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r257: dropped contained unitigs

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Heng Li
2020-06-08 15:43:21 -04:00
parent afa93e4bbb
commit 36bfb02298
4 changed files with 109 additions and 15 deletions
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CommandLines.cpp
+2
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@@ -19,6 +19,7 @@ static ko_longopt_t long_options[] = {
{ "max-od-final", ko_no_argument, 306 },
{ "ex-list", ko_required_argument, 307 },
{ "ex-iter", ko_required_argument, 308 },
{ "keep-contained",ko_no_argument, 309 },
{ 0, 0, 0 }
};
@@ -404,6 +405,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 306) asm_opt->max_ov_diff_final = atof(opt.arg);
else if (c == 307) asm_opt->extract_list = opt.arg;
else if (c == 308) asm_opt->extract_iter = atoi(opt.arg);
else if (c == 309) asm_opt->flag |= HA_F_KEEP_CONTAINED;
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);