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r823: mappy to index a single sequence

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Heng Li
2018-08-05 20:57:05 -04:00
parent 5ab6538757
commit b0f39a1a61
5 changed files with 37 additions and 10 deletions
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index.c
+6
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@@ -372,7 +372,9 @@ mm_idx_t *mm_idx_str(int w, int k, int is_hpc, int bucket_bits, int n, const cha
uint64_t sum_len = 0;
mm128_v a = {0,0,0};
mm_idx_t *mi;
khash_t(str) *h;
int i, flag = 0;
if (n <= 0) return 0;
for (i = 0; i < n; ++i) // get the total length
sum_len += strlen(seq[i]);
@@ -383,13 +385,17 @@ mm_idx_t *mm_idx_str(int w, int k, int is_hpc, int bucket_bits, int n, const cha
mi->n_seq = n;
mi->seq = (mm_idx_seq_t*)kcalloc(mi->km, n, sizeof(mm_idx_seq_t)); // ->seq is allocated from km
mi->S = (uint32_t*)calloc((sum_len + 7) / 8, 4);
mi->h = h = kh_init(str);
for (i = 0, sum_len = 0; i < n; ++i) {
const char *s = seq[i];
mm_idx_seq_t *p = &mi->seq[i];
uint32_t j;
if (name && name[i]) {
int absent;
p->name = (char*)kmalloc(mi->km, strlen(name[i]) + 1);
strcpy(p->name, name[i]);
kh_put(str, h, p->name, &absent);
assert(absent);
}
p->offset = sum_len;
p->len = strlen(s);