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An option to output SEQ field for secondary alignment (#687)

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* a new option --secondary-seq to output SEQ field for secondary alignments

* comments removed

* Fixed a conflict in #687

---------

Co-authored-by: Heng Li <lh3@me.com>
This commit is contained in:
Mikhail Kolmogorov
2023-04-21 08:06:13 -07:00
committed by GitHub
parent fc24c8a348
commit 704fbc6f5c
3 changed files with 9 additions and 4 deletions
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2
main.c
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@@ -76,6 +76,7 @@ static ko_longopt_t long_options[] = {
{ "chain-skip-scale",ko_required_argument,351 },
{ "print-chains", ko_no_argument, 352 },
{ "no-hash-name", ko_no_argument, 353 },
{ "secondary-seq", ko_no_argument, 354 },
{ "help", ko_no_argument, 'h' },
{ "max-intron-len", ko_required_argument, 'G' },
{ "version", ko_no_argument, 'V' },
@@ -241,6 +242,7 @@ int main(int argc, char *argv[])
else if (c == 350) opt.q_occ_frac = atof(o.arg); // --q-occ-frac
else if (c == 352) mm_dbg_flag |= MM_DBG_PRINT_CHAIN; // --print-chains
else if (c == 353) opt.flag |= MM_F_NO_HASH_NAME; // --no-hash-name
else if (c == 354) opt.flag |= MM_F_SECONDARY_SEQ; // --secondary-seq
else if (c == 330) {
fprintf(stderr, "[WARNING] \033[1;31m --lj-min-ratio has been deprecated.\033[0m\n");
} else if (c == 314) { // --frag