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r905: lower peak RAM for "shm -f"

This commit is contained in:
Heng Li 2014-10-16 11:22:09 -04:00
parent ad0da1418f
commit e318d8e7e5
2 changed files with 9 additions and 10 deletions
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17
bwa.c
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@ -282,8 +282,8 @@ int bwa_mem2idx(int64_t l_mem, uint8_t *mem, bwaidx_t *idx)
// generate idx->bwt // generate idx->bwt
x = sizeof(bwt_t); idx->bwt = malloc(x); memcpy(idx->bwt, mem + k, x); k += x; x = sizeof(bwt_t); idx->bwt = malloc(x); memcpy(idx->bwt, mem + k, x); k += x;
x = idx->bwt->n_sa * sizeof(bwtint_t); idx->bwt->sa = (bwtint_t*)(mem + k); k += x;
x = idx->bwt->bwt_size * 4; idx->bwt->bwt = (uint32_t*)(mem + k); k += x; x = idx->bwt->bwt_size * 4; idx->bwt->bwt = (uint32_t*)(mem + k); k += x;
x = idx->bwt->n_sa * sizeof(bwtint_t); idx->bwt->sa = (bwtint_t*)(mem + k); k += x;
// generate idx->bns and idx->pac // generate idx->bns and idx->pac
x = sizeof(bntseq_t); idx->bns = malloc(x); memcpy(idx->bns, mem + k, x); k += x; x = sizeof(bntseq_t); idx->bns = malloc(x); memcpy(idx->bns, mem + k, x); k += x;
@ -303,17 +303,16 @@ int bwa_mem2idx(int64_t l_mem, uint8_t *mem, bwaidx_t *idx)
int bwa_idx2mem(bwaidx_t *idx) int bwa_idx2mem(bwaidx_t *idx)
{ {
int i; int i;
int64_t k = 0, x, tmp; int64_t k, x, tmp;
uint8_t *mem = 0; uint8_t *mem;
// copy idx->bwt // copy idx->bwt
mem = malloc(sizeof(bwt_t) + idx->bwt->n_sa * sizeof(bwtint_t)); x = idx->bwt->bwt_size * 4;
x = sizeof(bwt_t); memcpy(mem + k, idx->bwt, x); k += x; mem = realloc(idx->bwt->bwt, sizeof(bwt_t) + x); idx->bwt->bwt = 0;
x = idx->bwt->n_sa * sizeof(bwtint_t); memcpy(mem + k, idx->bwt->sa, x); k += x; memmove(mem + sizeof(bwt_t), mem, x);
memcpy(mem, idx->bwt, sizeof(bwt_t)); k = sizeof(bwt_t) + x;
x = idx->bwt->n_sa * sizeof(bwtint_t); mem = realloc(mem, k + x); memcpy(mem + k, idx->bwt->sa, x); k += x;
free(idx->bwt->sa); free(idx->bwt->sa);
mem = realloc(mem, k + idx->bwt->bwt_size * 4);
x = idx->bwt->bwt_size * 4; memcpy(mem + k, idx->bwt->bwt, x); k += x;
free(idx->bwt->bwt);
free(idx->bwt); idx->bwt = 0; free(idx->bwt); idx->bwt = 0;
// copy idx->bns // copy idx->bns

2
main.c
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@ -4,7 +4,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.10-r904-dirty" #define PACKAGE_VERSION "0.7.10-r905-dirty"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);