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r36: bring back primary; don't output all mappings

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This commit is contained in:
Heng Li
2017-06-08 15:28:19 -04:00
parent 6c099bef89
commit b04e4b9215
3 changed files with 63 additions and 7 deletions
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main.c
+5 -2
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@@ -9,7 +9,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r34-pre"
#define MM_VERSION "2.0-r36-pre"
void liftrlimit()
{
@@ -54,7 +54,7 @@ int main(int argc, char *argv[])
mm_realtime0 = realtime();
mm_mapopt_init(&opt);
while ((c = getopt(argc, argv, "w:k:B:b:t:r:f:Vv:Ng:I:d:ST:s:Dx:H")) >= 0) {
while ((c = getopt(argc, argv, "w:k:B:b:t:r:f:Vv:Ng:I:d:ST:s:Dx:Hp:m:")) >= 0) {
if (c == 'w') w = atoi(optarg);
else if (c == 'k') k = atoi(optarg);
else if (c == 'b') b = atoi(optarg);
@@ -66,6 +66,8 @@ int main(int argc, char *argv[])
else if (c == 'v') mm_verbose = atoi(optarg);
else if (c == 'g') opt.max_gap = atoi(optarg);
else if (c == 'N') keep_name = 0;
else if (c == 'p') opt.pri_ratio = atof(optarg);
else if (c == 'm') opt.mask_level = atof(optarg);
else if (c == 'D') opt.flag |= MM_F_NO_SELF;
else if (c == 'S') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
else if (c == 'T') opt.sdust_thres = atoi(optarg);
@@ -110,6 +112,7 @@ int main(int argc, char *argv[])
fprintf(stderr, " -T INT SDUST threshold; 0 to disable SDUST [%d]\n", opt.sdust_thres);
// fprintf(stderr, " -D skip self mappings but keep dual mappings\n"); // too confusing to expose to end users
fprintf(stderr, " -S skip self and dual mappings\n");
fprintf(stderr, " -p FLOAT threshold to output a mapping [%g]\n", opt.pri_ratio);
fprintf(stderr, " -x STR preset (recommended to be applied before other options) []\n");
fprintf(stderr, " ava10k: -Sw5 -L100 -m0 (PacBio/ONT all-vs-all read mapping)\n");
fprintf(stderr, " Input/Output:\n");