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r424: reduce memory for long query seqs

This commit is contained in:
Heng Li 2017-09-20 12:22:13 -04:00
parent 75e6bbc9f6
commit e3b5802b2e
2 changed files with 12 additions and 1 deletions
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2
main.c
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@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.2-r421-dirty"
#define MM_VERSION "2.2-r424-dirty"
#ifdef __linux__
#include <sys/resource.h>

11
map.c
View File

@ -237,6 +237,17 @@ mm_reg1_t *mm_map(const mm_idx_t *mi, int qlen, const char *seq, int *n_regs, mm
max_gap_ref = opt->max_gap_ref >= 0? opt->max_gap_ref : opt->max_gap;
n_u = mm_chain_dp(max_gap_ref, opt->max_gap, opt->bw, opt->max_chain_skip, opt->min_cnt, opt->min_chain_score, !!(opt->flag&MM_F_SPLICE), n_a, a, &u, b->km);
if (n_u > 0) { // shrink _a_ because after chaining, the size of _a_ may be much reduced
int64_t n_a0 = n_a;
for (j = 0, n_a = 0; j < n_u; ++j)
n_a += (int32_t)u[j];
if (n_a < n_a0>>1) {
mm128_t *a0 = a;
a = (mm128_t*)kmalloc(b->km, n_a * sizeof(mm128_t));
memcpy(a, a0, n_a * sizeof(mm128_t)); // anything beyond n_a is not used
kfree(b->km, a0);
}
}
regs = mm_gen_regs(b->km, qlen, n_u, u, a);
*n_regs = n_u;