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