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added two more filters

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Heng Li
2019-12-24 00:06:44 -05:00
parent 43b0399991
commit de6ad4c1d9
4 changed files with 19 additions and 0 deletions
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main.c
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@@ -69,6 +69,8 @@ static ko_longopt_t long_options[] = {
{ "sam-hit-only", ko_no_argument, 342 },
{ "idx-min-occ", ko_required_argument, 343 },
{ "idx-max-occ", ko_required_argument, 344 },
{ "flt-max-dv", ko_required_argument, 345 },
{ "flt-min-blen", ko_required_argument, 346 },
{ "help", ko_no_argument, 'h' },
{ "max-intron-len", ko_required_argument, 'G' },
{ "version", ko_no_argument, 'V' },
@@ -214,6 +216,8 @@ int main(int argc, char *argv[])
else if (c == 342) opt.flag |= MM_F_SAM_HIT_ONLY; // --sam-hit-only
else if (c == 343) ipt.min_occ = mm_parse_num(o.arg); // --idx-min-occ
else if (c == 344) ipt.max_occ = mm_parse_num(o.arg); // --idx-max-occ
else if (c == 345) opt.flt_max_dv = atof(o.arg); // --flt-max-dv
else if (c == 346) opt.flt_min_blen = mm_parse_num(o.arg); // --flt-min-blen
else if (c == 314) { // --frag
yes_or_no(&opt, MM_F_FRAG_MODE, o.longidx, o.arg, 1);
} else if (c == 315) { // --secondary