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moved array shrinking into chain_dp()

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Heng Li
2017-09-20 14:58:57 -04:00
parent 9943e5fdd0
commit 19d8eca3a1
3 changed files with 12 additions and 20 deletions
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chain.c
+7 -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_x, int max_dist_y, int bw, int max_skip, int min_cnt, int min_sc, int is_cdna, int n_segs, int64_t n, mm128_t *a, uint64_t **_u, void *km)
mm128_t *mm_chain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int min_cnt, int min_sc, int is_cdna, int n_segs, int64_t n, mm128_t *a, int *n_u_, uint64_t **_u, void *km)
{ // TODO: make sure this works when n has more than 32 bits
int32_t st = 0, k, *f, *p, *t, *v, n_u, n_v;
int64_t i, j;
@@ -148,6 +148,10 @@ int mm_chain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int min_cn
k += n;
}
memcpy(u, u2, n_u * 8);
kfree(km, b); kfree(km, w); kfree(km, u2);
return n_u;
// write _a_ to _b_ and deallocate _a_ because _a_ is oversized, sometimes a lot
memcpy(b, a, n_v * sizeof(mm128_t));
*n_u_ = n_u;
kfree(km, a); kfree(km, w); kfree(km, u2);
return b;
}