fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-10-07 03:28:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

r774: Merge branch 'hot-fix' into fix-long-gap

Browse Source
This commit is contained in:
Heng Li
2018-05-11 10:02:17 -04:00
parent e61812ee55 10c6dd2551
commit 881b4ca3a2
9 changed files with 21 additions and 12 deletions
Download Patch File Download Diff File Expand all files Collapse all files
main.c
+4 -2
View File
@@ -10,7 +10,7 @@
#include "getopt.h"
#endif
#define MM_VERSION "2.10-r769-dirty"
#define MM_VERSION "2.10-r774-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -58,6 +58,7 @@ static struct option long_options[] = {
{ "min-occ-floor", required_argument, 0, 0 }, // 28
{ "MD", no_argument, 0, 0 }, // 29
{ "lj-min-ratio", required_argument, 0, 0 }, // 30
{ "score-N", required_argument, 0, 0 }, // 31
{ "help", no_argument, 0, 'h' },
{ "max-intron-len", required_argument, 0, 'G' },
{ "version", no_argument, 0, 'V' },
@@ -95,7 +96,7 @@ static inline void yes_or_no(mm_mapopt_t *opt, int flag, int long_idx, const cha
int main(int argc, char *argv[])
{
const char *opt_str = "2aSDw: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:y";
const char *opt_str = "2aSDw: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:yY";
mm_mapopt_t opt;
mm_idxopt_t ipt;
int i, c, n_threads = 3, long_idx;
@@ -175,6 +176,7 @@ int main(int argc, char *argv[])
else if (c == 0 && long_idx ==28) opt.min_mid_occ = atoi(optarg); // --min-occ-floor
else if (c == 0 && long_idx ==29) opt.flag |= MM_F_OUT_MD; // --MD
else if (c == 0 && long_idx ==30) opt.min_join_flank_ratio = atof(optarg); // --lj-min-ratio
else if (c == 0 && long_idx ==31) opt.sc_ambi = atoi(optarg); // --score-N
else if (c == 0 && long_idx == 14) { // --frag
yes_or_no(&opt, MM_F_FRAG_MODE, long_idx, optarg, 1);
} else if (c == 0 && long_idx == 15) { // --secondary