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r360: allow to set integer max occ

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Heng Li
2017-09-13 11:37:00 -04:00
parent 1b44275802
commit 3c91d652dd
5 changed files with 16 additions and 10 deletions
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main.c
+7 -3
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@@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.1.1-r347-dirty"
#define MM_VERSION "2.1.1-r360-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -78,7 +78,6 @@ int main(int argc, char *argv[])
else if (c == 'H') is_hpc = 1, idx_par_set = 1;
else if (c == 'd') fnw = optarg; // the above are indexing related options, except -I
else if (c == 'r') opt.bw = (int)mm_parse_num(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 = (int)mm_parse_num(optarg);
@@ -117,6 +116,11 @@ int main(int argc, char *argv[])
else if (c == 'V') {
puts(MM_VERSION);
return 0;
} else if (c == 'f') {
double x;
x = atof(optarg);
if (x < 1.0) opt.mid_occ_frac = x, opt.mid_occ = 0;
else opt.mid_occ = (int)(x + .499);
} else if (c == 'u') {
if (*optarg == 'b') opt.flag |= MM_F_SPLICE_FOR|MM_F_SPLICE_REV;
else if (*optarg == 'B') opt.flag |= MM_F_SPLICE_BOTH;
@@ -168,7 +172,7 @@ int main(int argc, char *argv[])
opt.min_dp_max = 40;
opt.best_n = 20;
opt.bw = 50;
opt.mid_occ_frac = 2e-5f;
opt.mid_occ = 1000;
} else if (strcmp(optarg, "splice") == 0 || strcmp(optarg, "cdna") == 0) {
k = 15, w = 5;
opt.flag |= MM_F_SPLICE | MM_F_SPLICE_FOR | MM_F_SPLICE_REV;