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dev-r1087: added --cap-kalloc

This commit is contained in:
Heng Li 2021-07-19 21:20:04 -04:00
parent c4fe52fb07
commit 7e33fde82b
3 changed files with 7 additions and 2 deletions
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4
main.c
View File

@ -7,7 +7,7 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "ketopt.h" #include "ketopt.h"
#define MM_VERSION "2.21-dev-r1084-dirty" #define MM_VERSION "2.21-dev-r1087-dirty"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>
@ -73,6 +73,7 @@ static ko_longopt_t long_options[] = {
{ "mask-len", ko_required_argument, 346 }, { "mask-len", ko_required_argument, 346 },
{ "rmq", ko_optional_argument, 347 }, { "rmq", ko_optional_argument, 347 },
{ "qstrand", ko_no_argument, 348 }, { "qstrand", ko_no_argument, 348 },
{ "cap-kalloc", ko_required_argument, 349 },
{ "help", ko_no_argument, 'h' }, { "help", ko_no_argument, 'h' },
{ "max-intron-len", ko_required_argument, 'G' }, { "max-intron-len", ko_required_argument, 'G' },
{ "version", ko_no_argument, 'V' }, { "version", ko_no_argument, 'V' },
@ -227,6 +228,7 @@ int main(int argc, char *argv[])
else if (c == 345) opt.alt_drop = atof(o.arg); // --alt-drop else if (c == 345) opt.alt_drop = atof(o.arg); // --alt-drop
else if (c == 346) opt.mask_len = mm_parse_num(o.arg); // --mask-len else if (c == 346) opt.mask_len = mm_parse_num(o.arg); // --mask-len
else if (c == 348) opt.flag |= MM_F_QSTRAND | MM_F_NO_INV; // --qstrand else if (c == 348) opt.flag |= MM_F_QSTRAND | MM_F_NO_INV; // --qstrand
else if (c == 349) opt.cap_kalloc = mm_parse_num(o.arg); // --cap-kalloc
else if (c == 330) { else if (c == 330) {
fprintf(stderr, "[WARNING] \033[1;31m --lj-min-ratio has been deprecated.\033[0m\n"); fprintf(stderr, "[WARNING] \033[1;31m --lj-min-ratio has been deprecated.\033[0m\n");
} else if (c == 314) { // --frag } else if (c == 314) { // --frag

4
map.c
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@ -362,7 +362,9 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
if (mm_dbg_flag & MM_DBG_PRINT_QNAME) if (mm_dbg_flag & MM_DBG_PRINT_QNAME)
fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest); fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest);
assert(kmst.n_blocks == kmst.n_cores); // otherwise, there is a memory leak assert(kmst.n_blocks == kmst.n_cores); // otherwise, there is a memory leak
if (kmst.largest > 1U<<28) { if (kmst.largest > 1U<<28 || (opt->cap_kalloc > 0 && kmst.capacity > opt->cap_kalloc)) {
if (mm_dbg_flag & MM_DBG_PRINT_QNAME)
fprintf(stderr, "[W::%s] reset thread-local memory after read %s\n", __func__, qname);
km_destroy(b->km); km_destroy(b->km);
b->km = km_init(); b->km = km_init();
} }

1
minimap.h
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@ -168,6 +168,7 @@ typedef struct {
int32_t max_occ, max_max_occ, occ_dist; int32_t max_occ, max_max_occ, occ_dist;
int64_t mini_batch_size; // size of a batch of query bases to process in parallel int64_t mini_batch_size; // size of a batch of query bases to process in parallel
int64_t max_sw_mat; int64_t max_sw_mat;
int64_t cap_kalloc;
const char *split_prefix; const char *split_prefix;
} mm_mapopt_t; } mm_mapopt_t;