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optionally output unmapped query in PAF

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Heng Li
2018-07-07 10:26:08 -05:00
parent bcf92b3c46
commit a609a07f8c
4 changed files with 16 additions and 0 deletions
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main.c
+2
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@@ -60,6 +60,7 @@ static struct option long_options[] = {
{ "lj-min-ratio", required_argument, 0, 0 }, // 30
{ "score-N", required_argument, 0, 0 }, // 31
{ "eqx", no_argument, 0, 0 }, // 32
{ "paf-no-hit", no_argument, 0, 0 }, // 33
{ "help", no_argument, 0, 'h' },
{ "max-intron-len", required_argument, 0, 'G' },
{ "version", no_argument, 0, 'V' },
@@ -179,6 +180,7 @@ int main(int argc, char *argv[])
else if (c == 0 && long_idx ==30) opt.min_join_flank_ratio = atof(optarg); // --lj-min-ratio
else if (c == 0 && long_idx ==31) opt.sc_ambi = atoi(optarg); // --score-N
else if (c == 0 && long_idx ==32) opt.flag |= MM_F_EQX; // --eqx
else if (c == 0 && long_idx ==33) opt.flag |= MM_F_PAF_NO_HIT; // --paf-no-hit
else if (c == 0 && long_idx == 14) { // --frag
yes_or_no(&opt, MM_F_FRAG_MODE, long_idx, optarg, 1);
} else if (c == 0 && long_idx == 15) { // --secondary