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r819: mappy to support cs/MD

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This commit is contained in:
Heng Li
2018-07-24 23:29:55 -04:00
parent 8c064a5f29
commit ff9917a1c4
11 changed files with 115 additions and 28 deletions
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map.c
+6 -1
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@@ -29,6 +29,11 @@ void mm_tbuf_destroy(mm_tbuf_t *b)
free(b);
}
void *mm_tbuf_get_km(mm_tbuf_t *b)
{
return b->km;
}
static int mm_dust_minier(void *km, int n, mm128_t *a, int l_seq, const char *seq, int sdust_thres)
{
int n_dreg, j, k, u = 0;
@@ -682,7 +687,7 @@ int mm_split_merge(int n_segs, const char **fn, const mm_mapopt_t *opt, int n_sp
for (pl.rid_shift[0] = 0, i = 1; i < n_split_idx; ++i)
pl.rid_shift[i] += pl.rid_shift[i - 1];
if (opt->flag & MM_F_OUT_SAM)
for (i = 0; i < pl.mi->n_seq; ++i)
for (i = 0; i < (int32_t)pl.mi->n_seq; ++i)
printf("@SQ\tSN:%s\tLN:%d\n", pl.mi->seq[i].name, pl.mi->seq[i].len);
kt_pipeline(2, worker_pipeline, &pl, 3);