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fixed a bug in ksw2

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This commit is contained in:
Heng Li
2017-06-25 10:22:13 -04:00
parent ef5dd318ca
commit 72dfb0c99e
3 changed files with 6 additions and 2 deletions
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main.c
+3 -1
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@@ -54,7 +54,7 @@ int main(int argc, char *argv[])
mm_realtime0 = realtime();
mm_mapopt_init(&opt);
while ((c = getopt(argc, argv, "w:k:B:b:t:r:f:Vv:Ng:I:d:ST:s:Dx:Hp:m:")) >= 0) {
while ((c = getopt(argc, argv, "w:k:B:b:t:r:f:Vv:Ng:I:d:ST:s:Dx:Hp:m:z:")) >= 0) {
if (c == 'w') w = atoi(optarg);
else if (c == 'k') k = atoi(optarg);
else if (c == 'b') b = atoi(optarg);
@@ -72,6 +72,7 @@ int main(int argc, char *argv[])
else if (c == 'S') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
else if (c == 'T') opt.sdust_thres = atoi(optarg);
else if (c == 's') opt.min_score = atoi(optarg);
else if (c == 'z') opt.zdrop = atoi(optarg);
else if (c == 'V') {
puts(MM_VERSION);
return 0;
@@ -113,6 +114,7 @@ int main(int argc, char *argv[])
// fprintf(stderr, " -D skip self mappings but keep dual mappings\n"); // too confusing to expose to end users
fprintf(stderr, " -S skip self and dual mappings\n");
fprintf(stderr, " -p FLOAT threshold to output a mapping [%g]\n", opt.pri_ratio);
fprintf(stderr, " -z INT Z-drop score [%d]\n", opt.zdrop);
fprintf(stderr, " -x STR preset (recommended to be applied before other options) []\n");
fprintf(stderr, " ava10k: -Sw5 -L100 -m0 (PacBio/ONT all-vs-all read mapping)\n");
fprintf(stderr, " Input/Output:\n");