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r966: minimap2 returns 1 on file failure (#532)

This commit is contained in:
Heng Li 2020-01-18 10:58:59 -05:00
parent 040f74102c
commit 04e015d803
1 changed files with 11 additions and 5 deletions
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16
main.c
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@ -7,7 +7,7 @@
#include "mmpriv.h"
#include "ketopt.h"
#define MM_VERSION "2.17-r965-dirty"
#define MM_VERSION "2.17-r966-dirty"
#ifdef __linux__
#include <sys/resource.h>
@ -352,6 +352,7 @@ int main(int argc, char *argv[])
if (opt.best_n == 0 && (opt.flag&MM_F_CIGAR) && mm_verbose >= 2)
fprintf(stderr, "[WARNING]\033[1;31m `-N 0' reduces alignment accuracy. Please use --secondary=no to suppress secondary alignments.\033[0m\n");
while ((mi = mm_idx_reader_read(idx_rdr, n_threads)) != 0) {
int ret;
if ((opt.flag & MM_F_CIGAR) && (mi->flag & MM_I_NO_SEQ)) {
fprintf(stderr, "[ERROR] the prebuilt index doesn't contain sequences.\n");
mm_idx_destroy(mi);
@ -359,7 +360,6 @@ int main(int argc, char *argv[])
return 1;
}
if ((opt.flag & MM_F_OUT_SAM) && idx_rdr->n_parts == 1) {
int ret;
if (mm_idx_reader_eof(idx_rdr)) {
ret = mm_write_sam_hdr(mi, rg, MM_VERSION, argc, argv);
} else {
@ -380,12 +380,18 @@ int main(int argc, char *argv[])
if (mm_verbose >= 3) mm_idx_stat(mi);
if (junc_bed) mm_idx_bed_read(mi, junc_bed, 1);
if (!(opt.flag & MM_F_FRAG_MODE)) {
for (i = o.ind + 1; i < argc; ++i)
mm_map_file(mi, argv[i], &opt, n_threads);
for (i = o.ind + 1; i < argc; ++i) {
ret = mm_map_file(mi, argv[i], &opt, n_threads);
if (ret < 0) break;
}
} else {
mm_map_file_frag(mi, argc - (o.ind + 1), (const char**)&argv[o.ind + 1], &opt, n_threads);
ret = mm_map_file_frag(mi, argc - (o.ind + 1), (const char**)&argv[o.ind + 1], &opt, n_threads);
}
mm_idx_destroy(mi);
if (ret < 0) {
fprintf(stderr, "ERROR: failed to map the query file\n");
exit(EXIT_FAILURE);
}
}
n_parts = idx_rdr->n_parts;
mm_idx_reader_close(idx_rdr);