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r89: added minimal number of minimizer counts

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Heng Li
2017-06-27 18:43:15 -04:00
parent 8977f07269
commit fa80177e58
5 changed files with 19 additions and 11 deletions
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chain.c
+5 -3
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@@ -19,7 +19,7 @@ static inline int ilog2_32(uint32_t v)
return (t = v>>8) ? 8 + LogTable256[t] : LogTable256[v];
}
int mm_chain_dp(int max_dist, int bw, int max_skip, int min_sc, int n, mm128_t *a, uint64_t **_u, void *km)
int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int n, mm128_t *a, uint64_t **_u, void *km)
{
int32_t st = 0, i, j, k, *f, *p, *t, *v, n_u, n_v;
uint64_t *u;
@@ -88,8 +88,10 @@ int mm_chain_dp(int max_dist, int bw, int max_skip, int min_sc, int n, mm128_t *
t[j] = 1;
j = p[j];
} while (j >= 0 && t[j] == 0);
if (j < 0) u[k++] = u[i]>>32<<32 | (n_v - n_v0);
else if ((int32_t)(u[i]>>32) - f[j] >= min_sc) u[k++] = ((u[i]>>32) - f[j]) << 32 | (n_v - n_v0);
if (j < 0 && n_v - n_v0 >= min_cnt)
u[k++] = u[i]>>32<<32 | (n_v - n_v0);
else if ((int32_t)(u[i]>>32) - f[j] >= min_sc && n_v - n_v0 >= min_cnt)
u[k++] = ((u[i]>>32) - f[j]) << 32 | (n_v - n_v0);
else n_v = n_v0;
}
n_u = k, *_u = u;