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root/gclib/tophat_cpp/fragments.cpp
Revision: 135
Committed: Mon Dec 12 22:28:38 2011 UTC (7 years, 10 months ago) by gpertea
File size: 1314 byte(s)
Log Message:
wip - SplicedSAMHitFactory() still not implemented

Line File contents
1 /*
2 * fragments.cpp
3 * TopHat
4 *
5 * Created by Cole Trapnell on 1/14/09.
6 * Copyright 2009 Cole Trapnell. All rights reserved.
7 *
8 */
9
10 #ifdef HAVE_CONFIG_H
11 #include <config.h>
12 #endif
13
14 #include <cassert>
15 #include "bwt_map.h"
16 #include "fragments.h"
17
18 void best_fragment_mappings(uint64_t refid,
19 const string& name,
20 HitList& hits_in_ref,
21 ReadTable& it,
22 BestFragmentAlignmentTable& best_status_for_fragments)
23 {
24 for (size_t i = 0; i < hits_in_ref.size(); ++i)
25 {
26 BowtieHit& h1 = hits_in_ref[i];
27 uint64_t fragment_id = h1.insert_id();
28 uint32_t obs_order = it.observation_order(fragment_id);
29
30 JunctionSet dummy;
31 FragmentAlignmentGrade s(h1, dummy);
32
33 pair<FragmentAlignmentGrade, vector<FragmentAlignment*> >& fragment_best
34 = best_status_for_fragments[obs_order];
35 FragmentAlignmentGrade& current = fragment_best.first;
36 // Is the new status better than the current best one?
37 if (current < s)
38 {
39 fragment_best.second.clear();
40 current = s;
41 fragment_best.second.push_back(&h1);
42 }
43 else if (! (s < current)) // is it just as good?
44 {
45 fragment_best.second.push_back(&h1);
46 }
47 }
48 }
49
50 bool valid_fragment_alignment(const FragmentAlignmentGrade& g, const FragmentAlignment& a)
51 {
52 // stub
53 return true;
54 }