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disable postjoin for the ul assembly

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chhylp123
2023-03-13 15:43:22 -04:00
parent f67faa9c34
commit d4773a497f
2 changed files with 26 additions and 5 deletions
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28
CommandLines.cpp
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@@ -100,7 +100,9 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " -x FLOAT max overlap drop ratio [%.2g]\n", asm_opt->max_drop_rate);
fprintf(stderr, " -y FLOAT min overlap drop ratio [%.2g]\n", asm_opt->min_drop_rate);
fprintf(stderr, " -i ignore saved read correction and overlaps\n");
fprintf(stderr, " -u disable post-join step for contigs which may improve N50\n");
fprintf(stderr, " -u post-join step for contigs which may improve N50; 0 to disable; 1 to enable\n");
fprintf(stderr, " [%u] and [%u] in default for the UL+HiFi assembly and the HiFi assembly, respectively\n",
asm_opt->ul_pst_join, asm_opt->hifi_pst_join);
fprintf(stderr, " --hom-cov INT\n");
fprintf(stderr, " homozygous read coverage [auto]\n");
fprintf(stderr, " --lowQ INT\n");
@@ -282,6 +284,8 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->dbg_ovec_cal = 0;
asm_opt->min_path_drop_rate = 0.2;
asm_opt->max_path_drop_rate = 0.6;
asm_opt->hifi_pst_join = 1;
asm_opt->ul_pst_join = 0;
}
void destory_enzyme(enzyme* f)
@@ -719,7 +723,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
int c;
while ((c = ketopt(&opt, argc, argv, 1, "hvt:o:k:w:m:n:r:a:b:z:x:y:p:c:d:M:P:if:D:FN:1:2:3:4:5:l:s:O:eu", long_options)) >= 0) {
while ((c = ketopt(&opt, argc, argv, 1, "hvt:o:k:w:m:n:r:a:b:z:x:y:p:c:d:M:P:if:D:FN:1:2:3:4:5:l:s:O:eu:", long_options)) >= 0) {
if (c == 'h')
{
Print_H(asm_opt);
@@ -756,8 +760,14 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 'm') asm_opt->large_pop_bubble_size = atoll(opt.arg);
else if (c == 'n') asm_opt->max_short_tip = atoll(opt.arg);
else if (c == 'e') asm_opt->flag |= HA_F_BAN_ASSEMBLY;
else if (c == 'u') asm_opt->flag |= HA_F_BAN_POST_JOIN;
else if (c == 301) asm_opt->flag |= HA_F_VERBOSE_GFA;
else if (c == 'u') {
if(atoll(opt.arg)) {
asm_opt->hifi_pst_join = asm_opt->ul_pst_join = 1;
} else {
asm_opt->hifi_pst_join = asm_opt->ul_pst_join = 0;
}
}
else if (c == 301) asm_opt->flag |= HA_F_VERBOSE_GFA;
else if (c == 302) asm_opt->flag |= HA_F_WRITE_PAF;
else if (c == 303) asm_opt->flag |= HA_F_WRITE_EC;
else if (c == 304) asm_opt->flag |= HA_F_SKIP_TRIOBIN;
@@ -848,5 +858,15 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
get_queries(argc, argv, &opt, asm_opt);
c = ((asm_opt->ar)?(asm_opt->ul_pst_join):(asm_opt->hifi_pst_join));
if(c) {
if((asm_opt->flag&HA_F_BAN_POST_JOIN)) asm_opt->flag-=HA_F_BAN_POST_JOIN;
} else {
asm_opt->flag |= HA_F_BAN_POST_JOIN;
}
// fprintf(stderr, "[M::%s::] post join::%u\n", __func__, (uint32_t)(!(asm_opt->flag & HA_F_BAN_POST_JOIN)));
// exit(1);
return check_option(asm_opt);
}

3
CommandLines.h
View File

@@ -5,7 +5,7 @@
#include <pthread.h>
#include <stdint.h>
#define HA_VERSION "0.19.1-r559"
#define HA_VERSION "0.19.2-r560"
#define VERBOSE 0
@@ -145,6 +145,7 @@ typedef struct {
int32_t prt_dbg_gfa;
int32_t integer_correct_round;
uint8_t dbg_ovec_cal;
uint8_t hifi_pst_join, ul_pst_join;
} hifiasm_opt_t;
extern hifiasm_opt_t asm_opt;