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added idx_stat

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This commit is contained in:
Heng Li
2017-04-26 22:52:28 +08:00
parent de367a340c
commit 7b7fabef4d
4 changed files with 23 additions and 7 deletions
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main.c
+2 -5
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@@ -34,7 +34,7 @@ int main(int argc, char *argv[])
mm_realtime0 = realtime();
mm_mapopt_init(&opt);
while ((c = getopt(argc, argv, "w:k:B:b:t:r:c:f:Vv:NOg:I:d:lRPST:L:Dx:H")) >= 0) {
while ((c = getopt(argc, argv, "w:k:B:b:t:r:c:f:Vv:NOg:I:d:lST:L:Dx:H")) >= 0) {
if (c == 'w') w = atoi(optarg);
else if (c == 'k') k = atoi(optarg);
else if (c == 'b') b = atoi(optarg);
@@ -48,8 +48,6 @@ int main(int argc, char *argv[])
else if (c == 'v') mm_verbose = atoi(optarg);
else if (c == 'g') opt.max_gap = atoi(optarg);
else if (c == 'N') keep_name = 0;
else if (c == 'R') opt.flag |= MM_F_WITH_REP;
else if (c == 'P') opt.flag &= ~MM_F_WITH_REP;
else if (c == 'D') opt.flag |= MM_F_NO_SELF;
else if (c == 'O') opt.flag |= MM_F_NO_ISO;
else if (c == 'S') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
@@ -98,8 +96,6 @@ int main(int argc, char *argv[])
// fprintf(stderr, " -D skip self mappings but keep dual mappings\n"); // too confusing to expose to end users
fprintf(stderr, " -S skip self and dual mappings\n");
fprintf(stderr, " -O drop isolated hits before chaining (EXPERIMENTAL)\n");
fprintf(stderr, " -P filtering potential repeats after mapping (EXPERIMENTAL)\n");
// fprintf(stderr, " -R skip post-mapping repeat filtering\n"); // deprecated option for backward compatibility
fprintf(stderr, " -x STR preset (recommended to be applied before other options) []\n");
fprintf(stderr, " ava10k: -Sw5 -L100 -m0 (PacBio/ONT all-vs-all read mapping)\n");
fprintf(stderr, " Input/Output:\n");
@@ -130,6 +126,7 @@ int main(int argc, char *argv[])
fprintf(stderr, "[M::%s::%.3f*%.2f] dumpped the (partial) index to disk\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0));
}
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, mini_batch_size);
mm_idx_destroy(mi);