diff --git a/mpileup.c b/mpileup.c index b5e02c3d..847fbd95 100644 --- a/mpileup.c +++ b/mpileup.c @@ -1286,27 +1286,27 @@ static void print_usage(FILE *fp, const mplp_conf_t *mplp) " --indel-size INT Approximate maximum indel size considered [%d]\n", mplp->indel_win_size); fprintf(fp, " --indels-2.0 New EXPERIMENTAL indel calling model (diploid reference consensus)\n" - " --edlib New EXPERIMENTAL indel calling model with edlib\n" - " --no-edlib Disable edlib mode, to use after a -X profile\n" + " --indels-cns New EXPERIMENTAL indel calling model with edlib\n" + " --no-indels-cns Disable CNS mode, to use after a -X profile\n" " --poly-mqual (Edlib mode) Use minimum quality within homopolymers\n"); fprintf(fp,"\n"); fprintf(fp, "Configuration profiles activated with -X, --config:\n" " 1.12: -Q13 -h100 -m1 -F0.002\n" " illumina-1.18: --indel-size 110\n" - " illumina or illumina-1.20: --edlib\n" + " illumina or illumina-1.20: --indels-cns\n" " ont: -B -Q5 --max-BQ 30 -I [also try eg |bcftools call -P0.01]\n" " ont-sup or ont-sup-1.20:\n" " -B -Q1 --max-BQ 99 -F0.20 -o15 -e1 -h80 --delta-BQ 60 \\\n" - " --del-bias 0.4 --poly-mqual --edlib\n" + " --del-bias 0.4 --poly-mqual --indels-cns\n" " pacbio-ccs-1.18: -D -Q5 --max-BQ 50 -F0.1 -o25 -e1 --delta-BQ 10 \\\n" " -M99999 --indel-size 110\n" " pacbio-ccs or pacbio-ccs-1.20:\n" " -B -Q5 --max-BQ 50 -F0.10 -o25 -e1 -h300 --delta-BQ 10 \\\n" - " --del-bias 0.4 --poly-mqual --edlib\n" + " --del-bias 0.4 --poly-mqual --indels-cns\n" " ultima or ultima-1.20:\n" - " -B --max-BQ 30 -F0.15 -o20 -e15 -h250 --delta-BQ 10 \\\n" - " --del-bias 0.3 --poly-mqual --edlib\n" + " -B --max-BQ 30 -F0.15 -o20 -e10 -h250 --delta-BQ 10 \\\n" + " --del-bias 0.3 --poly-mqual --indels-cns\n" "\n" "Notes: Assuming diploid individuals.\n" "\n" @@ -1412,8 +1412,8 @@ int main_mpileup(int argc, char *argv[]) {"indel-bias", required_argument, NULL, 10}, {"indel-size", required_argument, NULL, 15}, {"indels-2.0", no_argument, NULL, 20}, - {"edlib", no_argument, NULL, 22}, - {"no-edlib", no_argument, NULL, 25}, + {"indels-cns", no_argument, NULL, 22}, + {"no-indels-cns", no_argument, NULL, 25}, {"tandem-qual", required_argument, NULL, 'h'}, {"skip-indels", no_argument, NULL, 'I'}, {"max-idepth", required_argument, NULL, 'L'},