1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
|
/*++
Module Name:
SingleAligner.cpp
Abstract:
Functions for running the single end aligner sub-program.
Authors:
Matei Zaharia, February, 2012
Environment:
`
User mode service.
Revision History:
Adapted from cSNAP, which was in turn adapted from the scala prototype
--*/
#pragma once
#include "stdafx.h"
#include "AlignerContext.h"
#include "ReadSupplierQueue.h"
struct PairedAlignerStats;
class PairedAlignerContext : public AlignerContext
{
public:
PairedAlignerContext(AlignerExtension* i_extension = NULL);
protected:
// AlignerContext
virtual bool initialize();
virtual AlignerStats* newStats();
virtual void runTask();
virtual void runIterationThread();
// for subclasses
virtual void updateStats(PairedAlignerStats* stats, Read* read0, Read* read1, PairedAlignmentResult* result, bool useful0, bool useful1);
bool isPaired() {return true;}
protected:
virtual void typeSpecificBeginIteration();
virtual void typeSpecificNextIteration();
PairedReadSupplierGenerator *pairedReadSupplierGenerator;
int minSpacing;
int maxSpacing;
bool forceSpacing;
unsigned intersectingAlignerMaxHits;
unsigned maxCandidatePoolSize;
const char *fastqFile1;
bool ignoreMismatchedIDs;
bool quicklyDropUnpairedReads;
friend class AlignerContext2;
};
struct PairedAlignerOptions : public AlignerOptions
{
PairedAlignerOptions(const char* i_commandLine);
virtual void usageMessage();
virtual bool parse(const char** argv, int argc, int& n, bool *done);
virtual bool isPaired() { return true; }
int minSpacing;
int maxSpacing;
bool forceSpacing;
unsigned intersectingAlignerMaxHits;
unsigned maxCandidatePoolSize;
bool quicklyDropUnpairedReads;
};
|
