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r749: max_hits tunable on CMD; default to 5

This commit is contained in:
Heng Li 2014-05-04 10:17:03 -04:00
parent f21d6498bc
commit ce3c198245
3 changed files with 4 additions and 3 deletions
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2
bwamem.c
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@ -67,7 +67,7 @@ mem_opt_t *mem_opt_init()
o->split_factor = 1.5; o->split_factor = 1.5;
o->chunk_size = 10000000; o->chunk_size = 10000000;
o->n_threads = 1; o->n_threads = 1;
o->max_hits = 10; o->max_hits = 5;
o->max_matesw = 50; o->max_matesw = 50;
o->mask_level_redun = 0.95; o->mask_level_redun = 0.95;
o->min_chain_weight = 0; o->min_chain_weight = 0;

3
fastmap.c
View File

@ -53,7 +53,7 @@ int main_mem(int argc, char *argv[])
opt = mem_opt_init(); opt = mem_opt_init();
memset(&opt0, 0, sizeof(mem_opt_t)); memset(&opt0, 0, sizeof(mem_opt_t));
while ((c = getopt(argc, argv, "epaFMCSPHYk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:")) >= 0) { while ((c = getopt(argc, argv, "epaFMCSPHYk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:")) >= 0) {
if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1; if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
else if (c == 'x') mode = optarg; else if (c == 'x') mode = optarg;
else if (c == 'w') opt->w = atoi(optarg), opt0.w = 1; else if (c == 'w') opt->w = atoi(optarg), opt0.w = 1;
@ -76,6 +76,7 @@ int main_mem(int argc, char *argv[])
else if (c == 'r') opt->split_factor = atof(optarg), opt0.split_factor = 1.; else if (c == 'r') opt->split_factor = atof(optarg), opt0.split_factor = 1.;
else if (c == 'D') opt->drop_ratio = atof(optarg), opt0.drop_ratio = 1.; else if (c == 'D') opt->drop_ratio = atof(optarg), opt0.drop_ratio = 1.;
else if (c == 'm') opt->max_matesw = atoi(optarg), opt0.max_matesw = 1; else if (c == 'm') opt->max_matesw = atoi(optarg), opt0.max_matesw = 1;
else if (c == 'h') opt->max_hits = atoi(optarg), opt0.max_hits = 1;
else if (c == 's') opt->split_width = atoi(optarg), opt0.split_width = 1; else if (c == 's') opt->split_width = atoi(optarg), opt0.split_width = 1;
else if (c == 'G') opt->max_chain_gap = atoi(optarg), opt0.max_chain_gap = 1; else if (c == 'G') opt->max_chain_gap = atoi(optarg), opt0.max_chain_gap = 1;
else if (c == 'N') opt->max_chain_extend = atoi(optarg), opt0.max_chain_extend = 1; else if (c == 'N') opt->max_chain_extend = atoi(optarg), opt0.max_chain_extend = 1;

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 "0.7.8-r748-dirty" #define PACKAGE_VERSION "0.7.8-r749-dirty"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);