gclib/tophat_cpp/align_status.h

#ifndef ALIGN_STATUS_H
#define ALIGN_STATUS_H

#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <stdint.h>
#include <stdio.h>
#include <stdlib.h>
#include <string>
#include <map>
#include <vector>
#include <cassert>
#include <cstring>
#include <seqan/sequence.h>
#include <bam/sam.h>
#include "common.h"
#include "junctions.h"


using namespace std;


/**
 * The main purpose of this struct is to provide a
 * (fairly primitive) method for ranking competing alignments
 * for a read. In general,
 * continguous > spliced > in/dels = fusions
 * Ties are broken with the number of mismatches
 */
struct AlignStatus
{


private:
  /**
   * Is this alignment free of indels. Note, if there is no alignment
   * this should still be false.
   */
  bool _indelFreeAlignment;
  
  /**
   * Is this alignment free of unannotated splices? Note, if there is no alignment
   * this should still be false
   */
  bool _unannotatedSpliceFreeAlignment;
  
  bool _fusionFreeAlignment;
  
  /**
   * Is there an alignment?
   */
  bool _aligned;
  unsigned char _edit_dist;
public:
  AlignStatus();
  AlignStatus(const BowtieHit& bh, const JunctionSet& gtf_junctions);

  bool operator<(const AlignStatus& rhs) const;
  bool operator==(const AlignStatus& rhs) const;
  bool operator!=(const AlignStatus& rhs) const;
};

#endif
Revision:	154
Committed:	Tue Jan 24 02:29:21 2012 UTC (12 years, 7 months ago) by gpertea
File size:	1321 byte(s)
Log Message:	massive update with Daehwan's work
Line	File contents
1	#ifndef ALIGN_STATUS_H
2	#define ALIGN_STATUS_H
3
4	#ifdef HAVE_CONFIG_H
5	#include <config.h>
6	#endif
7
8	#include <stdint.h>
9	#include <stdio.h>
10	#include <stdlib.h>
11	#include <string>
12	#include <map>
13	#include <vector>
14	#include <cassert>
15	#include <cstring>
16	#include <seqan/sequence.h>
17	#include <bam/sam.h>
18	#include "common.h"
19	#include "junctions.h"
20
21
22	using namespace std;
23
24
25	/**
26	* The main purpose of this struct is to provide a
27	* (fairly primitive) method for ranking competing alignments
28	* for a read. In general,
29	* continguous > spliced > in/dels = fusions
30	* Ties are broken with the number of mismatches
31	*/
32	struct AlignStatus
33	{
34
35
36	private:
37	/**
38	* Is this alignment free of indels. Note, if there is no alignment
39	* this should still be false.
40	*/
41	bool _indelFreeAlignment;
42
43	/**
44	* Is this alignment free of unannotated splices? Note, if there is no alignment
45	* this should still be false
46	*/
47	bool _unannotatedSpliceFreeAlignment;
48
49	bool _fusionFreeAlignment;
50
51	/**
52	* Is there an alignment?
53	*/
54	bool _aligned;
55	unsigned char _edit_dist;
56	public:
57	AlignStatus();
58	AlignStatus(const BowtieHit& bh, const JunctionSet& gtf_junctions);
59
60	bool operator<(const AlignStatus& rhs) const;
61	bool operator==(const AlignStatus& rhs) const;
62	bool operator!=(const AlignStatus& rhs) const;
63	};
64
65	#endif