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r1060: safer ways to use -rNUM1,NUM2

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Heng Li
2021-05-27 10:55:13 -04:00
parent 4f8d1bc360
commit ca19463268
4 changed files with 24 additions and 18 deletions
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main.c
+2 -4
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@@ -7,7 +7,7 @@
#include "mmpriv.h"
#include "ketopt.h"
#define MM_VERSION "2.19-r1059-dirty"
#define MM_VERSION "2.19-r1060-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -296,8 +296,6 @@ int main(int argc, char *argv[])
}
if (!fnw && !(opt.flag&MM_F_CIGAR))
ipt.flag |= MM_I_NO_SEQ;
if (opt.bw < opt.bw_long && (opt.flag&MM_F_RMQ))
opt.bw = opt.bw_long;
if (mm_check_opt(&ipt, &opt) < 0)
return 1;
if (opt.best_n == 0) {
@@ -319,7 +317,7 @@ int main(int argc, char *argv[])
fprintf(fp_help, " -g NUM stop chain enlongation if there are no minimizers in INT-bp [%d]\n", opt.max_gap);
fprintf(fp_help, " -G NUM max intron length (effective with -xsplice; changing -r) [200k]\n");
fprintf(fp_help, " -F NUM max fragment length (effective with -xsr or in the fragment mode) [800]\n");
fprintf(fp_help, " -r NUM bandwidth used in chaining and DP-based alignment [%d]\n", opt.bw);
fprintf(fp_help, " -r NUM[,NUM] chaining/alignment bandwidth and long-join bandwidth [%d,%d]\n", opt.bw, opt.bw_long);
fprintf(fp_help, " -n INT minimal number of minimizers on a chain [%d]\n", opt.min_cnt);
fprintf(fp_help, " -m INT minimal chaining score (matching bases minus log gap penalty) [%d]\n", opt.min_chain_score);
// fprintf(fp_help, " -T INT SDUST threshold; 0 to disable SDUST [%d]\n", opt.sdust_thres); // TODO: this option is never used; might be buggy