#define MINUS_CONST 0x10000000
-bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, const bam_pileup1_t *pl, const char *ref)
+bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, const bam_pileup1_t *pl, const char *ref,
+ int _n_types, int *_types)
{
int i, j, n_types, *types, left, right;
bam_maqindel_ret_t *ret = 0;
- for (i = 0; i < n; ++i) {
- const bam_pileup1_t *p = pl + i;
- if (!(p->b->core.flag&BAM_FUNMAP) && p->indel != 0) break;
+ // if there is no proposed indel, check if there is an indel from the alignment
+ if (_n_types == 0) {
+ for (i = 0; i < n; ++i) {
+ const bam_pileup1_t *p = pl + i;
+ if (!(p->b->core.flag&BAM_FUNMAP) && p->indel != 0) break;
+ }
+ if (i == n) return 0; // no indel
}
- if (i == n) return 0; // no indel
{ // calculate how many types of indels are available (set n_types and types)
int m;
uint32_t *aux;
- aux = (uint32_t*)calloc(n+1, 4);
+ aux = (uint32_t*)calloc(n + _n_types + 1, 4);
m = 0;
aux[m++] = MINUS_CONST; // zero indel is always a type
for (i = 0; i < n; ++i) {
if (!(p->b->core.flag&BAM_FUNMAP) && p->indel != 0)
aux[m++] = MINUS_CONST + p->indel;
}
+ if (_n_types) // then also add this to aux[]
+ for (i = 0; i < _n_types; ++i)
+ if (_types[i]) aux[m++] = MINUS_CONST + _types[i];
ks_introsort(uint32_t, m, aux);
- n_types = 1;
- for (i = 1; i < m; ++i)
+ // squeeze out identical types
+ for (i = 1, n_types = 1; i < m; ++i)
if (aux[i] != aux[i-1]) ++n_types;
types = (int*)calloc(n_types, sizeof(int));
j = 0;
ret->s[1][k+1] = ref[pos + k + 1];
} else ret->s[1][0] = '*';
// write count
- for (j = 0; j < n; ++j) {
- if (score[max1_i*n+j] < 0 && score[max2_i*n+j] < 0) ++ret->cnt_anti;
- else {
- int diff = score[max1_i*n+j] - score[max2_i*n+j];
- if (diff > mi->ambi_thres) ++ret->cnt1;
- else if (diff < -mi->ambi_thres) ++ret->cnt2;
- else ++ret->cnt_ambi;
- }
+ for (i = 0; i < n; ++i) {
+ const bam_pileup1_t *p = pl + i;
+ if (p->indel == ret->indel1) ++ret->cnt1;
+ else if (p->indel == ret->indel2) ++ret->cnt2;
+ else ++ret->cnt_anti;
}
// write gl[]
ret->gl[0] = ret->gl[1] = 0;