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chhylp123
2020-06-08 17:51:36 -04:00
parent 97f6efc4da
commit 71f6c93d58
4 changed files with 52 additions and 39 deletions
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CommandLines.cpp
+4 -1
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@@ -50,6 +50,7 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " -n INT small removed unitig threshold [%d]\n", asm_opt->max_short_tip);
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, " -u disable post join contigs step which may improve N50. Don't disable in default.\n");
fprintf(stderr, " --version show version number\n");
fprintf(stderr, " -h show help information\n");
@@ -361,7 +362,7 @@ 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:l:s:O:", 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:l:s:O:eu", long_options)) >= 0) {
if (c == 'h')
{
Print_H(asm_opt);
@@ -396,6 +397,8 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 'p') asm_opt->small_pop_bubble_size = atoll(opt.arg);
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 == 302) asm_opt->flag |= HA_F_WRITE_PAF;
else if (c == 303) asm_opt->flag |= HA_F_WRITE_EC;