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
92
93
94
95
96
97
98
99
|
/*++
Module Name:
AlignerStats.h
Abstract:
Common statistics for running single & paired alignment.
Authors:
Ravi Pandya, May, 2012
Environment:
User mode service.
Revision History:
Integrated from SingleAligner.cpp & PairedAligner.cpp
--*/
#pragma once
#include "stdafx.h"
#include "Compat.h"
#include "options.h"
struct AbstractStats
{
virtual ~AbstractStats();
virtual void add(const AbstractStats* other) = 0;
virtual void printHistograms(FILE* out) = 0;
};
//#define TIME_STRING_DISTANCE 1
struct AlignerStats : public AbstractStats
{
AlignerStats(AbstractStats* i_extra = NULL);
_int64 totalReads;
_int64 uselessReads; // Too short or too many Ns, so unalignable
_int64 singleHits;
_int64 multiHits;
_int64 notFound;
_int64 alignedAsPairs;
_int64 lvCalls;
_int64 affineGapCalls;
_int64 millisReading;
_int64 millisAligning;
_int64 millisWriting;
_int64 filtered;
_int64 extraAlignments;
_int64 sameComplement;
_int64 agForcedSingleEndAlignment;
_int64 agUsedSingleEndAlignment;
static const unsigned maxMapq = 70;
unsigned mapqHistogram[maxMapq+1];
#if TIME_HISTOGRAM
//
// Histogram of alignment times. Time buckets are divided by powers-of-two nanoseconds, so time bucket 0 is
// <= 1 ns, time bucket 10 is <= 1.024 us, etc. Time bucket 30 is > 1s.
//
_int64 countByTimeBucket[31];
_int64 nanosByTimeBucket[31];
_int64 countByMAPQ[71];
_int64 timeByMAPQ[71];
_int64 countByNM[31];
_int64 timeByNM[31];
_int64 countOfUnaligned;
_int64 timeOfUnaligned;
_int64 backwardsTimeStamps;
_int64 totalBackwardsTimeStamps;
#endif // TIME_HISTOGRAM
static const unsigned maxMaxHits = 50;
unsigned countOfBestHitsByWeightDepth[maxMaxHits];
unsigned countOfAllHitsByWeightDepth[maxMaxHits];
double probabilityMassByWeightDepth[maxMaxHits];
AbstractStats* extra;
virtual ~AlignerStats();
virtual void add(const AbstractStats* other);
virtual void printHistograms(FILE* out);
};
|
