) - int(match_iter->first /* query offset */ + flanking_bases_5),
0);
unsigned int target_stop = min( target_start + target_length, SEQ_SIZE(m_seq) );
// Is there a result already in the cache?
BindCacheKey key(m_oligo, target_start, target_stop);
unordered_map<BindCacheKey, BindCacheValue>::const_iterator cache_iter = m_melt_cache.find(key);
if( cache_iter == m_melt_cache.end() ){ // Cache miss
// Clear the target buffer to make room for the bases we're about to add
m_melt.clear_target();
// The first valid base of the target
SEQPTR seq_ptr = SEQ_START(m_seq) + target_start;
// Attempt to extract target_length bases from the start
for(unsigned int i = target_start;i < target_stop;i++, seq_ptr++){
// Bind to the plus strand
switch(*seq_ptr){
case DB_A:
m_melt.push_back_target(BASE::A);
break;
case DB_T:
m_melt.push_back_target(BASE::T);
break;
case DB_C:
m_melt.push_back_target(BASE::C);
break;
case DB_G:
m_melt.push_back_target(BASE::G);
break;
case DB_I:
m_melt.push_back_target(BASE::I);
break;
// IUPAC degenerate bases
case DB_M: // A or C
m_melt.push_back_target(BASE::M);
break;
case DB_R: // G or A
m_melt.push_back_target(BASE::R);
break;
case DB_S: // G or C
m_melt.push_back_target(BASE::S);
break;
case DB_V: // G or C or A
m_melt.push_back_target(BASE::V);
break;
case DB_W: // A or T
m_melt.push_back_target(BASE::W);
break;
case DB_Y: // T or C
m_melt.push_back_target(BASE::Y);
break;
case DB_H: // A or C or T
m_melt.push_back_target(BASE::H);
break;
case DB_K: // G or T
m_melt.push_back_target(BASE::K);
break;
case DB_D: // G or A or T
m_melt.push_back_target(BASE::D);
break;
case DB_B: // G or T or C
m_melt.push_back_target(BASE::B);
break;
case DB_N: // A or T or G or C
m_melt.push_back_target(BASE::N);
break;
default:
// Are we closer to the start or the end?
if( (i - target_start) > (target_stop - (i + 1) ) ){
// Closer to the end
target_stop = i;
}
else{
// Closer to the start
m_melt.clear_target();
target_start = i + 1;
}
break;
};
}
#ifdef PROFILE
num_plus_tm_eval ++;
#endif // PROFILE
const float tm = m_melt.approximate_tm_heterodimer();
if( (tm < m_min_oligo_tm) || (tm > m_max_oligo_tm) ){
// Add this partial result to the cache
m_melt_cache[key] = BindCacheValue(tm, 0.0f /*dg*/, 0.0f /*dH*/, 0.0f /*dS*/,
0 /*anchor_5*/, 0 /*anchor_3*/, 0 /*target_5*/, 0 /*target_3*/,
0 /*num_mismatch*/, 0 /*num_gap*/, 0.0f /*fraction_real_base_pairs*/, string() /*align*/);
continue;
}
const float dg = m_melt.delta_G();
if( (dg < m_min_oligo_dg) || (dg > m_max_oligo_dg) ){
// Add this partial result to the cache
m_melt_cache[key] = BindCacheValue(tm, dg, 0.0f /*dH*/, 0.0f /*dS*/,
0 /*anchor_5*/, 0 /*anchor_3*/, 0 /*target_5*/, 0 /*target_3*/,
0 /*num_mismatch*/, 0 /*num_gap*/, 0.0f /*fraction_real_base_pairs*/, string() /*align*/);
continue;
}
const unsigned int anchor_5 = m_melt.anchor5_query();
if(anchor_5 < m_clamp_5){
// Add this partial result to the cache
m_melt_cache[key] = BindCacheValue(tm, dg, 0.0f /*dH*/, 0.0f /*dS*/,
anchor_5, 0 /*anchor_3*/, 0 /*target_5*/, 0 /*target_3*/,
0 /*num_mismatch*/, 0 /*num_gap*/, 0.0f /*fraction_real_base_pairs*/, string() /*align*/);
continue;
}
const unsigned int anchor_3 = m_melt.anchor3_query();
if(anchor_3 < m_clamp_3){
// Add this partial result to the cache
m_melt_cache[key] = BindCacheValue(tm, dg, 0.0f /*dH*/, 0.0f /*dS*/,
anchor_5, anchor_3, 0 /*target_5*/, 0 /*target_3*/,
0 /*num_mismatch*/, 0 /*num_gap*/, 0.0f /*fraction_real_base_pairs*/, string() /*align*/);
continue;
}
const unsigned int num_mismatch = m_melt.num_mismatch();
if(num_mismatch > m_max_mismatch){
// Add this partial result to the cache
m_melt_cache[key] = BindCacheValue(tm, dg, 0.0f /*dH*/, 0.0f /*dS*/,
anchor_5, anchor_3, 0 /*target_5*/, 0 /*target_3*/,
num_mismatch, 0 /*num_gap*/, 0.0f /*fraction_real_base_pairs*/, string() /*align*/);
continue;
}
const unsigned int num_gap = m_melt.num_gap();
if(num_gap > m_max_gap){
// Add this partial result to the cache
m_melt_cache[key] = BindCacheValue(tm, dg, 0.0 /*dH*/, 0.0 /*dS*/,
anchor_5, anchor_3, 0 /*target_5*/, 0 /*target_3*/,
num_mismatch, num_gap, 0.0 /*fraction_real_base_pairs*/, string() /*align*/);
continue;
}
// How many "real" (non-degenerate, non-virtual) bases make up the target sequence?
// Since degenerate bases get turned into 'N' by the hash function, we can
// end up with spurious matches to poly-N sequences. Require that at least