-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathcli.c
224 lines (214 loc) · 8.51 KB
/
cli.c
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
#include <stdio.h>
#include <string.h>
#include <unistd.h>
#include <zlib.h>
#include "ksw2.h"
#include "kseq.h"
KSEQ_INIT(gzFile, gzread)
#ifdef HAVE_GABA
#include "gaba.h"
#endif
#ifdef HAVE_PARASAIL
#include "parasail.h"
#endif
unsigned char seq_nt4_table[256] = {
0, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4
};
static void ksw_gen_simple_mat(int m, int8_t *mat, int8_t a, int8_t b)
{
int i, j;
a = a < 0? -a : a;
b = b > 0? -b : b;
for (i = 0; i < m - 1; ++i) {
for (j = 0; j < m - 1; ++j)
mat[i * m + j] = i == j? a : b;
mat[i * m + m - 1] = 0;
}
for (j = 0; j < m; ++j)
mat[(m - 1) * m + j] = 0;
}
static void global_aln(const char *algo, void *km, const char *qseq_, const char *tseq_, int8_t m, const int8_t *mat, int8_t q, int8_t e, int8_t q2, int8_t e2,
int w, int zdrop, int flag, ksw_extz_t *ez)
{
int i, qlen, tlen;
uint8_t *qseq, *tseq;
ez->max_q = ez->max_t = ez->mqe_t = ez->mte_q = -1;
ez->max = 0, ez->mqe = ez->mte = KSW_NEG_INF;
ez->n_cigar = 0;
qlen = strlen(qseq_);
tlen = strlen(tseq_);
qseq = (uint8_t*)calloc(qlen + 33, 1); // 32 for gaba
tseq = (uint8_t*)calloc(tlen + 33, 1);
for (i = 0; i < qlen; ++i)
qseq[i] = seq_nt4_table[(uint8_t)qseq_[i]];
for (i = 0; i < tlen; ++i)
tseq[i] = seq_nt4_table[(uint8_t)tseq_[i]];
if (strcmp(algo, "gg") == 0) {
if (flag & KSW_EZ_SCORE_ONLY) ez->score = ksw_gg(km, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, m, mat, q, e, w, 0, 0, 0);
else ez->score = ksw_gg(km, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, m, mat, q, e, w, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
} else if (strcmp(algo, "gg2") == 0) {
if (flag & KSW_EZ_SCORE_ONLY) ez->score = ksw_gg2(km, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, m, mat, q, e, w, 0, 0, 0);
else ez->score = ksw_gg2(km, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, m, mat, q, e, w, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
}
else if (strcmp(algo, "gg2_sse") == 0) ez->score = ksw_gg2_sse(km, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, m, mat, q, e, w, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
else if (strcmp(algo, "extz") == 0) ksw_extz(km, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, m, mat, q, e, w, zdrop, flag, ez);
else if (strcmp(algo, "extz2_sse") == 0) ksw_extz2_sse(km, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, m, mat, q, e, w, zdrop, flag, ez);
else if (strcmp(algo, "extd") == 0) ksw_extd(km, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, m, mat, q, e, q2, e2, w, zdrop, flag, ez);
else if (strcmp(algo, "extd2_sse") == 0) ksw_extd2_sse(km, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, m, mat, q, e, q2, e2, w, zdrop, flag, ez);
else if (strcmp(algo, "extf2_sse") == 0) ksw_extf2_sse(km, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, mat[0], mat[1], e, w, zdrop, ez);
else if (strcmp(algo, "exts2_sse") == 0) {
int8_t mat[25];
ksw_gen_simple_mat(5, mat, 1, 2);
ksw_exts2_sse(km, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, m, mat, 2, 1, 32, 4, zdrop, flag|KSW_EZ_SPLICE_FOR, ez);
}
else if (strcmp(algo, "test") == 0) ksw_extd2_sse(km, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, m, mat, 4, 2, 24, 1, 751, 400, 8, ez);
#ifdef HAVE_GABA
else if (strcmp(algo, "gaba") == 0) { // libgaba. Note that gaba may not align to the end
int buf_len = 0x10000;
char *cigar = (char*)calloc(buf_len, 1);
for (i = 0; i < qlen; ++i)
qseq[i] = qseq[i] < 4? 1<<qseq[i] : 15;
for (i = 0; i < tlen; ++i)
tseq[i] = tseq[i] < 4? 1<<tseq[i] : 15;
struct gaba_section_s qs = gaba_build_section(0, qseq, qlen);
struct gaba_section_s ts = gaba_build_section(2, tseq, tlen);
gaba_t *ctx = gaba_init(GABA_PARAMS(.xdrop = (zdrop<120?zdrop:120), GABA_SCORE_SIMPLE(mat[0], abs(mat[1]), q, e)));
void const *lim = (void const *)0x800000000000;
gaba_dp_t *dp = gaba_dp_init(ctx, lim, lim);
struct gaba_fill_s *f = gaba_dp_fill_root(dp, &qs, 0, &ts, 0);
f = gaba_dp_fill(dp, f, &qs, &ts);
gaba_alignment_t *r = gaba_dp_trace(dp, 0, f, 0);
ez->score = r->score;
gaba_dp_dump_cigar_forward(cigar, buf_len, r->path->array, 0, r->path->len);
printf("gaba cigar: %s\n", cigar);
gaba_dp_clean(dp);
gaba_clean(ctx);
free(cigar);
}
#endif
#ifdef HAVE_PARASAIL
else if (strncmp(algo, "ps_", 3) == 0) {
parasail_matrix_t *ps_mat;
parasail_function_t *func;
parasail_result_t *res;
ps_mat = parasail_matrix_create("ACGTN", mat[0], mat[1]); // TODO: call parasail_matrix_set_value() to change N<->A/C/G/T scores
func = parasail_lookup_function(algo + 3);
if (func == 0) {
fprintf(stderr, "ERROR: can't find parasail function '%s'\n", algo + 3);
exit(1);
}
res = func(qseq_, qlen, tseq_, tlen, q+e, e, ps_mat);
ez->score = res->score;
parasail_matrix_free(ps_mat);
parasail_result_free(res);
}
#endif
else {
fprintf(stderr, "ERROR: can't find algorithm '%s'\n", algo);
exit(1);
}
free(qseq); free(tseq);
}
static void print_aln(const char *tname, const char *qname, ksw_extz_t *ez)
{
printf("%s\t%s\t%d", tname, qname, ez->score);
printf("\t%d\t%d\t%d", ez->max, ez->max_t, ez->max_q);
if (ez->n_cigar > 0) {
int i;
putchar('\t');
for (i = 0; i < ez->n_cigar; ++i)
printf("%d%c", ez->cigar[i]>>4, "MID"[ez->cigar[i]&0xf]);
}
putchar('\n');
}
int main(int argc, char *argv[])
{
void *km = 0;
int8_t a = 2, b = 4, q = 4, e = 2, q2 = 13, e2 = 1;
int c, i, pair = 1, w = -1, flag = 0, rep = 1, zdrop = -1, no_kalloc = 0;
char *algo = "extd", *s;
int8_t mat[25];
ksw_extz_t ez;
gzFile fp[2];
while ((c = getopt(argc, argv, "t:w:R:rsgz:A:B:O:E:K")) >= 0) {
if (c == 't') algo = optarg;
else if (c == 'w') w = atoi(optarg);
else if (c == 'R') rep = atoi(optarg);
else if (c == 'z') zdrop = atoi(optarg);
else if (c == 'r') flag |= KSW_EZ_RIGHT;
else if (c == 's') flag |= KSW_EZ_SCORE_ONLY;
else if (c == 'g') flag |= KSW_EZ_APPROX_MAX | KSW_EZ_APPROX_DROP;
else if (c == 'K') no_kalloc = 1;
else if (c == 'A') a = atoi(optarg);
else if (c == 'B') b = atoi(optarg);
else if (c == 'O') {
q = q2 = strtol(optarg, &s, 10);
if (*s == ',') q2 = strtol(s+1, &s, 10);
} else if (c == 'E') {
e = e2 = strtol(optarg, &s, 10);
if (*s == ',') e2 = strtol(s+1, &s, 10);
}
}
if (argc - optind < 2) {
fprintf(stderr, "Usage: ksw2-test [options] <DNA-target> <DNA-query>\n");
fprintf(stderr, "Options:\n");
fprintf(stderr, " -t STR algorithm: gg, gg2, gg2_sse, extz, extz2_sse, extd, extd2_sse [%s]\n", algo);
fprintf(stderr, " -R INT repeat INT times (for benchmarking) [1]\n");
fprintf(stderr, " -w INT band width [inf]\n");
fprintf(stderr, " -z INT Z-drop [%d]\n", zdrop);
fprintf(stderr, " -r gap right alignment\n");
fprintf(stderr, " -s score only\n");
fprintf(stderr, " -A INT match score [%d]\n", a);
fprintf(stderr, " -B INT mismatch penalty [%d]\n", b);
fprintf(stderr, " -O INT[,INT] gap open penalty [%d,%d]\n", q, q2);
fprintf(stderr, " -E INT[,INT] gap extension penalty [%d,%d]\n", e, e2);
return 1;
}
#ifdef HAVE_KALLOC
km = no_kalloc? 0 : km_init();
#endif
memset(&ez, 0, sizeof(ksw_extz_t));
ksw_gen_simple_mat(5, mat, a, -b);
fp[0] = gzopen(argv[optind], "r");
fp[1] = gzopen(argv[optind+1], "r");
if (fp[0] == 0 && fp[1] == 0) {
global_aln(algo, km, argv[optind+1], argv[optind], 5, mat, q, e, q2, e2, w, zdrop, flag, &ez);
print_aln("first", "second", &ez);
} else if (fp[0] && fp[1]) {
kseq_t *ks[2];
ks[0] = kseq_init(fp[0]);
ks[1] = kseq_init(fp[1]);
if (pair) {
while (kseq_read(ks[0]) > 0) {
if (kseq_read(ks[1]) <= 0) break;
for (i = 0; i < rep; ++i)
global_aln(algo, km, ks[1]->seq.s, ks[0]->seq.s, 5, mat, q, e, q2, e2, w, zdrop, flag, &ez);
print_aln(ks[0]->name.s, ks[1]->name.s, &ez);
}
}
kseq_destroy(ks[0]);
kseq_destroy(ks[1]);
gzclose(fp[0]);
gzclose(fp[1]);
}
kfree(km, ez.cigar);
#ifdef HAVE_KALLOC
km_destroy(km);
#endif
return 0;
}