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r516: throw a warning if -N0 is used

This commit is contained in:
Heng Li 2017-10-16 14:55:35 -04:00
parent addb61bcb2
commit aa2d9d4e1b
1 changed files with 3 additions and 1 deletions
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4
main.c
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@ -6,7 +6,7 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "getopt.h" #include "getopt.h"
#define MM_VERSION "2.2-r515-dirty" #define MM_VERSION "2.2-r516-dirty"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>
@ -257,6 +257,8 @@ 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"); fprintf(stderr, "[ERROR] missing input: please specify a query file to map or option -d to keep the index\n");
return 1; return 1;
} }
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 --print-2nd=no to suppress secondary alignments.\033[0m\n");
while ((mi = mm_idx_reader_read(idx_rdr, n_threads)) != 0) { while ((mi = mm_idx_reader_read(idx_rdr, n_threads)) != 0) {
if ((opt.flag & MM_F_OUT_SAM) && idx_rdr->n_parts == 1) { if ((opt.flag & MM_F_OUT_SAM) && idx_rdr->n_parts == 1) {
if (mm_idx_reader_eof(idx_rdr)) { if (mm_idx_reader_eof(idx_rdr)) {