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gpertea |
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/* |
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* closures.cpp |
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* TopHat |
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* |
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* Created by Cole Trapnell on 1/15/09. |
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* Copyright 2009 Cole Trapnell. All rights reserved. |
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* |
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*/ |
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#ifdef HAVE_CONFIG_H |
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#include <config.h> |
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#endif |
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#include <iostream> |
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#include <fstream> |
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#include <getopt.h> |
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gpertea |
154 |
#include <seqan/sequence.h> |
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#include <seqan/file.h> |
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gpertea |
29 |
#include "bwt_map.h" |
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#include "inserts.h" |
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#include "closures.h" |
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#include "reads.h" |
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#include "tokenize.h" |
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gpertea |
154 |
#include "fusions.h" |
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gpertea |
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using namespace seqan; |
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using namespace std; |
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bool possible_cotranscript(const BowtieHit& h1, const BowtieHit& h2, bool check_strand = true) |
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{ |
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if (h1.insert_id() != h2.insert_id()) |
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return false; |
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gpertea |
233 |
InsertAlignmentGrade grade(h1, h2); |
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gpertea |
29 |
return (!grade.too_far && !grade.too_close && grade.opposite_strands); |
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} |
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void check_mates(const HitList& hits1_in_ref, |
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const HitList& hits2_in_ref, |
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vector<pair<size_t, size_t> >& happy_mates, |
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vector<size_t>& map1_singletons, |
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vector<size_t>& map2_singletons) |
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{ |
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std::set<size_t> marked; |
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// TODO: if this shows up on the profile, replace it with a linear |
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// time algorithm. This one is 2*n*lg(n). |
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HitList::const_iterator last_good = hits2_in_ref.begin(); |
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for (size_t i = 0; i < hits1_in_ref.size(); ++i) |
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{ |
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pair<HitList::const_iterator, HitList::const_iterator> range_pair; |
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range_pair = equal_range(last_good, hits2_in_ref.end(), |
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hits1_in_ref[i], hit_insert_id_lt); |
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bool found_hit = false; |
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if (range_pair.first != range_pair.second) |
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last_good = range_pair.first; |
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for (HitList::const_iterator f = range_pair.first; |
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f != range_pair.second; |
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++f) |
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{ |
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if (possible_cotranscript(hits1_in_ref[i], *f)) |
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{ |
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happy_mates.push_back(make_pair(i,f - hits2_in_ref.begin())); |
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marked.insert(f - hits2_in_ref.begin()); |
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found_hit = true; |
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} |
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} |
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if (!found_hit) |
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map1_singletons.push_back(i); |
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} |
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for (size_t i = 0; i < hits2_in_ref.size(); ++i) |
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{ |
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if (marked.find(i) == marked.end()) |
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{ |
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map2_singletons.push_back(i); |
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} |
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} |
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} |
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gpertea |
154 |
void find_fusion_closure(HitsForRead& left_hits, |
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HitsForRead& right_hits, |
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std::set<Fusion>& fusions) |
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{ |
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if (left_hits.hits.size() > 3 || right_hits.hits.size() > 3) |
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return; |
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for (size_t left_index = 0; left_index < left_hits.hits.size(); ++left_index) |
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{ |
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for (size_t right_index = 0; right_index < right_hits.hits.size(); ++right_index) |
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{ |
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BowtieHit* leftHit = &left_hits.hits[left_index]; |
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BowtieHit* rightHit = &right_hits.hits[right_index]; |
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uint32_t dir = FUSION_FF; |
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if (leftHit->antisense_align() != rightHit->antisense_align()) |
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dir = FUSION_FF; |
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else if (!leftHit->antisense_align()) |
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dir = FUSION_FR; |
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else |
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dir = FUSION_RF; |
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if (dir == FUSION_FF && leftHit->antisense_align()) |
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{ |
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BowtieHit * tmp = leftHit; |
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leftHit = rightHit; |
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rightHit = tmp; |
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} |
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uint32_t left, right; |
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if (dir == FUSION_FF || dir == FUSION_FR) |
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left = leftHit->right() - 4; |
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else |
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left = leftHit->left() + 4; |
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if (dir == FUSION_FF || dir == FUSION_RF) |
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right = rightHit->left() + 4; |
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else |
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right = rightHit->right() - 4; |
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if (leftHit->ref_id() == rightHit->ref_id() && dir == FUSION_FF) |
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{ |
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int dist = 0; |
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dist = rightHit->left() - leftHit->right(); |
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if (dist >= 0 && dist <= (int)fusion_min_dist) |
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continue; |
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} |
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uint32_t ref_id1 = leftHit->ref_id(); |
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uint32_t ref_id2 = rightHit->ref_id(); |
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if (dir == FUSION_FR || dir == FUSION_RF) |
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{ |
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if ((ref_id2 < ref_id1) || (ref_id1 == ref_id2 && left > right)) |
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{ |
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uint32_t temp = ref_id1; |
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ref_id1 = ref_id2; |
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ref_id2 = temp; |
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temp = left; |
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left = right; |
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right = temp; |
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} |
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} |
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fusions.insert(Fusion(ref_id1, ref_id2, left, right, dir)); |
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} |
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} |
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} |
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gpertea |
29 |
bool prefer_shorter_pairs = true; |
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typedef pair<InsertAlignmentGrade, vector<InsertAlignment> > BestPairingHits; |
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template<typename Visitor> |
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void visit_best_pairing(HitsForRead& left_hit_group, |
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HitsForRead& right_hit_group, |
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Visitor& visitor) |
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{ |
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BestPairingHits insert_best; |
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for (size_t i = 0; i < left_hit_group.hits.size(); ++i) |
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{ |
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BowtieHit& h1 = left_hit_group.hits[i]; |
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for (size_t j = 0; j < right_hit_group.hits.size(); j++) |
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{ |
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BowtieHit& h2 = right_hit_group.hits[j]; |
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if (h1.ref_id() != h2.ref_id()) |
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continue; |
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uint32_t refid = h1.ref_id(); |
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gpertea |
233 |
InsertAlignmentGrade s(h1, h2); |
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gpertea |
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//pair<InsertAlignmentGrade, vector<InsertAlignment> >& insert_best |
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// = best_status_for_inserts[curr_left_obs_order]; |
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InsertAlignmentGrade& current = insert_best.first; |
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// Is the new status better than the current best one? |
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if (current < s) |
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{ |
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insert_best.second.clear(); |
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current = s; |
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insert_best.second.push_back(InsertAlignment(refid, &h1, &h2)); |
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} |
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else if (! (s < current)) |
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{ |
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if (prefer_shorter_pairs && current.num_mapped == 2) |
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{ |
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pair<int, int> dc = pair_distances(*(insert_best.second[0].left_alignment), *(insert_best.second[0].right_alignment)); |
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pair<int, int> ds = pair_distances(h1,h2); |
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if (ds.second < dc.second) |
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{ |
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//chucked_for_shorter_pair += insert_best.second.size(); |
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insert_best.second.clear(); |
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current = s; |
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insert_best.second.push_back(InsertAlignment(refid, &h1, &h2)); |
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} |
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} |
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else |
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{ |
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insert_best.second.push_back(InsertAlignment(refid, &h1, &h2)); |
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} |
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} |
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} |
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} |
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visitor.visit(insert_best); |
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} |
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class CovMapIntronFinder |
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{ |
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std::set<SpliceMotif> _tmp_hits; |
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vector<SpliceMotif> _hits; |
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RefSequenceTable::Sequence* _ref_seq; |
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public: |
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CovMapIntronFinder() : _ref_seq(NULL) {} |
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CovMapIntronFinder(RefSequenceTable::Sequence* ref_seq) : |
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_ref_seq(ref_seq), |
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_lms(vector<bool>(length(*ref_seq), false)), |
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_rms(vector<bool>(length(*ref_seq), false)){} |
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void add_motifs_in_window(int left, |
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int right, |
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const string& left_motif, |
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const string& right_motif) |
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{ |
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size_t l_start = max(0,left); |
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for (int i = l_start; |
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i < min(right, (int)length(*_ref_seq) - 2); |
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++i) |
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{ |
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seqan::Infix<RefSequenceTable::Sequence>::Type curr |
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= seqan::infix(*_ref_seq,i, i + 2); |
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if (curr == left_motif) |
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_lms[i] = true; |
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else if (curr == right_motif) |
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_rms[i] = true; |
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} |
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} |
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void finalize() |
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{ |
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int pos = 0; |
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for (vector<bool>::iterator itr = _lms.begin(); |
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itr != _lms.end(); |
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++itr, ++pos) |
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{ |
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if (*itr) |
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_hits.push_back(SpliceMotif(pos, true)); |
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} |
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pos = 0; |
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for (vector<bool>::iterator itr = _rms.begin(); |
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itr != _rms.end(); |
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++itr, ++pos) |
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{ |
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if (*itr) |
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_hits.push_back(SpliceMotif(pos, false)); |
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} |
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sort(_hits.begin(), _hits.end()); |
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} |
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size_t seq_len() const { return length(*_ref_seq); } |
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const vector<SpliceMotif>& hits() const { return _hits; } |
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vector<bool> _lms; |
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vector<bool> _rms; |
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}; |
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typedef CovMapIntronFinder CIF; |
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struct RefCIF |
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{ |
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RefCIF() : ref_seq(NULL) {} |
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RefCIF(const CIF& f, const CIF& r, RefSequenceTable::Sequence* s) : |
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fwd_cif(f), rev_cif(r), ref_seq(s) {} |
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CIF fwd_cif; |
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CIF rev_cif; |
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RefSequenceTable::Sequence* ref_seq; |
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}; |
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class CoverageMapVisitor |
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{ |
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public: |
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map<uint32_t, RefCIF> finders; |
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CoverageMapVisitor(istream& ref_stream, |
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RefSequenceTable& rt) |
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{ |
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while(ref_stream.good() && |
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!ref_stream.eof()) |
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{ |
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RefSequenceTable::Sequence* ref_str = new RefSequenceTable::Sequence; |
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string name; |
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readMeta(ref_stream, name, Fasta()); |
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string::size_type space_pos = name.find_first_of(" \t\r"); |
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if (space_pos != string::npos) |
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{ |
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name.resize(space_pos); |
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} |
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read(ref_stream, *ref_str, Fasta()); |
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uint32_t ref_id = rt.get_id(name, NULL, 0); |
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finders[ref_id] = RefCIF(CIF(ref_str), CIF(ref_str), ref_str); |
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} |
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} |
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void visit(BestPairingHits& pairings) |
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{ |
| 316 |
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if (!pairings.first.num_mapped == 2) |
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return; |
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static string fwd_lm("GT"); |
| 320 |
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static string fwd_rm("AG"); |
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static string rev_lm("CT"); |
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static string rev_rm("AC"); |
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for (size_t i = 0; |
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i < pairings.second.size(); |
| 326 |
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++i) |
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{ |
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InsertAlignment& al = pairings.second[i]; |
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BowtieHit& bh_left = *(al.left_alignment); |
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BowtieHit& bh_right = *(al.right_alignment); |
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| 334 |
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assert (bh_left.ref_id() == bh_right.ref_id()); |
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| 336 |
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map<uint32_t, RefCIF >::iterator if_itr = finders.find(bh_left.ref_id()); |
| 337 |
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assert (if_itr != finders.end()); |
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| 339 |
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RefCIF& ref_finders = if_itr->second; |
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pair<int, int> ds = pair_distances(bh_left, bh_right); |
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| 343 |
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int minor_hit_start, major_hit_start; |
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int minor_hit_end, major_hit_end; |
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if (bh_left.left() < bh_right.left()) |
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{ |
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minor_hit_start = (int)bh_left.left(); |
| 348 |
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minor_hit_end = (int)bh_left.right(); |
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major_hit_start = (int)bh_right.left(); |
| 350 |
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major_hit_end = (int)bh_right.right(); |
| 351 |
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} |
| 352 |
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else |
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{ |
| 354 |
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minor_hit_start = (int)bh_right.left(); |
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minor_hit_end = (int)bh_right.right(); |
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major_hit_start = (int)bh_left.left(); |
| 357 |
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major_hit_end = (int)bh_left.right(); |
| 358 |
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} |
| 359 |
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| 360 |
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int inner_dist = major_hit_start - minor_hit_end; |
| 361 |
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| 362 |
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bool skip_fwd = false; |
| 363 |
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bool skip_rev = false; |
| 364 |
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| 365 |
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if (library_type == FR_FIRSTSTRAND) |
| 366 |
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{ |
| 367 |
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if (bh_left.antisense_align()) skip_rev = true; |
| 368 |
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else skip_fwd = true; |
| 369 |
|
|
} |
| 370 |
|
|
|
| 371 |
|
|
if (library_type == FR_SECONDSTRAND) |
| 372 |
|
|
{ |
| 373 |
|
|
if (bh_left.antisense_align()) skip_fwd = true; |
| 374 |
|
|
else skip_rev = true; |
| 375 |
|
|
} |
| 376 |
|
|
|
| 377 |
|
|
if (inner_dist > inner_dist_mean + 2 * inner_dist_std_dev) |
| 378 |
|
|
{ |
| 379 |
|
|
// Forward strand |
| 380 |
|
|
if (!skip_fwd) |
| 381 |
|
|
{ |
| 382 |
|
|
ref_finders.fwd_cif.add_motifs_in_window((int)bh_left.left() - 10, |
| 383 |
|
|
bh_left.right() + 10, |
| 384 |
|
|
fwd_lm, |
| 385 |
|
|
fwd_rm); |
| 386 |
|
|
|
| 387 |
|
|
ref_finders.fwd_cif.add_motifs_in_window((int)bh_right.left() - 10, |
| 388 |
|
|
bh_right.right() + 10, |
| 389 |
|
|
fwd_lm, |
| 390 |
|
|
fwd_rm); |
| 391 |
|
|
} |
| 392 |
|
|
|
| 393 |
|
|
// Reverse strand |
| 394 |
|
|
if (!skip_rev) |
| 395 |
|
|
{ |
| 396 |
|
|
ref_finders.rev_cif.add_motifs_in_window((int)bh_left.left() - 10, |
| 397 |
|
|
bh_left.right() + 10, |
| 398 |
|
|
rev_lm, |
| 399 |
|
|
rev_rm); |
| 400 |
|
|
|
| 401 |
|
|
ref_finders.rev_cif.add_motifs_in_window((int)bh_right.left() - 10, |
| 402 |
|
|
bh_right.right() + 10, |
| 403 |
|
|
rev_lm, |
| 404 |
|
|
rev_rm); |
| 405 |
|
|
} |
| 406 |
|
|
} |
| 407 |
|
|
} |
| 408 |
|
|
} |
| 409 |
|
|
|
| 410 |
|
|
void finalize() |
| 411 |
|
|
{ |
| 412 |
|
|
for (map<uint32_t, RefCIF >::iterator itr = finders.begin(); |
| 413 |
|
|
itr != finders.end(); |
| 414 |
|
|
++itr) |
| 415 |
|
|
{ |
| 416 |
|
|
itr->second.fwd_cif.finalize(); |
| 417 |
|
|
itr->second.rev_cif.finalize(); |
| 418 |
|
|
delete itr->second.ref_seq; |
| 419 |
|
|
itr->second.ref_seq = NULL; |
| 420 |
|
|
} |
| 421 |
|
|
} |
| 422 |
|
|
}; |
| 423 |
|
|
|
| 424 |
|
|
|
| 425 |
|
|
class JunctionMapVisitor |
| 426 |
|
|
{ |
| 427 |
|
|
public: |
| 428 |
|
|
typedef JunctionFinder<RefSequenceTable::Sequence, CIF> JF; |
| 429 |
|
|
|
| 430 |
|
|
struct JunctionTable |
| 431 |
|
|
{ |
| 432 |
|
|
JunctionTable() : jf(NULL), possible_splices(NULL) {} |
| 433 |
|
|
JunctionTable(ClosureJunctionSet* ps, JF* _jf, bool as) |
| 434 |
|
|
: jf(_jf), possible_splices(ps), antisense(as) {} |
| 435 |
|
|
|
| 436 |
|
|
JF* jf; |
| 437 |
|
|
ClosureJunctionSet* possible_splices; |
| 438 |
|
|
bool antisense; |
| 439 |
|
|
}; |
| 440 |
|
|
|
| 441 |
|
|
|
| 442 |
|
|
map<uint32_t, pair<JunctionTable, JunctionTable> > _finders; |
| 443 |
|
|
|
| 444 |
|
|
JunctionMapVisitor(ClosureJunctionSet& fwd_splices, |
| 445 |
|
|
ClosureJunctionSet& rev_splices, |
| 446 |
|
|
map<uint32_t, RefCIF >& finders) |
| 447 |
|
|
{ |
| 448 |
|
|
static const uint32_t bowtie_padding = 5; |
| 449 |
|
|
for (map<uint32_t, RefCIF >::iterator itr = finders.begin(); |
| 450 |
|
|
itr != finders.end(); |
| 451 |
|
|
++itr) |
| 452 |
|
|
{ |
| 453 |
|
|
JF* fwd_jf = new JF(itr->second.fwd_cif, |
| 454 |
|
|
inner_dist_mean, |
| 455 |
|
|
inner_dist_std_dev, |
| 456 |
|
|
min_closure_intron_length, |
| 457 |
|
|
min_closure_exon_length, |
| 458 |
|
|
bowtie_padding, |
| 459 |
|
|
island_extension); |
| 460 |
|
|
JF* rev_jf = new JF(itr->second.rev_cif, |
| 461 |
|
|
inner_dist_mean, |
| 462 |
|
|
inner_dist_std_dev, |
| 463 |
|
|
min_closure_intron_length, |
| 464 |
|
|
min_closure_exon_length, |
| 465 |
|
|
bowtie_padding, |
| 466 |
|
|
island_extension); |
| 467 |
|
|
|
| 468 |
|
|
_finders[itr->first] = make_pair(JunctionTable(&fwd_splices, fwd_jf,false), |
| 469 |
|
|
JunctionTable(&rev_splices, rev_jf, true)); |
| 470 |
|
|
} |
| 471 |
|
|
} |
| 472 |
|
|
|
| 473 |
|
|
|
| 474 |
|
|
void visit(BestPairingHits& pairings) |
| 475 |
|
|
{ |
| 476 |
|
|
if (!pairings.first.num_mapped == 2) |
| 477 |
|
|
return; |
| 478 |
|
|
for (size_t i = 0; |
| 479 |
|
|
i < pairings.second.size(); |
| 480 |
|
|
++i) |
| 481 |
|
|
{ |
| 482 |
|
|
|
| 483 |
|
|
InsertAlignment& al = pairings.second[i]; |
| 484 |
|
|
|
| 485 |
|
|
BowtieHit& bh_left = *(al.left_alignment); |
| 486 |
|
|
BowtieHit& bh_right = *(al.right_alignment); |
| 487 |
|
|
|
| 488 |
|
|
assert (bh_left.ref_id() == bh_right.ref_id()); |
| 489 |
|
|
|
| 490 |
|
|
map<uint32_t, pair<JunctionTable, JunctionTable> >::iterator if_itr = _finders.find(bh_left.ref_id()); |
| 491 |
|
|
assert (if_itr != _finders.end()); |
| 492 |
|
|
|
| 493 |
|
|
JF& fwd_jf = *(if_itr->second.first.jf); |
| 494 |
|
|
fwd_jf.possible_junctions(*(if_itr->second.first.possible_splices), bh_left, bh_right); |
| 495 |
|
|
|
| 496 |
|
|
JF& rev_jf = *(if_itr->second.second.jf); |
| 497 |
|
|
rev_jf.possible_junctions(*(if_itr->second.second.possible_splices), bh_left, bh_right); |
| 498 |
|
|
} |
| 499 |
|
|
} |
| 500 |
|
|
}; |
| 501 |
|
|
|
| 502 |
|
|
void closure_driver(vector<FZPipe>& map1, |
| 503 |
|
|
vector<FZPipe>& map2, |
| 504 |
|
|
ifstream& ref_stream, |
| 505 |
gpertea |
154 |
FILE* juncs_file, |
| 506 |
|
|
FILE* fusions_out) |
| 507 |
gpertea |
29 |
{ |
| 508 |
|
|
typedef RefSequenceTable::Sequence Reference; |
| 509 |
|
|
|
| 510 |
|
|
ReadTable it; |
| 511 |
|
|
RefSequenceTable rt(true); |
| 512 |
gpertea |
154 |
|
| 513 |
|
|
BowtieHitFactory hit_factory(it, rt); |
| 514 |
|
|
|
| 515 |
|
|
std::set<Fusion> fusions; |
| 516 |
gpertea |
29 |
|
| 517 |
|
|
fprintf (stderr, "Finding near-covered motifs..."); |
| 518 |
|
|
CoverageMapVisitor cov_map_visitor(ref_stream, rt); |
| 519 |
|
|
uint32_t coverage_attempts = 0; |
| 520 |
|
|
|
| 521 |
|
|
assert(map1.size() == map2.size()); |
| 522 |
|
|
for (size_t num = 0; num < map1.size(); ++num) |
| 523 |
|
|
{ |
| 524 |
|
|
HitStream left_hs(map1[num].file, &hit_factory, false, true, false); |
| 525 |
|
|
HitStream right_hs(map2[num].file, &hit_factory, false, true, false); |
| 526 |
|
|
|
| 527 |
|
|
HitsForRead curr_left_hit_group; |
| 528 |
|
|
HitsForRead curr_right_hit_group; |
| 529 |
|
|
|
| 530 |
|
|
left_hs.next_read_hits(curr_left_hit_group); |
| 531 |
|
|
right_hs.next_read_hits(curr_right_hit_group); |
| 532 |
|
|
|
| 533 |
|
|
uint32_t curr_right_obs_order = it.observation_order(curr_left_hit_group.insert_id); |
| 534 |
|
|
uint32_t curr_left_obs_order = it.observation_order(curr_right_hit_group.insert_id); |
| 535 |
|
|
|
| 536 |
gpertea |
135 |
while(curr_left_obs_order != VMAXINT32 && |
| 537 |
|
|
curr_right_obs_order != VMAXINT32) |
| 538 |
gpertea |
29 |
{ |
| 539 |
|
|
while (curr_left_obs_order < curr_right_obs_order&& |
| 540 |
gpertea |
135 |
curr_left_obs_order != VMAXINT32 && curr_right_obs_order != VMAXINT32) |
| 541 |
gpertea |
29 |
{ |
| 542 |
|
|
// Get hit group |
| 543 |
|
|
|
| 544 |
|
|
left_hs.next_read_hits(curr_left_hit_group); |
| 545 |
|
|
curr_left_obs_order = it.observation_order(curr_left_hit_group.insert_id); |
| 546 |
|
|
} |
| 547 |
|
|
|
| 548 |
|
|
while (curr_left_obs_order > curr_right_obs_order && |
| 549 |
gpertea |
135 |
curr_left_obs_order != VMAXINT32 && curr_right_obs_order != VMAXINT32) |
| 550 |
gpertea |
29 |
{ |
| 551 |
|
|
// Get hit group |
| 552 |
|
|
|
| 553 |
|
|
right_hs.next_read_hits(curr_right_hit_group); |
| 554 |
|
|
curr_right_obs_order = it.observation_order(curr_right_hit_group.insert_id); |
| 555 |
|
|
} |
| 556 |
|
|
|
| 557 |
|
|
while (curr_left_obs_order == curr_right_obs_order && |
| 558 |
gpertea |
135 |
curr_left_obs_order != VMAXINT32 && curr_right_obs_order != VMAXINT32) |
| 559 |
gpertea |
154 |
{ |
| 560 |
|
|
if (num == 0) |
| 561 |
|
|
find_fusion_closure(curr_left_hit_group, curr_right_hit_group, fusions); |
| 562 |
|
|
|
| 563 |
|
|
if (coverage_attempts++ % 10000 == 0) |
| 564 |
|
|
fprintf (stderr, "Adding covered motifs from pair %d\n", coverage_attempts); |
| 565 |
|
|
|
| 566 |
gpertea |
29 |
visit_best_pairing(curr_left_hit_group, curr_right_hit_group, cov_map_visitor); |
| 567 |
|
|
|
| 568 |
|
|
left_hs.next_read_hits(curr_left_hit_group); |
| 569 |
|
|
curr_left_obs_order = it.observation_order(curr_left_hit_group.insert_id); |
| 570 |
|
|
|
| 571 |
|
|
right_hs.next_read_hits(curr_right_hit_group); |
| 572 |
|
|
curr_right_obs_order = it.observation_order(curr_right_hit_group.insert_id); |
| 573 |
|
|
} |
| 574 |
|
|
} |
| 575 |
|
|
} |
| 576 |
|
|
|
| 577 |
|
|
cov_map_visitor.finalize(); |
| 578 |
|
|
fprintf (stderr, "done\n"); |
| 579 |
|
|
|
| 580 |
|
|
ClosureJunctionSet fwd_splices; |
| 581 |
|
|
ClosureJunctionSet rev_splices; |
| 582 |
|
|
|
| 583 |
|
|
JunctionMapVisitor junc_map_visitor(fwd_splices, rev_splices, cov_map_visitor.finders); |
| 584 |
|
|
fprintf (stderr, "Searching for closures..."); |
| 585 |
|
|
uint32_t closure_attempts = 0; |
| 586 |
|
|
|
| 587 |
|
|
for (size_t num = 0; num < map1.size(); ++num) |
| 588 |
|
|
{ |
| 589 |
|
|
map1[num].rewind(); |
| 590 |
|
|
map2[num].rewind(); |
| 591 |
|
|
|
| 592 |
|
|
HitStream left_hs = HitStream(map1[num].file, &hit_factory, false, true, false); |
| 593 |
|
|
HitStream right_hs = HitStream(map2[num].file, &hit_factory, false, true, false); |
| 594 |
|
|
|
| 595 |
|
|
HitsForRead curr_left_hit_group; |
| 596 |
|
|
HitsForRead curr_right_hit_group; |
| 597 |
|
|
|
| 598 |
|
|
left_hs.next_read_hits(curr_left_hit_group); |
| 599 |
|
|
right_hs.next_read_hits(curr_right_hit_group); |
| 600 |
|
|
|
| 601 |
|
|
uint32_t curr_right_obs_order = it.observation_order(curr_left_hit_group.insert_id); |
| 602 |
|
|
uint32_t curr_left_obs_order = it.observation_order(curr_right_hit_group.insert_id); |
| 603 |
|
|
|
| 604 |
gpertea |
135 |
while(curr_left_obs_order != VMAXINT32 && |
| 605 |
|
|
curr_right_obs_order != VMAXINT32) |
| 606 |
gpertea |
29 |
{ |
| 607 |
|
|
while (curr_left_obs_order < curr_right_obs_order && |
| 608 |
gpertea |
135 |
curr_left_obs_order != VMAXINT32 && curr_right_obs_order != VMAXINT32) |
| 609 |
gpertea |
29 |
{ |
| 610 |
|
|
// Get hit group |
| 611 |
|
|
|
| 612 |
|
|
left_hs.next_read_hits(curr_left_hit_group); |
| 613 |
|
|
curr_left_obs_order = it.observation_order(curr_left_hit_group.insert_id); |
| 614 |
|
|
} |
| 615 |
|
|
|
| 616 |
|
|
while (curr_left_obs_order > curr_right_obs_order && |
| 617 |
gpertea |
135 |
curr_left_obs_order != VMAXINT32 && curr_right_obs_order != VMAXINT32) |
| 618 |
gpertea |
29 |
{ |
| 619 |
|
|
// Get hit group |
| 620 |
|
|
|
| 621 |
|
|
right_hs.next_read_hits(curr_right_hit_group); |
| 622 |
|
|
curr_right_obs_order = it.observation_order(curr_right_hit_group.insert_id); |
| 623 |
|
|
} |
| 624 |
|
|
|
| 625 |
|
|
while (curr_left_obs_order == curr_right_obs_order && |
| 626 |
gpertea |
135 |
curr_left_obs_order != VMAXINT32 && curr_right_obs_order != VMAXINT32) |
| 627 |
gpertea |
29 |
{ |
| 628 |
gpertea |
154 |
if (closure_attempts++ % 10000 == 0) |
| 629 |
|
|
fprintf (stderr, "Trying to close pair %d\n", closure_attempts); |
| 630 |
|
|
|
| 631 |
gpertea |
29 |
visit_best_pairing(curr_left_hit_group, curr_right_hit_group, junc_map_visitor); |
| 632 |
|
|
left_hs.next_read_hits(curr_left_hit_group); |
| 633 |
|
|
curr_left_obs_order = it.observation_order(curr_left_hit_group.insert_id); |
| 634 |
|
|
|
| 635 |
|
|
right_hs.next_read_hits(curr_right_hit_group); |
| 636 |
|
|
curr_right_obs_order = it.observation_order(curr_right_hit_group.insert_id); |
| 637 |
|
|
} |
| 638 |
|
|
} |
| 639 |
|
|
} |
| 640 |
|
|
|
| 641 |
|
|
for (size_t num = 0; num < map1.size(); ++num) |
| 642 |
|
|
{ |
| 643 |
|
|
map1[num].close(); |
| 644 |
|
|
map2[num].close(); |
| 645 |
|
|
} |
| 646 |
|
|
|
| 647 |
|
|
fprintf(stderr, "%lu Forward strand splices\n", fwd_splices.size()); |
| 648 |
|
|
fprintf(stderr, "%lu Reverse strand splices\n", rev_splices.size()); |
| 649 |
|
|
|
| 650 |
|
|
fprintf (stderr, "done\n"); |
| 651 |
|
|
uint32_t num_potential_splices = 0; |
| 652 |
|
|
fprintf (stderr, "Reporting possible junctions..."); |
| 653 |
|
|
map<uint32_t, pair<JunctionMapVisitor::JunctionTable, JunctionMapVisitor::JunctionTable> >::iterator f_itr; |
| 654 |
|
|
f_itr = junc_map_visitor._finders.begin(); |
| 655 |
|
|
|
| 656 |
|
|
ClosureJunctionSet::iterator j_itr; |
| 657 |
|
|
j_itr = fwd_splices.begin(); |
| 658 |
|
|
while (j_itr != fwd_splices.end()) |
| 659 |
|
|
{ |
| 660 |
|
|
fprintf (juncs_file,"%s\t%u\t%u\t%c\n", |
| 661 |
|
|
rt.get_name(j_itr->refid), |
| 662 |
|
|
j_itr->left,j_itr->right,'+'); |
| 663 |
|
|
++num_potential_splices; |
| 664 |
|
|
++j_itr; |
| 665 |
|
|
} |
| 666 |
|
|
|
| 667 |
|
|
j_itr = rev_splices.begin(); |
| 668 |
|
|
while (j_itr != rev_splices.end()) |
| 669 |
|
|
{ |
| 670 |
|
|
fprintf (juncs_file,"%s\t%u\t%u\t%c\n", |
| 671 |
|
|
rt.get_name(j_itr->refid), |
| 672 |
|
|
j_itr->left,j_itr->right,'-'); |
| 673 |
|
|
++num_potential_splices; |
| 674 |
|
|
++j_itr; |
| 675 |
|
|
} |
| 676 |
|
|
|
| 677 |
|
|
//accept_all_best_hits(best_status_for_inserts); |
| 678 |
|
|
fprintf(stderr, "done\n"); |
| 679 |
|
|
fprintf(stderr, "Searched for closures between %d pairs\n", searched); |
| 680 |
|
|
fprintf(stderr, "Successfully closed %d pairs\n", closed); |
| 681 |
|
|
|
| 682 |
|
|
fprintf(stderr, "Found %d total possible splices\n", num_potential_splices); |
| 683 |
gpertea |
154 |
|
| 684 |
|
|
// daehwan |
| 685 |
|
|
#if 0 |
| 686 |
|
|
fprintf (stderr, "Reporting potential fusions...\n"); |
| 687 |
|
|
if(fusions_out){ |
| 688 |
|
|
for(std::set<Fusion>::iterator itr = fusions.begin(); itr != fusions.end(); ++itr){ |
| 689 |
|
|
const char* ref_name1 = rt.get_name(itr->refid1); |
| 690 |
|
|
const char* ref_name2 = rt.get_name(itr->refid2); |
| 691 |
|
|
|
| 692 |
|
|
const char* dir = ""; |
| 693 |
|
|
if (itr->dir == FUSION_FR) |
| 694 |
|
|
dir = "fr"; |
| 695 |
|
|
else if(itr->dir == FUSION_RF) |
| 696 |
|
|
dir = "rf"; |
| 697 |
|
|
else |
| 698 |
|
|
dir = "ff"; |
| 699 |
|
|
|
| 700 |
|
|
fprintf(fusions_out, |
| 701 |
|
|
"%s\t%d\t%s\t%d\t%s\n", |
| 702 |
|
|
ref_name1, |
| 703 |
|
|
itr->left, |
| 704 |
|
|
ref_name2, |
| 705 |
|
|
itr->right, |
| 706 |
|
|
dir); |
| 707 |
|
|
} |
| 708 |
|
|
fclose(fusions_out); |
| 709 |
|
|
}else{ |
| 710 |
|
|
fprintf(stderr, "Failed to open fusions file for writing\n"); |
| 711 |
|
|
} |
| 712 |
|
|
#endif |
| 713 |
gpertea |
29 |
} |
| 714 |
|
|
|
| 715 |
|
|
void print_usage() |
| 716 |
|
|
{ |
| 717 |
|
|
fprintf(stderr, "Usage: closure_juncs <closure.juncs> <ref.fa> <left_map.bwtout> <right_map.bwtout>\n"); |
| 718 |
|
|
} |
| 719 |
|
|
|
| 720 |
|
|
int main(int argc, char** argv) |
| 721 |
|
|
{ |
| 722 |
|
|
fprintf(stderr, "closure_juncs v%s (%s)\n", PACKAGE_VERSION, SVN_REVISION); |
| 723 |
|
|
fprintf(stderr, "---------------------------\n"); |
| 724 |
|
|
|
| 725 |
|
|
int parse_ret = parse_options(argc, argv, print_usage); |
| 726 |
|
|
if (parse_ret) |
| 727 |
|
|
return parse_ret; |
| 728 |
|
|
|
| 729 |
|
|
if(optind >= argc) |
| 730 |
|
|
{ |
| 731 |
|
|
print_usage(); |
| 732 |
|
|
return 1; |
| 733 |
|
|
} |
| 734 |
|
|
|
| 735 |
|
|
string junctions_file_name = argv[optind++]; |
| 736 |
|
|
|
| 737 |
|
|
if(optind >= argc) |
| 738 |
|
|
{ |
| 739 |
|
|
print_usage(); |
| 740 |
|
|
return 1; |
| 741 |
|
|
} |
| 742 |
gpertea |
154 |
|
| 743 |
|
|
string fusions_file_name = argv[optind++]; |
| 744 |
gpertea |
29 |
|
| 745 |
gpertea |
154 |
if(optind >= argc) |
| 746 |
|
|
{ |
| 747 |
|
|
print_usage(); |
| 748 |
|
|
return 1; |
| 749 |
|
|
} |
| 750 |
|
|
|
| 751 |
gpertea |
29 |
string ref_fasta = argv[optind++]; |
| 752 |
gpertea |
154 |
|
| 753 |
gpertea |
29 |
if(optind >= argc) |
| 754 |
|
|
{ |
| 755 |
|
|
print_usage(); |
| 756 |
|
|
return 1; |
| 757 |
|
|
} |
| 758 |
|
|
|
| 759 |
|
|
string left_file_list = argv[optind++]; |
| 760 |
|
|
vector<string> left_file_names; |
| 761 |
|
|
vector<FZPipe> left_files; |
| 762 |
|
|
tokenize(left_file_list, ",", left_file_names); |
| 763 |
|
|
|
| 764 |
|
|
string unzcmd = getUnpackCmd(left_file_names[0], false); |
| 765 |
|
|
for (size_t i = 0; i < left_file_names.size(); ++i) |
| 766 |
|
|
{ |
| 767 |
|
|
FZPipe seg_file(left_file_names[i], unzcmd); |
| 768 |
|
|
if (seg_file.file == NULL) |
| 769 |
|
|
{ |
| 770 |
|
|
fprintf(stderr, "Error: cannot open file %s for reading\n", |
| 771 |
|
|
left_file_names[i].c_str()); |
| 772 |
|
|
exit(1); |
| 773 |
|
|
} |
| 774 |
|
|
left_files.push_back(seg_file); |
| 775 |
|
|
} |
| 776 |
|
|
|
| 777 |
|
|
if(optind >= argc) |
| 778 |
|
|
{ |
| 779 |
|
|
print_usage(); |
| 780 |
|
|
return 1; |
| 781 |
|
|
} |
| 782 |
|
|
|
| 783 |
|
|
string right_file_list = argv[optind++]; |
| 784 |
|
|
vector<string> right_file_names; |
| 785 |
|
|
vector<FZPipe> right_files; |
| 786 |
|
|
tokenize(right_file_list, ",", right_file_names); |
| 787 |
|
|
for (size_t i = 0; i < right_file_names.size(); ++i) |
| 788 |
|
|
{ |
| 789 |
|
|
FZPipe seg_file(right_file_names[i], unzcmd); |
| 790 |
|
|
if (seg_file.file == NULL) |
| 791 |
|
|
{ |
| 792 |
|
|
fprintf(stderr, "Error: cannot open %s for reading\n", |
| 793 |
|
|
right_file_names[i].c_str()); |
| 794 |
|
|
exit(1); |
| 795 |
|
|
} |
| 796 |
|
|
right_files.push_back(seg_file); |
| 797 |
|
|
} |
| 798 |
|
|
|
| 799 |
|
|
ifstream ref_stream(ref_fasta.c_str(), ifstream::in); |
| 800 |
|
|
|
| 801 |
|
|
FILE* splice_db = fopen(junctions_file_name.c_str(), "w"); |
| 802 |
|
|
if (splice_db == NULL) |
| 803 |
|
|
{ |
| 804 |
|
|
fprintf(stderr, "Error: cannot open junctions file %s for writing\n", |
| 805 |
|
|
junctions_file_name.c_str()); |
| 806 |
|
|
exit(1); |
| 807 |
|
|
} |
| 808 |
gpertea |
154 |
|
| 809 |
|
|
FILE* fusion_db = fopen(fusions_file_name.c_str(), "w"); |
| 810 |
|
|
if (splice_db == NULL) |
| 811 |
|
|
{ |
| 812 |
|
|
fprintf(stderr, "Error: cannot open fusions file %s for writing\n", |
| 813 |
|
|
fusions_file_name.c_str()); |
| 814 |
|
|
exit(1); |
| 815 |
|
|
} |
| 816 |
|
|
|
| 817 |
gpertea |
29 |
closure_driver(left_files, |
| 818 |
|
|
right_files, |
| 819 |
|
|
ref_stream, |
| 820 |
gpertea |
154 |
splice_db, |
| 821 |
|
|
fusion_db); |
| 822 |
gpertea |
29 |
|
| 823 |
|
|
return 0; |
| 824 |
|
|
} |
