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ensure FORMAT column is in vcf output (even if excluded from input vcf) #24

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ensure FORMAT column is in vcf output (even if excluded from input vcf) #24

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3 changes: 3 additions & 0 deletions sufam/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -202,6 +202,8 @@ def determine_genotype(bp):
record.samples = calls
if record.FILTER is None:
record.FILTER = []
if record.INFO is None:
record.INFO = {}
vcf_writer.write_record(record)


Expand All @@ -226,6 +228,7 @@ def validate_mutations(vcffile, bams, reffa, chr_reffa, samples, output_format,
vcf_reader.formats['GT'] = vcf.parser._Format(id='GT', num=1, type='String', desc="Genotype")
vcf_reader.formats['AD'] = vcf.parser._Format(id='AD', num='R', type='Integer', desc="Allelic depth")
vcf_reader.formats['DP'] = vcf.parser._Format(id='DP', num=1, type='Integer', desc="Depth")
vcf_reader.column_headers = ['CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO', 'FORMAT']
vcf_writer = vcf.Writer(outfile, vcf_reader)
else:
vcf_reader = open(vcffile)
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