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r1109: disable chain_skip_scale by default 

Enabling the option slows down alignment, possibly because it fragments chains
in difficult regions.
This commit is contained in:
Heng Li 2021-10-04 21:24:35 -04:00
parent 39bdd45875
commit 546623dcb4
2 changed files with 3 additions and 3 deletions
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2
main.c
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@ -7,7 +7,7 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "ketopt.h" #include "ketopt.h"
#define MM_VERSION "2.22-r1108-dirty" #define MM_VERSION "2.22-r1109-dirty"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>

4
options.c
View File

@ -19,7 +19,7 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->min_mid_occ = 10; opt->min_mid_occ = 10;
opt->max_mid_occ = 1000000; opt->max_mid_occ = 1000000;
opt->sdust_thres = 0; // no SDUST masking opt->sdust_thres = 0; // no SDUST masking
opt->q_occ_frac = 0.02f; opt->q_occ_frac = 0.01f;
opt->min_cnt = 3; opt->min_cnt = 3;
opt->min_chain_score = 40; opt->min_chain_score = 40;
@ -33,7 +33,7 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->rmq_rescue_size = 1000; opt->rmq_rescue_size = 1000;
opt->rmq_rescue_ratio = 0.1f; opt->rmq_rescue_ratio = 0.1f;
opt->chain_gap_scale = 0.8f; opt->chain_gap_scale = 0.8f;
opt->chain_skip_scale = 0.04f; opt->chain_skip_scale = 0.0f;
opt->max_max_occ = 4095; opt->max_max_occ = 4095;
opt->occ_dist = 500; opt->occ_dist = 500;