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fixed bug when retaining 2ndary aln; still buggy

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This commit is contained in:
Heng Li
2017-07-02 19:08:30 -04:00
parent da90b614db
commit 74d306a596
5 changed files with 31 additions and 15 deletions
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main.c
+3 -2
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@@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r141-pre"
#define MM_VERSION "2.0-r142-pre"
void liftrlimit()
{
@@ -68,7 +68,7 @@ int main(int argc, char *argv[])
mm_realtime0 = realtime();
mm_mapopt_init(&opt);
while ((c = getopt_long(argc, argv, "aw:k:t:r:f:Vv:g:I:d:ST:s:x:Hcp:M:n:z:A:B:O:E:m:D:", long_options, &long_idx)) >= 0) {
while ((c = getopt_long(argc, argv, "aw:k:t:r:f:Vv:g:I:d:ST:s:x:Hcp:M:n:z:A:B:O:E:m:D:N:", long_options, &long_idx)) >= 0) {
if (c == 'w') w = atoi(optarg);
else if (c == 'k') k = atoi(optarg);
else if (c == 'H') is_hpc = 1;
@@ -78,6 +78,7 @@ 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 == 'N') opt.best_n = atoi(optarg);
else if (c == 'p') opt.pri_ratio = atof(optarg);
else if (c == 'D') opt.min_seedcov_ratio = atof(optarg);
else if (c == 'M') opt.mask_level = atof(optarg);