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miniprot-like splice model

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slightly worse on iso-seq and slightly better on direct-RNA
This commit is contained in:
Heng Li
2022-10-06 09:10:17 -04:00
parent 5aa4355ca8
commit 6c2cbf7903
7 changed files with 104 additions and 7 deletions
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main.c
+2
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@@ -35,6 +35,7 @@ static ko_longopt_t long_options[] = {
{ "min-dp-len", ko_required_argument, 308 },
{ "print-aln-seq", ko_no_argument, 309 },
{ "splice", ko_no_argument, 310 },
{ "splice-model", ko_no_argument, 311 },
{ "cost-non-gt-ag", ko_required_argument, 'C' },
{ "no-long-join", ko_no_argument, 312 },
{ "sr", ko_no_argument, 313 },
@@ -205,6 +206,7 @@ int main(int argc, char *argv[])
else if (c == 308) opt.min_ksw_len = atoi(o.arg); // --min-dp-len
else if (c == 309) mm_dbg_flag |= MM_DBG_PRINT_QNAME | MM_DBG_PRINT_ALN_SEQ, n_threads = 1; // --print-aln-seq
else if (c == 310) opt.flag |= MM_F_SPLICE; // --splice
else if (c == 311) opt.flag |= MM_F_SPLICE_CMPLX; // --splice-model
else if (c == 312) opt.flag |= MM_F_NO_LJOIN; // --no-long-join
else if (c == 313) opt.flag |= MM_F_SR; // --sr
else if (c == 317) opt.end_bonus = atoi(o.arg); // --end-bonus