diff --git a/varifier/dnadiff.py b/varifier/dnadiff.py index 04c67a9..b32fe74 100644 --- a/varifier/dnadiff.py +++ b/varifier/dnadiff.py @@ -30,7 +30,7 @@ def _run_dnadiff(ref_fasta, query_fasta, outprefix): logging.info(f"dnadiff command finished ({command})") -def _snps_file_file_to_vcf(snps_file, query_fasta, outfile): +def _snps_file_to_vcf(snps_file, query_fasta, outfile): """Loads the .snps file made by dnadiff. query_fasta = fasta file of query sequences. Writes a new VCF file unmerged records.""" @@ -144,7 +144,7 @@ def make_truth_vcf(ref_fasta, truth_fasta, outfile, debug=False): tmp_outprefix = f"{outfile}.tmp" _run_dnadiff(truth_fasta, ref_fasta, tmp_outprefix) snps_file = f"{tmp_outprefix}.snps" - _snps_file_file_to_vcf(snps_file, ref_fasta, outfile) + _snps_file_to_vcf(snps_file, ref_fasta, outfile) if debug: return