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r963: --junc-bonus not working; resolves #513

This commit is contained in:
Heng Li 2020-01-06 22:03:50 -05:00
parent 3c0d05d272
commit cdb7857841
1 changed files with 2 additions and 1 deletions
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3
main.c
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@ -7,7 +7,7 @@
#include "mmpriv.h"
#include "ketopt.h"
#define MM_VERSION "2.17-r962-dirty"
#define MM_VERSION "2.17-r963-dirty"
#ifdef __linux__
#include <sys/resource.h>
@ -209,6 +209,7 @@ int main(int argc, char *argv[])
else if (c == 337) opt.max_sw_mat = mm_parse_num(o.arg); // --cap-sw-mat
else if (c == 338) opt.max_qlen = mm_parse_num(o.arg); // --max-qlen
else if (c == 340) junc_bed = o.arg; // --junc-bed
else if (c == 341) opt.junc_bonus = atoi(o.arg); // --junc-bonus
else if (c == 342) opt.flag |= MM_F_SAM_HIT_ONLY; // --sam-hit-only
else if (c == 314) { // --frag
yes_or_no(&opt, MM_F_FRAG_MODE, o.longidx, o.arg, 1);