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mostly debugging code

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Heng Li
2017-05-01 16:50:09 +08:00
parent 2c9f1bce3e
commit f2ae8eb670
2 changed files with 22 additions and 10 deletions
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main.c
+2 -3
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@@ -25,7 +25,6 @@ int main(int argc, char *argv[])
int i, c, k = 15, w = -1, b = MM_IDX_DEF_B, n_threads = 3, keep_name = 1, is_idx = 0, is_hpc = 0;
int mini_batch_size = 100000000;
uint64_t batch_size = 4000000000ULL;
float f = 0.001;
bseq_file_t *fp = 0;
char *fnw = 0;
FILE *fpr = 0, *fpw = 0;
@@ -43,7 +42,7 @@ int main(int argc, char *argv[])
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 == 'f') f = atof(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);
else if (c == 'g') opt.max_gap = atoi(optarg);
@@ -87,7 +86,7 @@ int main(int argc, char *argv[])
fprintf(stderr, " -l the 1st argument is a index file (overriding -k, -w and -I)\n");
// 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", f);
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);