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r274: CLI option to change max ref gap

This commit is contained in:
Heng Li 2017-08-08 11:39:23 -04:00
parent 1a7d782131
commit 7f9f659b6a
1 changed files with 3 additions and 2 deletions
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5
main.c
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@ -8,7 +8,7 @@
#include "minimap.h" #include "minimap.h"
#include "mmpriv.h" #include "mmpriv.h"
#define MM_VERSION "2.0rc1-r273-dirty" #define MM_VERSION "2.0rc1-r274-dirty"
void liftrlimit() void liftrlimit()
{ {
@ -54,7 +54,7 @@ int main(int argc, char *argv[])
mm_realtime0 = realtime(); mm_realtime0 = realtime();
mm_mapopt_init(&opt); 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; if (c == 'w') w = atoi(optarg), idx_par_set = 1;
else if (c == 'k') k = 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; 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 == 't') n_threads = atoi(optarg);
else if (c == 'v') mm_verbose = 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 = atoi(optarg);
else if (c == 'G') opt.max_gap_ref = atoi(optarg);
else if (c == 'N') opt.best_n = atoi(optarg); else if (c == 'N') opt.best_n = atoi(optarg);
else if (c == 'p') opt.pri_ratio = atof(optarg); else if (c == 'p') opt.pri_ratio = atof(optarg);
else if (c == 'M') opt.mask_level = atof(optarg); else if (c == 'M') opt.mask_level = atof(optarg);