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r477: renamed multi_seg to frag_mode

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This commit is contained in:
Heng Li
2017-10-05 15:48:17 -04:00
parent ae2adf04d4
commit 9c5767f9ed
5 changed files with 25 additions and 24 deletions
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main.c
+8 -7
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@@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.2-r476-dirty"
#define MM_VERSION "2.2-r477-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -131,8 +131,8 @@ int main(int argc, char *argv[])
else if (c == 0 && long_idx ==13) opt.flag |= MM_F_SR; // --sr
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;
opt.flag |= MM_F_FRAG_MODE;
else opt.flag &= ~MM_F_FRAG_MODE;
} else if (c == 0 && long_idx == 15) { // --print-2nd
if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
opt.flag &= ~MM_F_NO_PRINT_2ND;
@@ -180,7 +180,7 @@ int main(int argc, char *argv[])
}
}
if (max_gap_ref > 0) {
if (opt.flag & MM_F_MULTI_SEG)
if (opt.flag & MM_F_FRAG_MODE)
opt.max_gap_ref = max_gap_ref;
if (opt.flag & MM_F_SPLICE)
opt.max_gap_ref = opt.bw = max_gap_ref;
@@ -267,11 +267,12 @@ 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);
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
if (!(opt.flag & MM_F_FRAG_MODE)) {
for (i = optind + 1; i < argc; ++i)
mm_map_file(mi, argv[i], &opt, n_threads);
} else {
mm_map_file_frag(mi, argc - (optind + 1), (const char**)&argv[optind + 1], &opt, n_threads);
}
mm_idx_destroy(mi);
}
mm_idx_reader_close(idx_rdr);