fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-10-05 04:58:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

r461: randomize repetitive hits

Browse Source
This commit is contained in:
Heng Li
2017-10-04 13:05:18 -04:00
parent cf55c84056
commit 2a1e738a94
6 changed files with 52 additions and 25 deletions
Download Patch File Download Diff File Expand all files Collapse all files
main.c
+5 -3
View File
@@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.2-r460-dirty"
#define MM_VERSION "2.2-r461-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -37,8 +37,9 @@ static struct option long_options[] = {
{ "cost-non-gt-ag", required_argument, 0, 0 },
{ "no-sam-sq", no_argument, 0, 0 },
{ "sr", no_argument, 0, 0 },
{ "multi-seg", optional_argument, 0, 0 },
{ "multi", optional_argument, 0, 0 },
{ "no-long-join", no_argument, 0, 0 },
{ "seed", required_argument, 0, 0 },
{ "help", no_argument, 0, 'h' },
{ "max-intron-len", required_argument, 0, 'G' },
{ "version", no_argument, 0, 'V' },
@@ -118,7 +119,8 @@ int main(int argc, char *argv[])
else if (c == 0 && long_idx ==12) opt.flag |= MM_F_NO_SAM_SQ; // --no-sam-sq
else if (c == 0 && long_idx ==13) opt.flag |= MM_F_SR; // --sr
else if (c == 0 && long_idx ==15) opt.flag |= MM_F_NO_LJOIN; // --no-long-join
else if (c == 0 && long_idx ==14) { // --multi-seg
else if (c == 0 && long_idx ==16) opt.seed = atoi(optarg); // --seed
else if (c == 0 && long_idx ==14) { // --multi
if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
opt.flag |= MM_F_MULTI_SEG;
else opt.flag &= ~MM_F_MULTI_SEG;