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r249: make max overlap error rate CLI options

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Heng Li
2020-05-06 01:16:50 -04:00
parent 331e437c72
commit 3364a29b87
6 changed files with 56 additions and 49 deletions
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CommandLines.cpp
+21 -6
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@@ -10,11 +10,13 @@
hifiasm_opt_t asm_opt;
static ko_longopt_t long_options[] = {
{ "version", ko_no_argument, 300 },
{ "dbg-gfa", ko_no_argument, 301 },
{ "write-paf", ko_no_argument, 302 },
{ "write-ec", ko_no_argument, 303 },
{ "skip-triobin", ko_no_argument, 304 },
{ "version", ko_no_argument, 300 },
{ "dbg-gfa", ko_no_argument, 301 },
{ "write-paf", ko_no_argument, 302 },
{ "write-ec", ko_no_argument, 303 },
{ "skip-triobin", ko_no_argument, 304 },
{ "max-od-ec", ko_no_argument, 305 },
{ "max-od-final", ko_no_argument, 306 },
{ 0, 0, 0 }
};
@@ -83,7 +85,9 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->k_mer_length = 51;
asm_opt->mz_win = 51;
asm_opt->bf_shift = 37;
asm_opt->high_factor = 5.0f;
asm_opt->high_factor = 5.0;
asm_opt->max_ov_diff_ec = 0.04;
asm_opt->max_ov_diff_final = 0.03;
asm_opt->hom_cov = 20;
asm_opt->max_n_chain = 100;
asm_opt->k_mer_min_freq = 3;
@@ -264,6 +268,15 @@ int check_option(hifiasm_opt_t* asm_opt)
return 0;
}
if (asm_opt->max_ov_diff_ec < asm_opt->max_ov_diff_final) {
fprintf(stderr, "[ERROR] max_ov_diff_ec shouldn't be smaller than max_ov_diff_final\n");
return 0;
}
if (asm_opt->max_ov_diff_ec < HA_MIN_OV_DIFF) {
fprintf(stderr, "[ERROR] max_ov_diff_ec shouldn't be smaller than %g\n", HA_MIN_OV_DIFF);
return 0;
}
if(asm_opt->max_short_tip < 0)
{
@@ -385,6 +398,8 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
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;
else if (c == 305) asm_opt->max_ov_diff_ec = atof(opt.arg);
else if (c == 306) asm_opt->max_ov_diff_final = atof(opt.arg);
else if (c == 'l')
{ ///0: disable purge_dup; 1: purge containment; 2: purge overlap
asm_opt->purge_level_primary = asm_opt->purge_level_trio = atoi(opt.arg);