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
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
|
/*
* Copyright (c) Medical Research Council 2002. All rights reserved.
*
* Permission to use, copy, modify and distribute this software and its
* documentation for any purpose is hereby granted without fee, provided that
* this copyright and notice appears in all copies.
*
* This file was written as part of the Staden Package at the MRC Laboratory
* of Molecular Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
*
* MRC disclaims all warranties with regard to this software.
*
*/
#include <cstring> // For std::strcpy(), std::strlen()
#include <cstdlib> // For std::qsort()
#include <mutationtag_utils.hpp>
/*
Complements any base calls in the tag. ie.
A -> T
C -> G
G -> C
T -> A
*/
void CompTags( SimpleArray<mutlib_tag_t>& a )
{
for( int n=0; n<a.Length(); n++ )
{
// Find the -> arrow
char* pos = std::strstr( a[n].Comment, "->" );
if( pos )
{
pos--;
int p = 2;
while( p )
{
switch( *pos )
{
// Complement the bases
case 'A': *pos = 'T'; break;
case 'C': *pos = 'G'; break;
case 'G': *pos = 'C'; break;
case 'T': *pos = 'A'; break;
case 'K': *pos = 'M'; break;
case 'M': *pos = 'K'; break;
case 'R': *pos = 'Y'; break;
case 'Y': *pos = 'R'; break;
}
pos++;
pos++;
pos++;
p--;
}
}
}
}
/**
Sorts the tags in the array into ascending order of base position.
*/
extern "C" {
static int TagComparator( const void *t1, const void *t2 )
{
const mutlib_tag_t* pt1 = static_cast<const mutlib_tag_t*>( t1 );
const mutlib_tag_t* pt2 = static_cast<const mutlib_tag_t*>( t2 );
return pt1->Position[0] - pt2->Position[0];
}
}
void SortTags( SimpleArray<mutlib_tag_t>& a )
{
std::qsort( a.Raw(), a.Length(), sizeof(mutlib_tag_t), TagComparator );
}
/**
Copies the tags from the taglist into an array ready for output.
*/
void CopyTags( SimpleArray<mutlib_tag_t>& a, List<MutationTag>& l )
{
assert(a.Length()==l.Count());
int slen;
int n = 0;
MutationTag* pTag = l.First();
while( pTag )
{
std::strcpy( a[n].Type, pTag->Name() );
a[n].Strand = pTag->Strand();
a[n].Position[0] = pTag->Position();
a[n].Position[1] = (std::strcmp(pTag->Name(),"MCOV")==0) ? pTag->Position(1) : pTag->Position();
a[n].Marked = pTag->Marked();
slen = std::strlen( pTag->Comment() );
a[n].Comment = new char[ slen+1 ];
a[n].Comment[0] = 0;
if( slen > 0 )
std::strcpy( a[n].Comment, pTag->Comment() );
pTag = l.Next();
n++;
}
}
/**
Prunes the tag array so that there is only one tag at each position
which has not been marked for deletion. If there's a base-change MUTA
tag and a heterozygote HETE tag on the same base, the HETE tag is
given priority. Assumes the tags are already sorted in order of position.
*/
void PruneTags( SimpleArray<mutlib_tag_t>& a )
{
// Mark duplicate tags for deletion
const int len = a.Length();
for( int n=0; n<(len-1); n++ )
{
// If not a coverage tag
if( std::strcmp(a[n].Type,"MCOV") )
{
// If positions are identical
if( a[n].Position[0] == a[n+1].Position[0] )
{
if( std::strcmp(a[n].Type,"MUTA") == 0 )
a[n].Marked = 1;
else if( std::strcmp(a[n+1].Type,"MUTA") == 0 )
a[n+1].Marked = 1;
n++;
}
}
}
// Remove unwanted tags
int dst = 0;
for( int n=0; n<len; n++ )
{
if( a[n].Marked )
continue;
a[dst++] = a[n];
}
a.Length( dst );
}
|
