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compilable again

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This commit is contained in:
Heng Li
2017-04-26 19:36:46 +08:00
parent 56723ad580
commit de367a340c
4 changed files with 206 additions and 37 deletions
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main.c
+4 -8
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@@ -7,7 +7,7 @@
#include "bseq.h"
#include "minimap.h"
#define MM_VERSION "0.2-r124-dirty"
#define MM_VERSION "2.0-r14-pre"
void liftrlimit()
{
@@ -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:m:L:Dx:H")) >= 0) {
while ((c = getopt(argc, argv, "w:k:B:b:t:r:c:f:Vv:NOg:I:d:lRPST:L:Dx:H")) >= 0) {
if (c == 'w') w = atoi(optarg);
else if (c == 'k') k = atoi(optarg);
else if (c == 'b') b = atoi(optarg);
@@ -43,7 +43,6 @@ int main(int argc, char *argv[])
else if (c == 'd') fnw = optarg; // the above are indexing related options, except -I
else if (c == 'r') opt.radius = atoi(optarg);
else if (c == 'c') opt.min_cnt = atoi(optarg);
else if (c == 'm') opt.merge_frac = atof(optarg);
else if (c == 'f') f = atof(optarg);
else if (c == 't') n_threads = atoi(optarg);
else if (c == 'v') mm_verbose = atoi(optarg);
@@ -72,7 +71,6 @@ int main(int argc, char *argv[])
if (strcmp(optarg, "ava10k") == 0) {
opt.flag |= MM_F_AVA | MM_F_NO_SELF;
opt.min_match = 100;
opt.merge_frac = 0.0;
w = 5;
}
}
@@ -93,7 +91,6 @@ int main(int argc, char *argv[])
fprintf(stderr, " Mapping:\n");
fprintf(stderr, " -f FLOAT filter out top FLOAT fraction of repetitive minimizers [%.3f]\n", f);
fprintf(stderr, " -r INT bandwidth [%d]\n", opt.radius);
fprintf(stderr, " -m FLOAT merge two chains if FLOAT fraction of minimizers are shared [%.2f]\n", opt.merge_frac);
fprintf(stderr, " -c INT retain a mapping if it consists of >=INT minimizers [%d]\n", opt.min_cnt);
fprintf(stderr, " -L INT min matching length [%d]\n", opt.min_match);
fprintf(stderr, " -g INT split a mapping if there is a gap longer than INT [%d]\n", opt.max_gap);
@@ -129,13 +126,12 @@ int main(int argc, char *argv[])
__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), mi->n_seq);
if (fpw) {
mm_idx_dump(fpw, mi);
if (mm_verbose >= 2)
if (mm_verbose >= 3)
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);
for (i = optind + 1; i < argc; ++i)
mm_map_file(mi, argv[i], &opt, n_threads, mini_batch_size);
*/
mm_idx_destroy(mi);
}
if (fpw) fclose(fpw);