Escape characters

[Akazhiel]

• vcfpy version: 0.13.3
• Python version: 3.6.1
• Operating System: Linux (Ubuntu)

Description

I'm having a hard time understanding why there is a mapping of escape characters, because when I write a vcf if I have some % in my fields, this gets changed to %25 instead of remaining as % like in the original. And I believe this can cause conflicts when using tools on the VCF with the field formatted like %25.

What I Did

I ran this custom function to split the VCF in samples.

def split_vcf(vcf_path):
    reader_main = vcfpy.Reader.from_path(vcf_path)
    samples = list(set([x.replace('NORMAL.', '').replace('TUMOR.', '') for x in reader_main.header.samples.names]))
    reader_main.close()
    for sample in samples:
        reader_1 = vcfpy.Reader.from_path(vcf_path)
        reader_2 = vcfpy.Reader.from_path(vcf_path)
        header = reader_2.header
        header.samples.names = [x for x in header.samples.names if x in [f'NORMAL.{sample}', f'TUMOR.{sample}']]
        header.samples.name_to_idx = {x: header.samples.name_to_idx[x] for x in [f'NORMAL.{sample}', f'TUMOR.{sample}']}
        writer = vcfpy.Writer.from_path('./{}.vcf'.format(sample), header)
        for record in reader_1:
            if any(sample == s for s in record.INFO['set'].split('-')):
                writer.write_record(record)
        writer.close()