From 11698fc4e5a6f4cdd3d7fed91f9e2e6ff9e750f6 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Wed, 30 Apr 2014 13:12:43 -0400 Subject: [PATCH] r735: fixed a bug caused by merge --- fastmap.c | 4 ++-- main.c | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/fastmap.c b/fastmap.c index 655272d..3156ca3 100644 --- a/fastmap.c +++ b/fastmap.c @@ -53,7 +53,7 @@ int main_mem(int argc, char *argv[]) opt = mem_opt_init(); memset(&opt0, 0, sizeof(mem_opt_t)); - while ((c = getopt(argc, argv, "epaFMCSPHIk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:")) >= 0) { + while ((c = getopt(argc, argv, "epaFMCSPHYk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:")) >= 0) { if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1; else if (c == 'x') mode = optarg; else if (c == 'w') opt->w = atoi(optarg), opt0.w = 1; @@ -69,7 +69,7 @@ int main_mem(int argc, char *argv[]) else if (c == 'S') opt->flag |= MEM_F_NO_RESCUE; else if (c == 'e') opt->flag |= MEM_F_SELF_OVLP; else if (c == 'F') opt->flag |= MEM_F_ALN_REG; - else if (c == 'I') opt->flag |= MEM_F_SOFTCLIP; + else if (c == 'Y') opt->flag |= MEM_F_SOFTCLIP; else if (c == 'c') opt->max_occ = atoi(optarg), opt0.max_occ = 1; else if (c == 'd') opt->zdrop = atoi(optarg), opt0.zdrop = 1; else if (c == 'v') bwa_verbose = atoi(optarg); diff --git a/main.c b/main.c index fdbf555..48fcc36 100644 --- a/main.c +++ b/main.c @@ -4,7 +4,7 @@ #include "utils.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.7.8-r733-dirty" +#define PACKAGE_VERSION "0.7.8-r735-dirty" #endif int bwa_fa2pac(int argc, char *argv[]);