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added --junc-pen; it does nothing for now

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Heng Li
2024-10-11 21:27:25 -04:00
parent e4e1f7843b
commit 042c8d4d71
7 changed files with 15 additions and 11 deletions
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main.c
+3
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@@ -80,6 +80,8 @@ static ko_longopt_t long_options[] = {
{ "ds", ko_no_argument, 355 },
{ "rmq-inner", ko_required_argument, 356 },
{ "spsc", ko_required_argument, 357 },
{ "spsc0", ko_required_argument, 358 },
{ "junc-pen", ko_required_argument, 358 }, // an alias to --spsc0; this is not a typo
{ "dbg-seed-occ", ko_no_argument, 501 },
{ "help", ko_no_argument, 'h' },
{ "max-intron-len", ko_required_argument, 'G' },
@@ -235,6 +237,7 @@ 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 == 341) opt.junc_bonus = atoi(o.arg); // --junc-bonus
else if (c == 358) opt.junc_pen = atoi(o.arg); // --junc-pen
else if (c == 342) opt.flag |= MM_F_SAM_HIT_ONLY; // --sam-hit-only
else if (c == 343) opt.chain_gap_scale = atof(o.arg); // --chain-gap-scale
else if (c == 351) opt.chain_skip_scale = atof(o.arg); // --chain-skip-scale