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r517: replaced --print-2nd with --secondary

This commit is contained in:
Heng Li 2017-10-17 11:41:56 -04:00
parent aa2d9d4e1b
commit 25ffd72690
1 changed files with 4 additions and 4 deletions
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8
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-r516-dirty" #define MM_VERSION "2.2-r517-dirty"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>
@ -38,7 +38,7 @@ static struct option long_options[] = {
{ "no-long-join", no_argument, 0, 0 }, { "no-long-join", no_argument, 0, 0 },
{ "sr", no_argument, 0, 0 }, { "sr", no_argument, 0, 0 },
{ "frag", optional_argument, 0, 0 }, { "frag", optional_argument, 0, 0 },
{ "print-2nd", optional_argument, 0, 0 }, { "secondary", optional_argument, 0, 0 },
{ "cs", optional_argument, 0, 0 }, { "cs", optional_argument, 0, 0 },
{ "end-bonus", required_argument, 0, 0 }, { "end-bonus", required_argument, 0, 0 },
{ "help", no_argument, 0, 'h' }, { "help", no_argument, 0, 'h' },
@ -138,7 +138,7 @@ int main(int argc, char *argv[])
if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0) if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
opt.flag |= MM_F_FRAG_MODE; opt.flag |= MM_F_FRAG_MODE;
else opt.flag &= ~MM_F_FRAG_MODE; else opt.flag &= ~MM_F_FRAG_MODE;
} else if (c == 0 && long_idx == 15) { // --print-2nd } else if (c == 0 && long_idx == 15) { // --secondary
if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0) if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
opt.flag &= ~MM_F_NO_PRINT_2ND; opt.flag &= ~MM_F_NO_PRINT_2ND;
else opt.flag |= MM_F_NO_PRINT_2ND; else opt.flag |= MM_F_NO_PRINT_2ND;
@ -258,7 +258,7 @@ int main(int argc, char *argv[])
return 1; return 1;
} }
if (opt.best_n == 0 && (opt.flag&MM_F_CIGAR) && mm_verbose >= 2) 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"); 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) { 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)) {