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r499->false duplications

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chhylp123
2023-01-17 04:49:56 -05:00
parent 46391eba26
commit 25d6857d44
9 changed files with 641 additions and 65 deletions
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CommandLines.h
+5 -2
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@@ -4,7 +4,7 @@
#include <pthread.h>
#include <stdint.h>
#define HA_VERSION "0.18.4-r496"
#define HA_VERSION "0.18.5-r499"
#define VERBOSE 0
@@ -21,9 +21,10 @@
#define HA_F_HIGH_HET 0x400
#define HA_F_PARTITION 0x800
#define HA_F_FAST 0x1000
#define HA_F_USKEW 0x2000
#define HA_F_USKEW 0x2000
#define HA_MIN_OV_DIFF 0.02 // min sequence divergence in an overlap
#define MIN_N_CHAIN 100
typedef struct{
int *l, n;
@@ -135,6 +136,7 @@ typedef struct {
uint8_t is_read_trans;
uint8_t is_topo_trans;
uint8_t is_bub_trans;
uint8_t bin_only;
} hifiasm_opt_t;
extern hifiasm_opt_t asm_opt;
@@ -143,6 +145,7 @@ void init_opt(hifiasm_opt_t* asm_opt);
void destory_opt(hifiasm_opt_t* asm_opt);
void ha_opt_reset_to_round(hifiasm_opt_t* asm_opt, int round);
void ha_opt_update_cov(hifiasm_opt_t *opt, int hom_cov);
void ha_opt_update_cov_min(hifiasm_opt_t *opt, int hom_cov, int min_chain);
int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt);
double Get_T(void);