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added --idx-min-occ and --idx-max-occ

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Heng Li
2019-12-23 22:58:44 -05:00
parent d90583b83c
commit 43b0399991
4 changed files with 47 additions and 21 deletions
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main.c
+4
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@@ -67,6 +67,8 @@ static ko_longopt_t long_options[] = {
{ "junc-bed", ko_required_argument, 340 },
{ "junc-bonus", ko_required_argument, 341 },
{ "sam-hit-only", ko_no_argument, 342 },
{ "idx-min-occ", ko_required_argument, 343 },
{ "idx-max-occ", ko_required_argument, 344 },
{ "help", ko_no_argument, 'h' },
{ "max-intron-len", ko_required_argument, 'G' },
{ "version", ko_no_argument, 'V' },
@@ -210,6 +212,8 @@ int main(int argc, char *argv[])
else if (c == 338) opt.max_qlen = mm_parse_num(o.arg); // --max-qlen
else if (c == 340) junc_bed = o.arg; // --junc-bed
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 == 314) { // --frag
yes_or_no(&opt, MM_F_FRAG_MODE, o.longidx, o.arg, 1);
} else if (c == 315) { // --secondary