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
|
/****************************************************************************
*
* Copyright (c) 2003, The Institute for Genomic Research (TIGR), Rockville,
* Maryland, U.S.A. All rights reserved.
*
****************************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include "utils.h"
extern void giveup(char *);
static int Dlist[]={ 0, 2, 3}, Hlist[]={ 0, 1, 3},
rev_code[]={ 3, 2, 1, 0, 0, 6, 5, 10, 8, 9, 7, 12, 11, 14, 13, 15};
int tag_size;
static int tag_len;
static unsigned tag_mask;
static unsigned *tag_well;
int tag_code(c)
int c;
{
register int tmp;
switch (c) {
case 0: tmp=0; break;
case 1: tmp=1; break;
case 2: tmp=2; break;
case 3:
case 4: tmp=3; break;
case 5: tmp=random()%2 ? 2 : 0; break;
case 6: tmp=random()%2 ? 3 : 1; break;
case 7: tmp=random()%2 ; break;
case 8: tmp=random()%2 ? 3 : 0; break;
case 9: tmp=random()%2 ? 2 : 1; break;
case 10: tmp=random()%2 ? 3 : 2; break;
case 11: tmp=Dlist[random()%3]; break;
case 12: tmp=Hlist[random()%3]; break;
case 13: tmp=random()%3; break;
case 14: tmp=random()%3+1; break;
case 15: tmp=random()%4; break;
default:
giveup("how can other cases happen in tag_code?");
}
return tmp;
}
void tag_sort(l, r)
unsigned *l, *r;
{
register unsigned v, *i, *j, tmp;
if (r>l) {
v = *r; i = l-1; j = r;
while (1) {
while (*(++i) < v) ;
while (j>l && *(--j) > v) ;
if (i>=j) break;
tmp = *i; *i = *j; *j = tmp;
}
tmp = *i; *i = *r; *r = tmp;
tag_sort(l, i-1);
tag_sort(i+1, r);
}
}
void construct_vector_tags(seq, len)
char *seq;
int len;
{
register int i, j, k;
register unsigned accf, accr;
/* Note: this breaks the vector into non-overlapping tags of size tag_size */
tag_len=len/tag_size+(len%tag_size ? 1 : 0);
tag_well=(unsigned*)malloc(sizeof(unsigned)*tag_len*2);
if (tag_well==NULL)
giveup("Memory allocation failure.");
for (i=k=0; i<tag_len; i++) {
accf=accr=0;
for (j=0; j<tag_size; j++, k++) {
accf<<=2;
accf|=tag_code(seq[k%len]);
accr<<=2;
accr|=tag_code(rev_code[seq[len-k%len-1]]);
}
tag_well[i]=accf;
tag_well[i+tag_len]=accr;
}
tag_len*=2;
tag_sort(tag_well, &tag_well[tag_len-1]);
for (i=j=0; j<tag_len; j++)
if (tag_well[i]!=tag_well[j])
tag_well[++i]=tag_well[j];
tag_len=i+1;
for (accf=i=0; i<tag_size; i++) {
accf<<=2;
accf|=3;
}
tag_mask=accf;
}
int match_vector_tags(seq, len)
char *seq;
int len;
{
register unsigned acc;
register int i, l, r, m, hits, last_hit;
acc=0;
for (i=0; i<tag_size-1; i++, acc<<=2)
acc|=tag_code(seq[i]);
for (hits=0, last_hit=-1; i<len; i++, acc<<=2) {
acc&=tag_mask;
acc|=tag_code(seq[i]);
for (l=0, r=tag_len-1; l<=r; ) {
m=(l+r)/2;
if (acc<tag_well[m])
r=m-1;
else if (acc>tag_well[m])
l=m+1;
else {
/* this tag matches a vector tag -- count all bases in the tag as matching, */
/* without double-counting any bases from the previous hit */
if (i-last_hit>=tag_size)
hits+=tag_size;
else
hits+=i-last_hit;
last_hit=i;
break;
}
}
}
/* return the total number of matching bases */
return hits;
}
void destroy_vector_tags()
{
free(tag_well);
}
|
