From 7f9f659b6aa0e8dc1030501aec463a676cfb7dd0 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 8 Aug 2017 11:39:23 -0400 Subject: [PATCH] r274: CLI option to change max ref gap --- main.c | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/main.c b/main.c index 680d35f..4e1f897 100644 --- a/main.c +++ b/main.c @@ -8,7 +8,7 @@ #include "minimap.h" #include "mmpriv.h" -#define MM_VERSION "2.0rc1-r273-dirty" +#define MM_VERSION "2.0rc1-r274-dirty" void liftrlimit() { @@ -54,7 +54,7 @@ int main(int argc, char *argv[]) mm_realtime0 = realtime(); mm_mapopt_init(&opt); - while ((c = getopt_long(argc, argv, "aSw:k:K:t:r:f:Vv:g:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Q", long_options, &long_idx)) >= 0) { + while ((c = getopt_long(argc, argv, "aSw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Q", long_options, &long_idx)) >= 0) { if (c == 'w') w = atoi(optarg), idx_par_set = 1; else if (c == 'k') k = atoi(optarg), idx_par_set = 1; else if (c == 'H') is_hpc = 1, idx_par_set = 1; @@ -64,6 +64,7 @@ int main(int argc, char *argv[]) else if (c == 't') n_threads = atoi(optarg); else if (c == 'v') mm_verbose = atoi(optarg); else if (c == 'g') opt.max_gap = atoi(optarg); + else if (c == 'G') opt.max_gap_ref = atoi(optarg); else if (c == 'N') opt.best_n = atoi(optarg); else if (c == 'p') opt.pri_ratio = atof(optarg); else if (c == 'M') opt.mask_level = atof(optarg);