From b08591c7a0f98e4740c9e164abda94210c79e83a Mon Sep 17 00:00:00 2001 From: Heng Li Date: Fri, 30 Jun 2017 15:46:52 -0400 Subject: [PATCH] r124: a bit better CLI prompt --- main.c | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/main.c b/main.c index 8703e24..55312c5 100644 --- a/main.c +++ b/main.c @@ -10,7 +10,7 @@ #include "minimap.h" #include "mmpriv.h" -#define MM_VERSION "2.0-r123-pre" +#define MM_VERSION "2.0-r124-pre" void liftrlimit() { @@ -139,13 +139,13 @@ int main(int argc, char *argv[]) fprintf(stderr, " -I NUM split index for every ~NUM input bases [4G]\n"); fprintf(stderr, " -d FILE dump index to FILE []\n"); fprintf(stderr, " Mapping:\n"); - fprintf(stderr, " -f FLOAT filter out top FLOAT fraction of repetitive minimizers [%.3f]\n", opt.mid_occ_frac); + fprintf(stderr, " -f FLOAT filter out top FLOAT fraction of repetitive minimizers [%g]\n", opt.mid_occ_frac); + fprintf(stderr, " -g INT split a mapping if there are no minimizers in INT-bp [%d]\n", opt.max_gap); fprintf(stderr, " -r INT bandwidth [%d]\n", opt.bw); fprintf(stderr, " -n INT minimal number of minimizers [%d]\n", opt.min_cnt); - fprintf(stderr, " -m INT minimal chaining score [%d]\n", opt.min_chain_score); - fprintf(stderr, " -g INT split a mapping if there is a gap longer than INT [%d]\n", opt.max_gap); - fprintf(stderr, " -T INT SDUST threshold; 0 to disable SDUST [%d]\n", opt.sdust_thres); - fprintf(stderr, " -S skip self and dual mappings\n"); + fprintf(stderr, " -m INT minimal chaining score (matching bases minus log gap penalty) [%d]\n", opt.min_chain_score); +// fprintf(stderr, " -T INT SDUST threshold; 0 to disable SDUST [%d]\n", opt.sdust_thres); // TODO: this option is never used; might be buggy + fprintf(stderr, " -S skip self and dual mappings (for the all-vs-all mode)\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: -Hk19 -Sw5 -p0 -m100 (PacBio/ONT all-vs-all read mapping)\n");