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Refer to the correct option --samples, rather than --sample
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pd3 committed Dec 13, 2022
1 parent 9958cf4 commit 16b1874
Showing 1 changed file with 2 additions and 2 deletions.
4 changes: 2 additions & 2 deletions consensus.c
Original file line number Diff line number Diff line change
Expand Up @@ -266,7 +266,7 @@ static void init_data(args_t *args)
if ( ! args->fp_out ) error("Failed to create %s: %s\n", args->output_fname, strerror(errno));
}
else args->fp_out = stdout;
if ( args->isample<0 && !args->iupac_GTs ) fprintf(stderr,"Note: the --sample option not given, applying all records regardless of the genotype\n");
if ( args->isample<0 && !args->iupac_GTs ) fprintf(stderr,"Note: the --samples option not given, applying all records regardless of the genotype\n");
if ( args->filter_str )
args->filter = filter_init(args->hdr, args->filter_str);
args->rid = -1;
Expand Down Expand Up @@ -1082,7 +1082,7 @@ static void usage(args_t *args)
fprintf(stderr, "\n");
fprintf(stderr, "About: Create consensus sequence by applying VCF variants to a reference fasta\n");
fprintf(stderr, " file. By default, the program will apply all ALT variants. Using the\n");
fprintf(stderr, " --sample (and, optionally, --haplotype) option will apply genotype\n");
fprintf(stderr, " --samples (and, optionally, --haplotype) option will apply genotype\n");
fprintf(stderr, " (or haplotype) calls from FORMAT/GT. The program ignores allelic depth\n");
fprintf(stderr, " information, such as INFO/AD or FORMAT/AD.\n");
fprintf(stderr, "Usage: bcftools consensus [OPTIONS] <file.vcf.gz>\n");
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