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This commit is contained in:
Heng Li
2017-06-04 16:09:45 -04:00
parent 949d9be872
commit acc7382a30
3 changed files with 79 additions and 100 deletions
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main.c
+6 -8
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@@ -33,15 +33,14 @@ int main(int argc, char *argv[])
mm_realtime0 = realtime();
mm_mapopt_init(&opt);
while ((c = getopt(argc, argv, "w:k:B:b:t:r:c:f:Vv:NOg:I:d:lST:L:Dx:H")) >= 0) {
while ((c = getopt(argc, argv, "w:k:B:b:t:r:f:Vv:NOg:I:d:lST:s:Dx:H")) >= 0) {
if (c == 'w') w = atoi(optarg);
else if (c == 'k') k = atoi(optarg);
else if (c == 'b') b = atoi(optarg);
else if (c == 'H') is_hpc = 1;
else if (c == 'l') is_idx = 1;
else if (c == 'd') fnw = optarg; // the above are indexing related options, except -I
else if (c == 'r') opt.radius = atoi(optarg);
else if (c == 'c') opt.min_cnt = atoi(optarg);
else if (c == 'r') opt.bw = atoi(optarg);
else if (c == 'f') opt.mid_occ_frac = atof(optarg);
else if (c == 't') n_threads = atoi(optarg);
else if (c == 'v') mm_verbose = atoi(optarg);
@@ -51,7 +50,7 @@ int main(int argc, char *argv[])
else if (c == 'O') opt.flag |= MM_F_NO_ISO;
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 == 'L') opt.min_match = atoi(optarg);
else if (c == 's') opt.min_score = atoi(optarg);
else if (c == 'V') {
puts(MM_VERSION);
return 0;
@@ -67,7 +66,7 @@ int main(int argc, char *argv[])
} else if (c == 'x') {
if (strcmp(optarg, "ava10k") == 0) {
opt.flag |= MM_F_AVA | MM_F_NO_SELF;
opt.min_match = 100;
opt.min_score = 100;
w = 5;
}
}
@@ -87,9 +86,8 @@ int main(int argc, char *argv[])
// fprintf(stderr, " -b INT bucket bits [%d]\n", b); // most users wouldn't care about this
fprintf(stderr, " Mapping:\n");
fprintf(stderr, " -f FLOAT filter out top FLOAT fraction of repetitive minimizers [%.3f]\n", opt.mid_occ_frac);
fprintf(stderr, " -r INT bandwidth [%d]\n", opt.radius);
fprintf(stderr, " -c INT retain a mapping if it consists of >=INT minimizers [%d]\n", opt.min_cnt);
fprintf(stderr, " -L INT min matching length [%d]\n", opt.min_match);
fprintf(stderr, " -r INT bandwidth [%d]\n", opt.bw);
fprintf(stderr, " -s INT min score [%d]\n", opt.min_score);
fprintf(stderr, " -g INT split a mapping if there is a gap longer than INT [%d]\n", opt.max_gap);
fprintf(stderr, " -T INT SDUST threshold; 0 to disable SDUST [%d]\n", opt.sdust_thres);
// fprintf(stderr, " -D skip self mappings but keep dual mappings\n"); // too confusing to expose to end users