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replaced --approx-ext with --sr

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--sr disables Z-drop and may come with other heurstics
This commit is contained in:
Heng Li
2017-09-20 10:51:18 -04:00
parent 4979e66ff0
commit 7a9b4db874
5 changed files with 12 additions and 10 deletions
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main.c
+2 -2
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@@ -36,7 +36,7 @@ static struct option long_options[] = {
{ "splice", no_argument, 0, 0 },
{ "cost-non-gt-ag", required_argument, 0, 0 },
{ "no-sam-sq", no_argument, 0, 0 },
{ "approx-ext", no_argument, 0, 0 },
{ "sr", no_argument, 0, 0 },
{ "help", no_argument, 0, 'h' },
{ "max-intron-len", required_argument, 0, 'G' },
{ "version", no_argument, 0, 'V' },
@@ -114,7 +114,7 @@ int main(int argc, char *argv[])
else if (c == 0 && long_idx ==10) opt.flag |= MM_F_SPLICE; // --splice
else if (c == 0 && long_idx ==11) opt.noncan = atoi(optarg); // --cost-non-gt-ag
else if (c == 0 && long_idx ==12) opt.flag |= MM_F_NO_SAM_SQ; // --no-sam-sq
else if (c == 0 && long_idx ==13) opt.flag |= MM_F_APPROX_EXT; // --approx-ext
else if (c == 0 && long_idx ==13) opt.flag |= MM_F_SR; // --sr
else if (c == 'V') {
puts(MM_VERSION);
return 0;