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r124: a bit better CLI prompt

This commit is contained in:
Heng Li 2017-06-30 15:46:52 -04:00
parent 3a5486325a
commit b08591c7a0
1 changed files with 6 additions and 6 deletions
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12
main.c
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@ -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");