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r452: fixed - -G not working with -x sr

This commit is contained in:
Heng Li 2017-09-28 14:28:12 -04:00
parent 2a554a92e9
commit 0c63325985
1 changed files with 9 additions and 5 deletions
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14
main.c
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@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.2-r451-dirty"
#define MM_VERSION "2.2-r452-dirty"
#ifdef __linux__
#include <sys/resource.h>
@ -64,7 +64,7 @@ int main(int argc, char *argv[])
{
mm_mapopt_t opt;
mm_idxopt_t ipt;
int i, c, n_threads = 3, long_idx, max_intron_len = 0;
int i, c, n_threads = 3, long_idx, max_gap_ref = 0;
char *fnw = 0, *rg = 0, *s;
FILE *fp_help = stderr;
mm_idx_reader_t *idx_rdr;
@ -84,7 +84,7 @@ int main(int argc, char *argv[])
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);
else if (c == 'G') max_intron_len = (int)mm_parse_num(optarg);
else if (c == 'G') max_gap_ref = (int)mm_parse_num(optarg);
else if (c == 'N') opt.best_n = atoi(optarg);
else if (c == 'p') opt.pri_ratio = atof(optarg);
else if (c == 'M') opt.mask_level = atof(optarg);
@ -150,8 +150,12 @@ int main(int argc, char *argv[])
}
}
}
if ((opt.flag & MM_F_SPLICE) && max_intron_len > 0)
opt.max_gap_ref = opt.bw = max_intron_len;
if (max_gap_ref > 0) {
if (opt.flag & MM_F_MULTI_SEG)
opt.max_gap_ref = max_gap_ref;
if (opt.flag & MM_F_SPLICE)
opt.max_gap_ref = opt.bw = max_gap_ref;
}
if (argc == optind || fp_help == stdout) {
fprintf(fp_help, "Usage: minimap2 [options] <target.fa>|<target.idx> [query.fa] [...]\n");