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removed a useless bwa-sw CMD option

This commit is contained in:
Heng Li 2011-11-23 23:30:14 -05:00
parent 107a9870ef
commit b17b6577ac
3 changed files with 3 additions and 5 deletions
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2
bwtsw2.h
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@ -14,7 +14,7 @@
typedef struct {
int a, b, q, r, t, qr, bw;
int z, is, t_seeds, hard_clip;
float yita, mask_level, coef;
float mask_level, coef;
int n_threads, chunk_size;
} bsw2opt_t;

2
bwtsw2_aux.c
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@ -51,7 +51,7 @@ bsw2opt_t *bsw2_init_opt()
o->a = 1; o->b = 3; o->q = 5; o->r = 2; o->t = 30;
o->bw = 50;
o->z = 1; o->is = 3; o->t_seeds = 5; o->hard_clip = 0;
o->mask_level = 0.50f; o->yita = 5.5f; o->coef = 5.5f;
o->mask_level = 0.50f; o->coef = 5.5f;
o->qr = o->q + o->r; o->n_threads = 1; o->chunk_size = 10000000;
return o;
}

4
bwtsw2_main.c
View File

@ -17,7 +17,7 @@ int bwa_bwtsw2(int argc, char *argv[])
opt = bsw2_init_opt();
srand48(11);
while ((c = getopt(argc, argv, "q:r:a:b:t:T:w:d:z:m:y:s:c:N:Hf:")) >= 0) {
while ((c = getopt(argc, argv, "q:r:a:b:t:T:w:d:z:m:s:c:N:Hf:")) >= 0) {
switch (c) {
case 'q': opt->q = atoi(optarg); break;
case 'r': opt->r = atoi(optarg); break;
@ -27,7 +27,6 @@ int bwa_bwtsw2(int argc, char *argv[])
case 'T': opt->t = atoi(optarg); break;
case 't': opt->n_threads = atoi(optarg); break;
case 'z': opt->z = atoi(optarg); break;
case 'y': opt->yita = atof(optarg); break;
case 's': opt->is = atoi(optarg); break;
case 'm': opt->mask_level = atof(optarg); break;
case 'c': opt->coef = atof(optarg); break;
@ -45,7 +44,6 @@ int bwa_bwtsw2(int argc, char *argv[])
fprintf(stderr, " -b INT mismatch penalty [%d]\n", opt->b);
fprintf(stderr, " -q INT gap open penalty [%d]\n", opt->q);
fprintf(stderr, " -r INT gap extension penalty [%d]\n", opt->r);
// fprintf(stderr, " -y FLOAT error recurrence coef. (4..16) [%.1f]\n", opt->yita);
fprintf(stderr, "\n");
fprintf(stderr, " -t INT number of threads [%d]\n", opt->n_threads);
fprintf(stderr, "\n");