fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-10-02 22:58:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

r476: multi-file fragment mode working

Browse Source
This commit is contained in:
Heng Li
2017-10-05 15:39:26 -04:00
parent b839758335
commit ae2adf04d4
4 changed files with 12 additions and 6 deletions
Download Patch File Download Diff File Expand all files Collapse all files
main.c
+8 -5
View File
@@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.2-r475-dirty"
#define MM_VERSION "2.2-r476-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -37,7 +37,7 @@ static struct option long_options[] = {
{ "cost-non-gt-ag", required_argument, 0, 0 },
{ "no-long-join", no_argument, 0, 0 },
{ "sr", no_argument, 0, 0 },
{ "multi", optional_argument, 0, 0 },
{ "frag", optional_argument, 0, 0 },
{ "print-2nd", optional_argument, 0, 0 },
{ "cs", optional_argument, 0, 0 },
{ "help", no_argument, 0, 'h' },
@@ -129,7 +129,7 @@ int main(int argc, char *argv[])
else if (c == 0 && long_idx ==11) opt.noncan = atoi(optarg); // --cost-non-gt-ag
else if (c == 0 && long_idx ==12) opt.flag |= MM_F_NO_LJOIN; // --no-long-join
else if (c == 0 && long_idx ==13) opt.flag |= MM_F_SR; // --sr
else if (c == 0 && long_idx == 14) { // --multi
else if (c == 0 && long_idx == 14) { // --frag
if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
opt.flag |= MM_F_MULTI_SEG;
else opt.flag &= ~MM_F_MULTI_SEG;
@@ -267,8 +267,11 @@ int main(int argc, char *argv[])
__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), mi->n_seq);
if (argc != optind + 1) mm_mapopt_update(&opt, mi);
if (mm_verbose >= 3) mm_idx_stat(mi);
for (i = optind + 1; i < argc; ++i)
mm_map_file(mi, argv[i], &opt, n_threads);
if (opt.flag & MM_F_MULTI_SEG)
mm_map_file_multi_seg(mi, argc - (optind + 1), (const char**)&argv[optind + 1], &opt, n_threads);
else
for (i = optind + 1; i < argc; ++i)
mm_map_file(mi, argv[i], &opt, n_threads);
mm_idx_destroy(mi);
}
mm_idx_reader_close(idx_rdr);