@classmethod<EOL><INDENT>def _load_vcf_files(cls, filename_list, reference_seqs, homozygous_only=False, max_REF_len=None, min_SNP_qual=None, min_dp4=None, min_GT_conf=None):<DEDENT>
headers = {}<EOL>vcf_records = None<EOL>sample_name = None<EOL>for filename in filename_list:<EOL><INDENT>headers[filename], new_records = vcf_file_read.vcf_file_to_dict(filename, homozygous_only=homozygous_only, remove_asterisk_alts=True, max_REF_len=max_REF_len, remove_useless_start_nucleotides=True, min_SNP_qual=min_SNP_qual, min_dp4=min_dp4, min_GT_conf=min_GT_conf, reference_seqs=reference_seqs)<EOL>new_sample_name = vcf_file_read.get_sample_name_from_vcf_header_lines(headers[filename])<EOL>if sample_name is None and new_sample_name is not None:<EOL><INDENT>sample_name = new_sample_name<EOL><DEDENT>elif new_sample_name != sample_name:<EOL><INDENT>logging.warning('<STR_LIT>' + str(sample_name) + '<STR_LIT>' + str(new_sample_name) + '<STR_LIT>')<EOL><DEDENT>if vcf_records is None:<EOL><INDENT>vcf_records = new_records<EOL><DEDENT>else:<EOL><INDENT>for ref_name, record_list in new_records.items():<EOL><INDENT>if ref_name not in vcf_records:<EOL><INDENT>vcf_records[ref_name] = record_list<EOL><DEDENT>else:<EOL><INDENT>vcf_records[ref_name].extend(record_list)<EOL><DEDENT><DEDENT><DEDENT><DEDENT>for record_list in vcf_records.values():<EOL><INDENT>record_list.sort(key=operator.attrgetter('<STR_LIT>'))<EOL><DEDENT>if sample_name is None:<EOL><INDENT>logging.warning('<STR_LIT>')<EOL>sample_name = '<STR_LIT>'<EOL><DEDENT>return sample_name, headers, vcf_records<EOL>
Loads all the vcf files from filename_list. Returns tuple of:
        1. Sample name. If more than one sample name found, uses the first one
        and warns to stderr
        2. Dictionary. filename => list of header lines for that file
        3. Dictionary. ref name => list of VcfRecords sorted by position.

        reference_seqs should be a dictionary of sequence name -> sequence.
        This causes all records from the VCF to be sanity checked against the reference sequence,
        and any records where the REF seq does not match the expected sequence is removed.