diff --git a/main.c b/main.c index 27f36a6..88e3a93 100644 --- a/main.c +++ b/main.c @@ -9,7 +9,7 @@ #include "minimap.h" #include "mmpriv.h" -#define MM_VERSION "2.0-r14-pre" +#define MM_VERSION "2.0-r34-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: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); else if (c == 'k') k = 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 == 'N') keep_name = 0; 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 == 'T') opt.sdust_thres = 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, " -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, " -O drop isolated hits before chaining (EXPERIMENTAL)\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, " Input/Output:\n"); diff --git a/minimap.h b/minimap.h index 675b4c1..818498e 100644 --- a/minimap.h +++ b/minimap.h @@ -6,10 +6,8 @@ #include #define MM_IDX_DEF_B 14 -#define MM_DEREP_Q50 5.0 #define MM_F_NO_SELF 0x2 -#define MM_F_NO_ISO 0x4 #define MM_F_AVA 0x8 #define MM_IDX_MAGIC "MMI\2"