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
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
|
#include <stdlib.h>
#include <stdio.h>
#include <zlib.h>
#include <assert.h>
#include <string.h>
#include <unistd.h>
#include <ctype.h>
#include "const.h"
#include "main.h"
#define LINE_LEN 60
void cns_cns2snp(FILE *fpout, gzFile fp, int is_all, int is_alt)
{
int i, len, n_high = 0;
while (gzread(fp, &len, sizeof(int))) {
char *name = (char*)malloc(len);
gzread(fp, name, len);
gzread(fp, &len, sizeof(int));
for (i = 0; i != len; ++i) {
bit32_t low, high;
gzread(fp, &low, sizeof(bit32_t));
gzread(fp, &high, sizeof(bit32_t));
if (is_all || (high>>28 != (high>>24&0xf) && (high>>24&0xf) != 0xf)) {
// chr, pos, refB, cnsB, cnsQ, depth, avg01, mapQmax, refDiff
fprintf(fpout, "%s\t%d\t%c\t%c\t%d\t%d\t%.2f\t%d\t%d", name, i + 1, nst_nt16_rev_table[high>>28],
nst_nt16_rev_table[high>>24&0xf], high>>16&0xff, low&0xff, (float)(low>>20&0xfff)/16.0,
low>>8&0x3f, (low>>15&0x1f)<<1);
if (is_alt) fprintf(fpout, "\t%c\t%d\t%c\n", nst_nt16_rev_table[high>>12&0xf], high&0xff,
nst_nt16_rev_table[high>>8&0xf]);
else fputc('\n', fpout);
}
if ((low>>8&0x3f) >= 40 && (float)(low>>20&0xfff)/16.0 >= 0.25 && (low&0xff) >= 3) ++n_high;
}
free(name);
}
}
void cns_cns2win(FILE *fpout, gzFile fp, int win_size, const char *chr, int begin, int end, int minQ)
{
int i, len;
while (gzread(fp, &len, sizeof(int))) {
char *name = (char*)malloc(len);
int n_cvg, n_snp, n_het, depth, match, gc, is_chr, n_unique, uni_depth;
gzread(fp, name, len);
gzread(fp, &len, sizeof(int));
n_cvg = n_snp = n_het = depth = match = gc = 0;
n_unique = uni_depth = 0;
is_chr = (chr == 0 || strcmp(chr, name) == 0)? 1 : 0;
for (i = 0; i != len; ++i) {
bit32_t low, high;
gzread(fp, &low, sizeof(bit32_t));
gzread(fp, &high, sizeof(bit32_t));
if (high>>28 != 0xf) {
if ((high>>16&0xff) >= minQ) {
++n_cvg;
if ((low>>20&0xfff) >= 8 && (low>>20&0xfff) <= 32) {
++n_unique;
uni_depth += low&0xff;
}
if (nst_nt16_count_table[high>>24&0xf] == 2) ++n_het;
if (high>>28 != (high>>24&0xf)) ++n_snp;
if (high>>28 == 2 || high>>28 == 4) ++gc;
depth += low&0xff;
match += low>>20&0xfff;
}
}
if ((i+1)%win_size == 0 || i+1 == len) { // print
int pos = i+(win_size>>1)+1;
if (is_chr && (begin >= end || (pos >= begin && pos <= end))) {
float alt_depth = (n_unique == 0)? 0.0 : (float)uni_depth/n_unique;
// chr,pos,snpRate,hetRate,oriDepth,altDepth,01Match,GC%
if (n_cvg > 0) {
fprintf(fpout, "%s\t%.6f\t%g\t%g\t%.3f\t%.3f\t%.3f\t%.3f\n", name, pos/1000000.0,
(float)n_snp/n_cvg, (float)n_het/n_cvg, (float)depth/n_cvg, alt_depth,
(float)match/n_cvg/16.0, 100.0*gc/n_cvg);
} else {
fprintf(fpout, "%s\t%.6f\t%g\t%g\t%.3f\t%.3f\t%.3f\t%.3f\n", name, pos/1000000.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0);
}
n_cvg = n_snp = n_het = depth = match = gc = 0;
n_unique = uni_depth = 0;
}
}
}
free(name);
}
}
void cns_cns2ref(FILE *fpout, gzFile fp)
{
int i, len;
while (gzread(fp, &len, sizeof(int))) {
char *name = (char*)malloc(len);
gzread(fp, name, len);
fprintf(fpout, ">%s\n", name);
gzread(fp, &len, sizeof(int));
for (i = 0; i != len; ++i) {
bit32_t low, high;
gzread(fp, &low, sizeof(bit32_t));
gzread(fp, &high, sizeof(bit32_t));
fputc(nst_nt16_rev_table[high>>28], fpout);
if ((i+1)%LINE_LEN == 0) fputc('\n', fpout);
}
if (i%LINE_LEN != 0) fputc('\n', fpout);
free(name);
}
}
void cns_cns2cssnp(FILE *fpout, gzFile fp)
{
int i, len, q[2], b[2], r[2];
while (gzread(fp, &len, sizeof(int))) {
char *name = (char*)malloc(len);
gzread(fp, name, len);
gzread(fp, &len, sizeof(int));
r[0] = b[0] = 15; q[0] = 0;
for (i = 0; i != len; ++i) {
bit32_t low, high;
int is_snp = 0;
gzread(fp, &low, sizeof(bit32_t));
gzread(fp, &high, sizeof(bit32_t));
r[1] = high>>28; b[1] = high>>24&0xf; q[1] = high>>16&0xff;
if (r[0] != 15 && r[1] != 15 && b[0] != 15 && b[1] != 15 && r[0] != b[0] && r[1] != b[1]
&& (b[0]&r[0]) == (b[1]&r[1]))
{
int c = nst_nt16_count_table[b[0]|r[0]|b[1]|r[1]];
if (r[0] == r[1]) {
if (b[0] == b[1]) is_snp = 1;
} else {
if (c == 4 || c == 2) is_snp = 1;
}
}
if (is_snp) {
fprintf(fpout, "%s\t%d\t%c%c\t%c%c\t%d\t%d\n", name, i + 1, nst_nt16_rev_table[r[0]],
nst_nt16_rev_table[r[1]], nst_nt16_rev_table[b[0]], nst_nt16_rev_table[b[1]], q[0], q[1]);
}
r[0] = r[1]; b[0] = b[1]; q[0] = q[1];
}
free(name);
}
}
void cns_cns2fq(FILE *fpout, gzFile fp, bit32_t min_mapq, bit32_t min_depth, bit32_t max_depth, bit32_t min_nQ, float hidden)
{
int i, len;
while (gzread(fp, &len, sizeof(int))) {
char *name = (char*)malloc(len);
bit8_t *qual;
gzread(fp, name, len);
fprintf(fpout, "@%s", name);
gzread(fp, &len, sizeof(int));
qual = (bit8_t*)malloc(len);
for (i = 0; i != len; ++i) {
bit32_t low, high;
if (i%LINE_LEN == 0) fputc('\n', fpout);
gzread(fp, &low, sizeof(bit32_t));
gzread(fp, &high, sizeof(bit32_t));
if ((low>>8&0x3f) >= min_mapq && (float)(low>>20&0xfff)/16.0 >= hidden && (low&0xff) >= min_depth
&& (low&0xff) <= max_depth && (low>>15&0x1f)<<1 >= min_nQ)
{
fputc(nst_nt16_rev_table[high>>24&0xf], fpout);
} else fputc(tolower(nst_nt16_rev_table[high>>24&0xf]), fpout);
qual[i] = ((high>>16&0xff) + 33 > 126)? 126 : (high>>16&0xff) + 33;
}
fprintf(fpout, "\n+");
for (i = 0; i != len; ++i) {
if (i%LINE_LEN == 0) fputc('\n', fpout);
fputc(qual[i], fpout);
}
fputc('\n', fpout);
free(name); free(qual);
}
}
/* main() functions */
int ma_cns2ref(int argc, char *argv[])
{
gzFile fp;
if(argc < 2) {
fprintf(stderr, "Usage: maq cns2ref <in.cns>\n");
return 1;
}
fp = (strcmp(argv[1], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[1], "r");
assert(fp);
cns_cns2ref(stdout, fp);
gzclose(fp);
return 0;
}
int ma_cns2snp(int argc, char *argv[])
{
gzFile fp;
if(argc < 2) {
fprintf(stderr, "Usage: maq cns2snp <in.cns>\n");
return 1;
}
fp = (strcmp(argv[1], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[1], "r");
assert(fp);
cns_cns2snp(stdout, fp, 0, 1);
gzclose(fp);
return 0;
}
int ma_cns2cssnp(int argc, char *argv[])
{
gzFile fp;
if(argc < 2) {
fprintf(stderr, "Usage: maq cns2cssnp <in.cns>\n");
return 1;
}
fp = (strcmp(argv[1], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[1], "r");
assert(fp);
cns_cns2cssnp(stdout, fp);
gzclose(fp);
return 0;
}
int ma_cns2view(int argc, char *argv[])
{
gzFile fp;
if (argc < 2) {
fprintf(stderr, "Usage: maq cns2view <in.cns>\n");
return 1;
}
fp = (strcmp(argv[1], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[1], "r");
assert(fp);
cns_cns2snp(stdout, fp, 1, 1);
gzclose(fp);
return 0;
}
int ma_cns2win(int argc, char *argv[])
{
gzFile fp;
int win_size = 1000, begin, end, c, minQ;
char *chr;
begin = end = minQ = 0; chr = 0;
while ((c = getopt(argc, argv, "w:b:e:c:q:")) >= 0) {
switch (c) {
case 'w': win_size = atoi(optarg); break;
case 'b': begin = atoi(optarg); break;
case 'e': end = atoi(optarg); break;
case 'c': chr = strdup(optarg); break;
case 'q': minQ = atoi(optarg); break;
}
}
if (optind >= argc) {
fprintf(stderr, "Usage: maq cns2win [-w 1000] [-b 0] [-e 0] [-c null] [-q 0] <in.cns>\n");
return 1;
}
fp = (strcmp(argv[optind], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[optind], "r");
assert(fp);
cns_cns2win(stdout, fp, win_size, chr, begin, end, minQ);
gzclose(fp);
free(chr);
return 0;
}
int ma_cns2fq(int argc, char *argv[])
{
gzFile fp;
double hidden = 0.25;
int c, min_mapq = 40, min_depth = 3, max_depth = 255, min_nQ = 20;
while ((c = getopt(argc, argv, "Q:d:D:n:c:")) >= 0) {
switch (c) {
case 'Q': min_mapq = atoi(optarg); break;
case 'd': min_depth = atoi(optarg); break;
case 'D': max_depth = atoi(optarg); break;
case 'n': min_nQ = atoi(optarg); break;
case 'c': hidden = atof(optarg); break;
default: return 1;
}
}
if (optind == argc) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: maq cns2fq [options] <in.cns>\n\n");
fprintf(stderr, "Options: -Q INT minimum mapping quality [%d]\n", min_mapq);
fprintf(stderr, " -n INT minimum neighbouring quality [%d]\n", min_nQ);
fprintf(stderr, " -d INT minimum read depth [%d]\n", min_depth);
fprintf(stderr, " -D INT maximum read depth [%d]\n\n", max_depth);
return 1;
}
fp = (strcmp(argv[optind], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[optind], "r");
assert(fp);
cns_cns2fq(stdout, fp, min_mapq, min_depth, max_depth, min_nQ, hidden);
gzclose(fp);
return 0;
}
|
