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r34: removed a bit unused code

This commit is contained in:
Heng Li 2017-06-07 14:35:57 -04:00
parent be9a7f4e41
commit 19e43571c1
2 changed files with 2 additions and 6 deletions
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6
main.c
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@ -9,7 +9,7 @@
#include "minimap.h" #include "minimap.h"
#include "mmpriv.h" #include "mmpriv.h"
#define MM_VERSION "2.0-r14-pre" #define MM_VERSION "2.0-r34-pre"
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(argc, argv, "w:k:B:b:t:r:f:Vv:NOg: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:H")) >= 0) {
if (c == 'w') w = atoi(optarg); if (c == 'w') w = atoi(optarg);
else if (c == 'k') k = atoi(optarg); else if (c == 'k') k = atoi(optarg);
else if (c == 'b') b = atoi(optarg); else if (c == 'b') b = atoi(optarg);
@ -67,7 +67,6 @@ int main(int argc, char *argv[])
else if (c == 'g') opt.max_gap = atoi(optarg); else if (c == 'g') opt.max_gap = atoi(optarg);
else if (c == 'N') keep_name = 0; else if (c == 'N') keep_name = 0;
else if (c == 'D') opt.flag |= MM_F_NO_SELF; else if (c == 'D') opt.flag |= MM_F_NO_SELF;
else if (c == 'O') opt.flag |= MM_F_NO_ISO;
else if (c == 'S') opt.flag |= MM_F_AVA | 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); else if (c == 'T') opt.sdust_thres = atoi(optarg);
else if (c == 's') opt.min_score = atoi(optarg); else if (c == 's') opt.min_score = atoi(optarg);
@ -111,7 +110,6 @@ int main(int argc, char *argv[])
fprintf(stderr, " -T INT SDUST threshold; 0 to disable SDUST [%d]\n", opt.sdust_thres); 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, " -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, " -S skip self and dual mappings\n");
fprintf(stderr, " -O drop isolated hits before chaining (EXPERIMENTAL)\n");
fprintf(stderr, " -x STR preset (recommended to be applied before other options) []\n"); 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, " ava10k: -Sw5 -L100 -m0 (PacBio/ONT all-vs-all read mapping)\n");
fprintf(stderr, " Input/Output:\n"); fprintf(stderr, " Input/Output:\n");

2
minimap.h
View File

@ -6,10 +6,8 @@
#include <sys/types.h> #include <sys/types.h>
#define MM_IDX_DEF_B 14 #define MM_IDX_DEF_B 14
#define MM_DEREP_Q50 5.0
#define MM_F_NO_SELF 0x2 #define MM_F_NO_SELF 0x2
#define MM_F_NO_ISO 0x4
#define MM_F_AVA 0x8 #define MM_F_AVA 0x8
#define MM_IDX_MAGIC "MMI\2" #define MM_IDX_MAGIC "MMI\2"