1 #ifndef ASSEMBLE_H
2 #define ASSEMBLE_H
3 
4 /*
5  *  assemble.h
6  *  cufflinks
7  *
8  *  Created by Cole Trapnell on 3/23/09.
9  *  Copyright 2009 Cole Trapnell. All rights reserved.
10  *
11  */
12 
13 #ifdef HAVE_CONFIG_H
14 #include <config.h>
15 #endif
16 
17 #include <vector>
18 #include <map>
19 
20 
21 #include "bundles.h"
22 #include "scaffolds.h"
23 
24 class BiasLearner;
25 
26 bool assemble_hits(BundleFactory& bundle_factory, boost::shared_ptr<BiasLearner> bl_ptr);
27 
28 //bool intron_compatible(const MateHit& lhs, const MateHit& rhs);
29 bool read_hits_overlap(const ReadHit* lhs, const ReadHit* rhs);
30 bool read_hits_intron_agree(const ReadHit* h1, const ReadHit* h2);
31 
32 int  match_length(const MateHit& m, int left, int right);
33 
34 
35 bool mate_graphs(const HitBundle& bundle, BundleStats* stats);
36 
37 
38 
39 bool make_scaffolds(int bundle_left,
40 					int bundle_length,
41 					vector<Scaffold>& hits,
42 					vector<Scaffold>& scaffolds);
43 
44 #endif
45