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r367: index reader optionally writes index

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This commit is contained in:
Heng Li
2017-09-14 21:18:13 -04:00
parent eb00521d9b
commit e2823d4aee
5 changed files with 83 additions and 90 deletions
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main.c
+6 -13
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@@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.1.1-r365-dirty"
#define MM_VERSION "2.1.1-r367-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -65,13 +65,12 @@ int main(int argc, char *argv[])
mm_idxopt_t ipt;
int i, c, n_threads = 3, long_idx, max_intron_len = 0;
char *fnw = 0, *rg = 0, *s;
FILE *fpw = 0, *fp_help = stderr;
FILE *fp_help = stderr;
mm_idx_reader_t *idx_rdr;
liftrlimit();
mm_realtime0 = realtime();
mm_mapopt_init(&opt);
mm_idxopt_init(&ipt);
mm_set_opt(0, &ipt, &opt);
while ((c = getopt_long(argc, argv, "aSw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:h", long_options, &long_idx)) >= 0) {
if (c == 'w') ipt.w = atoi(optarg);
@@ -139,7 +138,7 @@ int main(int argc, char *argv[])
opt.e = opt.e2 = strtol(optarg, &s, 10);
if (*s == ',') opt.e2 = strtol(s + 1, &s, 10);
} else if (c == 'x') {
if (mm_preset(optarg, &ipt, &opt) < 0) {
if (mm_set_opt(optarg, &ipt, &opt) < 0) {
fprintf(stderr, "[E::%s] unknown preset '%s'\n", __func__, optarg);
return 1;
}
@@ -200,7 +199,7 @@ int main(int argc, char *argv[])
return fp_help == stdout? 0 : 1;
}
idx_rdr = mm_idx_reader_open(argv[optind], &ipt);
idx_rdr = mm_idx_reader_open(argv[optind], &ipt, fnw);
if (idx_rdr == 0) {
fprintf(stderr, "[ERROR] failed to open file '%s'\n", argv[optind]);
return 1;
@@ -209,7 +208,6 @@ int main(int argc, char *argv[])
fprintf(stderr, "[ERROR] missing input: please specify a query file to map or option -d to keep the index\n");
return 1;
}
if (fnw) fpw = fopen(fnw, "wb");
if (opt.flag & MM_F_OUT_SAM)
mm_write_sam_hdr_no_SQ(rg, MM_VERSION, argc, argv);
for (;;) {
@@ -220,18 +218,13 @@ int main(int argc, char *argv[])
if (mm_verbose >= 3)
fprintf(stderr, "[M::%s::%.3f*%.2f] loaded/built the index for %d target sequence(s)\n",
__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), mi->n_seq);
if (fpw) {
mm_idx_dump(fpw, mi);
if (mm_verbose >= 3)
fprintf(stderr, "[M::%s::%.3f*%.2f] dumpped the current part of the 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);
mm_idx_destroy(mi);
}
if (fpw) fclose(fpw);
mm_idx_reader_close(idx_rdr);
fprintf(stderr, "[M::%s] Version: %s\n", __func__, MM_VERSION);
fprintf(stderr, "[M::%s] CMD:", __func__);