diff --git a/README.md b/README.md index 6129530..fc6f30d 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@ Options: --minimum_coverage INTEGER Only consider SNP positions with a lest this coverage [default: 30] - --minimum_base_quality INTEGER Only count bases with a least this quality + --minimum_base_quality INTEGER Only count bases with at least this quality [default: 1] --homozygosity_threshold FLOAT Consider a SNP position homozygote if diff --git a/src/snpahoy/client.py b/src/snpahoy/client.py index 4e7f9a4..f903861 100644 --- a/src/snpahoy/client.py +++ b/src/snpahoy/client.py @@ -22,7 +22,7 @@ def get_counts(alignment: AlignmentFile, chromosome: str, position: int, minimum @click.group() @click.option('--minimum_coverage', default=30, show_default=True, help='Only consider SNP positions with a lest this coverage') -@click.option('--minimum_base_quality', default=1, show_default=True, help='Only count bases with a least this quality') +@click.option('--minimum_base_quality', default=1, show_default=True, help='Only count bases with at least this quality') @click.option('--homozygosity_threshold', default=0.95, show_default=True, help='Consider a SNP position homozygote if frequency of most common allele is this or higher') @click.pass_context def client(ctx, minimum_coverage, homozygosity_threshold, minimum_base_quality):