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/* |
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* fragments.cpp |
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* TopHat |
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* |
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* Created by Cole Trapnell on 1/14/09. |
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* Copyright 2009 Cole Trapnell. All rights reserved. |
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* |
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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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|
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#include <cassert> |
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#include "bwt_map.h" |
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#include "fragments.h" |
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|
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void best_fragment_mappings(uint64_t refid, |
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const string& name, |
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HitList& hits_in_ref, |
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ReadTable& it, |
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BestFragmentAlignmentTable& best_status_for_fragments) |
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{ |
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for (size_t i = 0; i < hits_in_ref.size(); ++i) |
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{ |
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BowtieHit& h1 = hits_in_ref[i]; |
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uint64_t fragment_id = h1.insert_id(); |
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uint32_t obs_order = it.observation_order(fragment_id); |
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|
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JunctionSet dummy; |
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FragmentAlignmentGrade s(h1, dummy); |
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|
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pair<FragmentAlignmentGrade, vector<FragmentAlignment*> >& fragment_best |
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= best_status_for_fragments[obs_order]; |
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FragmentAlignmentGrade& current = fragment_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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fragment_best.second.clear(); |
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current = s; |
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fragment_best.second.push_back(&h1); |
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} |
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else if (! (s < current)) // is it just as good? |
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{ |
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fragment_best.second.push_back(&h1); |
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} |
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} |
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} |
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|
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bool valid_fragment_alignment(const FragmentAlignmentGrade& g, const FragmentAlignment& a) |
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{ |
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// stub |
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return true; |
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} |
