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r332: increased mz sample dist from 200 to 500

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Heng Li
2021-01-22 10:31:29 -05:00
parent da672118e5
commit 3b8f73fbab
3 changed files with 4 additions and 4 deletions
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CommandLines.cpp
+1 -1
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@@ -101,7 +101,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->thread_num = 1; asm_opt->thread_num = 1;
asm_opt->k_mer_length = 51; asm_opt->k_mer_length = 51;
asm_opt->mz_win = 51; asm_opt->mz_win = 51;
asm_opt->sample_dist = 200; asm_opt->mz_sample_dist = 500;
asm_opt->bf_shift = 37; asm_opt->bf_shift = 37;
asm_opt->max_kmer_cnt = 2000; asm_opt->max_kmer_cnt = 2000;
asm_opt->high_factor = 5.0; asm_opt->high_factor = 5.0;
CommandLines.h
+2 -2
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@@ -3,7 +3,7 @@
#include <pthread.h> #include <pthread.h>
#define HA_VERSION "0.13-r330-dirty" #define HA_VERSION "0.13-r332-dirty"
#define VERBOSE 0 #define VERBOSE 0
@@ -34,7 +34,7 @@ typedef struct {
int thread_num; int thread_num;
int k_mer_length; int k_mer_length;
int mz_win; int mz_win;
int sample_dist; int mz_sample_dist;
int bf_shift; int bf_shift;
int max_kmer_cnt; int max_kmer_cnt;
double high_factor; // coverage cutoff set to high_factor*hom_cov double high_factor; // coverage cutoff set to high_factor*hom_cov
anchor.cpp
+1 -1
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@@ -73,7 +73,7 @@ void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_reg
rlen = Get_READ_LENGTH(R_INF, rid); // read length rlen = Get_READ_LENGTH(R_INF, rid); // read length
// get the list of anchors // get the list of anchors
ha_sketch(ucr->seq, ucr->length, asm_opt.mz_win, asm_opt.k_mer_length, 0, !(asm_opt.flag & HA_F_NO_HPC), &ab->mz, ha_flt_tab, asm_opt.sample_dist, k_flag, dbg_ct); ha_sketch(ucr->seq, ucr->length, asm_opt.mz_win, asm_opt.k_mer_length, 0, !(asm_opt.flag & HA_F_NO_HPC), &ab->mz, ha_flt_tab, asm_opt.mz_sample_dist, k_flag, dbg_ct);
// minimizer of queried read // minimizer of queried read
if (ab->mz.m > ab->old_mz_m) { if (ab->mz.m > ab->old_mz_m) {
ab->old_mz_m = ab->mz.m; ab->old_mz_m = ab->mz.m;