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r815: fixed a memory leak

This commit is contained in:
Heng Li 2018-07-15 22:11:32 -04:00
parent 830da7fa27
commit 395c8d678a
4 changed files with 15 additions and 8 deletions
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10
index.c
View File

@ -48,10 +48,12 @@ void mm_idx_destroy(mm_idx_t *mi)
uint32_t i;
if (mi == 0) return;
if (mi->h) kh_destroy(str, (khash_t(str)*)mi->h);
for (i = 0; i < 1U<<mi->b; ++i) {
free(mi->B[i].p);
free(mi->B[i].a.a);
kh_destroy(idx, (idxhash_t*)mi->B[i].h);
if (mi->B) {
for (i = 0; i < 1U<<mi->b; ++i) {
free(mi->B[i].p);
free(mi->B[i].a.a);
kh_destroy(idx, (idxhash_t*)mi->B[i].h);
}
}
if (!mi->km) {
for (i = 0; i < mi->n_seq; ++i)

4
main.c
View File

@ -10,7 +10,7 @@
#include "getopt.h"
#endif
#define MM_VERSION "2.11-r814-dirty"
#define MM_VERSION "2.11-r815-dirty"
#ifdef __linux__
#include <sys/resource.h>
@ -330,7 +330,7 @@ int main(int argc, char *argv[])
} else {
mm_write_sam_hdr(0, rg, MM_VERSION, argc, argv);
if (opt.split_prefix == 0 && mm_verbose >= 2)
fprintf(stderr, "[WARNING]\033[1;31m For a multi-part index, no @SQ lines will be outputted.\033[0m\n");
fprintf(stderr, "[WARNING]\033[1;31m For a multi-part index, no @SQ lines will be outputted. Please use --split-prefix.\033[0m\n");
}
}
if (mm_verbose >= 3)

4
map.c
View File

@ -659,6 +659,7 @@ int mm_split_merge(int n_segs, const char **fn, const mm_mapopt_t *opt, int n_sp
{
int i;
pipeline_t pl;
mm_idx_t *mi;
if (n_segs < 1 || n_split_idx < 1) return -1;
memset(&pl, 0, sizeof(pipeline_t));
pl.n_fp = n_segs;
@ -670,7 +671,7 @@ int mm_split_merge(int n_segs, const char **fn, const mm_mapopt_t *opt, int n_sp
pl.n_parts = n_split_idx;
pl.fp_parts = CALLOC(FILE*, pl.n_parts);
pl.rid_shift = CALLOC(uint32_t, pl.n_parts);
pl.mi = mm_split_merge_prep(opt->split_prefix, n_split_idx, pl.fp_parts, pl.rid_shift);
pl.mi = mi = mm_split_merge_prep(opt->split_prefix, n_split_idx, pl.fp_parts, pl.rid_shift);
if (pl.mi == 0) {
free(pl.fp_parts);
free(pl.rid_shift);
@ -687,6 +688,7 @@ int mm_split_merge(int n_segs, const char **fn, const mm_mapopt_t *opt, int n_sp
kt_pipeline(2, worker_pipeline, &pl, 3);
free(pl.str.s);
mm_idx_destroy(mi);
free(pl.rid_shift);
for (i = 0; i < n_split_idx; ++i)
fclose(pl.fp_parts[i]);

5
minimap2.1
View File

@ -239,7 +239,7 @@ Disable the long gap patching heuristic. When this option is applied, the
maximum alignment gap is mostly controlled by
.BR -r .
.TP
.B --lj-min-ratio \ FLOAT
.BI --lj-min-ratio \ FLOAT
Fraction of query sequence length required to bridge a long gap [0.5]. A
smaller value helps to recover longer gaps, at the cost of more false gaps.
.TP
@ -252,6 +252,9 @@ applies a second round of chaining with a higher minimizer occurrence threshold
if no good chain is found. In addition, minimap2 attempts to patch gaps between
seeds with ungapped alignment.
.TP
.BI --split-prefix \ STR
Prefix to create temporary files. Typically used for a multi-part index.
.TP
.BR --frag = no | yes
Whether to enable the fragment mode [no]
.TP