gclib/tophat_cpp/fragments.h

#ifndef FRAGMENTS_H
#define FRAGMENTS_H
/*
 *  fragments.h
 *  TopHat
 *
 *  Created by Cole Trapnell on 1/14/09.
 *  Copyright 2009 Cole Trapnell. All rights reserved.
 *
 */

#include "bwt_map.h"
#include "align_status.h"

typedef BowtieHit FragmentAlignment;

struct FragmentAlignmentGrade
{
  FragmentAlignmentGrade() 
  {
    //edit_dist = 0;
    num_alignments = 0;
    status = AlignStatus();
  }
  
  FragmentAlignmentGrade(const BowtieHit& h1, const JunctionSet& gtf_junctions) 
  {
    status = AlignStatus(h1, gtf_junctions);
    //edit_dist = h1.edit_dist();
    num_alignments = 1;
  }
  
  FragmentAlignmentGrade& operator=(const FragmentAlignmentGrade& rhs)
  {
    status = rhs.status;
    //edit_dist = rhs.edit_dist;
    num_alignments = rhs.num_alignments;
    
    return *this;
  }
    
  // Returns true if rhs is a "happier" alignment for the ends of this insert
  // than this InsertStatus.
    
  bool operator<(const FragmentAlignmentGrade& rhs)
  {
    // -- Geo: check this
    //if (status != rhs.status)
      return status < rhs.status;
    
    //return rhs.edit_dist < edit_dist;
  }
  
  AlignStatus status;
  //int edit_dist;
  int num_alignments; // number of equally good alignments for this fragment 
};

typedef vector<pair<FragmentAlignmentGrade, vector<FragmentAlignment*> > > BestFragmentAlignmentTable;

void best_fragment_mappings(uint64_t refid,
                            const string& name,
                            HitList& hits1_in_ref,
                            ReadTable& it,
                            BestFragmentAlignmentTable& best_status_for_fragments);

void accept_best_hits(BestFragmentAlignmentTable& best_status_for_fragments);
void accept_unique_hits(BestFragmentAlignmentTable& best_status_for_fragments);

#endif
Revision:	135
Committed:	Mon Dec 12 22:28:38 2011 UTC (9 years, 1 month ago) by gpertea
File size:	1700 byte(s)
Log Message:	wip - SplicedSAMHitFactory() still not implemented
Line	File contents
1	#ifndef FRAGMENTS_H
2	#define FRAGMENTS_H
3	/*
4	* fragments.h
5	* TopHat
6	*
7	* Created by Cole Trapnell on 1/14/09.
8	* Copyright 2009 Cole Trapnell. All rights reserved.
9	*
10	*/
11
12	#include "bwt_map.h"
13	#include "align_status.h"
14
15	typedef BowtieHit FragmentAlignment;
16
17	struct FragmentAlignmentGrade
18	{
19	FragmentAlignmentGrade()
20	{
21	//edit_dist = 0;
22	num_alignments = 0;
23	status = AlignStatus();
24	}
25
26	FragmentAlignmentGrade(const BowtieHit& h1, const JunctionSet& gtf_junctions)
27	{
28	status = AlignStatus(h1, gtf_junctions);
29	//edit_dist = h1.edit_dist();
30	num_alignments = 1;
31	}
32
33	FragmentAlignmentGrade& operator=(const FragmentAlignmentGrade& rhs)
34	{
35	status = rhs.status;
36	//edit_dist = rhs.edit_dist;
37	num_alignments = rhs.num_alignments;
38
39	return *this;
40	}
41
42	// Returns true if rhs is a "happier" alignment for the ends of this insert
43	// than this InsertStatus.
44
45	bool operator<(const FragmentAlignmentGrade& rhs)
46	{
47	// -- Geo: check this
48	//if (status != rhs.status)
49	return status < rhs.status;
50
51	//return rhs.edit_dist < edit_dist;
52	}
53
54	AlignStatus status;
55	//int edit_dist;
56	int num_alignments; // number of equally good alignments for this fragment
57	};
58
59	typedef vector<pair<FragmentAlignmentGrade, vector<FragmentAlignment*> > > BestFragmentAlignmentTable;
60
61	void best_fragment_mappings(uint64_t refid,
62	const string& name,
63	HitList& hits1_in_ref,
64	ReadTable& it,
65	BestFragmentAlignmentTable& best_status_for_fragments);
66
67	void accept_best_hits(BestFragmentAlignmentTable& best_status_for_fragments);
68	void accept_unique_hits(BestFragmentAlignmentTable& best_status_for_fragments);
69
70	#endif