From 25ffd7269070906b57bbe3754f9c8cd9215412e4 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 17 Oct 2017 11:41:56 -0400 Subject: [PATCH] r517: replaced --print-2nd with --secondary --- main.c | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/main.c b/main.c index d37ceba..a9928d9 100644 --- a/main.c +++ b/main.c @@ -6,7 +6,7 @@ #include "mmpriv.h" #include "getopt.h" -#define MM_VERSION "2.2-r516-dirty" +#define MM_VERSION "2.2-r517-dirty" #ifdef __linux__ #include @@ -38,7 +38,7 @@ static struct option long_options[] = { { "no-long-join", no_argument, 0, 0 }, { "sr", no_argument, 0, 0 }, { "frag", optional_argument, 0, 0 }, - { "print-2nd", optional_argument, 0, 0 }, + { "secondary", optional_argument, 0, 0 }, { "cs", optional_argument, 0, 0 }, { "end-bonus", required_argument, 0, 0 }, { "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) 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) 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; } 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) { if ((opt.flag & MM_F_OUT_SAM) && idx_rdr->n_parts == 1) { if (mm_idx_reader_eof(idx_rdr)) {