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r972: renamed --alt-diff to --alt-drop

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Heng Li
2020-01-21 10:33:39 -05:00
parent 20a3987082
commit 9dceae59a0
5 changed files with 15 additions and 10 deletions
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main.c
+2 -2
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@@ -69,7 +69,7 @@ static ko_longopt_t long_options[] = {
{ "sam-hit-only", ko_no_argument, 342 },
{ "chain-gap-scale",ko_required_argument, 343 },
{ "alt", ko_required_argument, 344 },
{ "alt-diff", ko_required_argument, 345 },
{ "alt-drop", ko_required_argument, 345 },
{ "help", ko_no_argument, 'h' },
{ "max-intron-len", ko_required_argument, 'G' },
{ "version", ko_no_argument, 'V' },
@@ -216,7 +216,7 @@ int main(int argc, char *argv[])
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 == 344) alt_list = o.arg; // --alt
else if (c == 345) opt.alt_diff_frac = atof(o.arg); // --alt-diff
else if (c == 345) opt.alt_drop = atof(o.arg); // --alt-drop
else if (c == 314) { // --frag
yes_or_no(&opt, MM_F_FRAG_MODE, o.longidx, o.arg, 1);
} else if (c == 315) { // --secondary