fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-09-24 09:38:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

r545: removed option -i, not working well

Browse Source
This commit is contained in:
Heng Li
2017-10-31 22:23:27 -04:00
parent b8e758df0f
commit cd24dc8834
6 changed files with 3 additions and 58 deletions
Download Patch File Download Diff File Expand all files Collapse all files
main.c
+2 -4
View File
@@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.3-r544-dirty"
#define MM_VERSION "2.3-r545-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -67,7 +67,7 @@ static inline int64_t mm_parse_num(const char *str)
int main(int argc, char *argv[])
{
const char *opt_str = "2aSw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:i:LC:";
const char *opt_str = "2aSw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:LC:";
mm_mapopt_t opt;
mm_idxopt_t ipt;
int i, c, n_threads = 3, long_idx;
@@ -102,7 +102,6 @@ int main(int argc, char *argv[])
else if (c == 'g') opt.max_gap = (int)mm_parse_num(optarg);
else if (c == 'G') mm_mapopt_max_intron_len(&opt, (int)mm_parse_num(optarg));
else if (c == 'F') opt.max_frag_len = (int)mm_parse_num(optarg);
else if (c == 'i') opt.min_iden = atof(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);
@@ -226,7 +225,6 @@ int main(int argc, char *argv[])
fprintf(fp_help, " -z INT Z-drop score [%d]\n", opt.zdrop);
fprintf(fp_help, " -s INT minimal peak DP alignment score [%d]\n", opt.min_dp_max);
fprintf(fp_help, " -u CHAR how to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG [n]\n");
fprintf(fp_help, " -i FLOAT min identity (mapQ reduced to 0 if below) [0]\n");
fprintf(fp_help, " Input/Output:\n");
fprintf(fp_help, " -a output in the SAM format (PAF by default)\n");
fprintf(fp_help, " -Q don't output base quality in SAM\n");