def get_vcf_header(self, sample_name, contigs):
header = VariantHeader()
items = [('ID', "PASS"), ('Description', "All filters passed")]
header.add_meta(key='FILTER', items=items)
items = [('ID', "refCall"), ('Description', "Call is homozygous")]
header.add_meta(key='FILTER', items=items)
items = [('ID', "lowGQ"), ('Description', "Low genotype quality")]
header.add_meta(key='FILTER', items=items)
items = [('ID', "lowQUAL"),
('Description', "Low variant call quality")]
header.add_meta(key='FILTER', items=items)
items = [('ID', "conflictPos"), ('Description', "Overlapping record")]
header.add_meta(key='FILTER', items=items)
items = [('ID', "GT"), ('Number', 1), ('Type', 'String'),
('Description', "Genotype")]
header.add_meta(key='FORMAT', items=items)
items = [('ID', "GQ"), ('Number', 1), ('Type', 'Float'),
('Description', "Genotype Quality")]
header.add_meta(key='FORMAT', items=items)
sqs = self.fasta_handler.get_chromosome_names()
for sq in sqs:
if sq not in contigs:
continue
sq_id = sq
ln = self.fasta_handler.get_chromosome_sequence_length(sq)
header.contigs.add(sq_id, length=ln)
header.add_sample(sample_name)
return header
def get_vcf_header(self, sample_name):
header = VariantHeader()
items = [('ID', "PASS"), ('Description', "All filters passed")]
header.add_meta(key='FILTER', items=items)
items = [('ID', "refCall"), ('Description', "Call is homozygous")]
header.add_meta(key='FILTER', items=items)
items = [('ID', "lowGQ"), ('Description', "Low genotype quality")]
header.add_meta(key='FILTER', items=items)
items = [('ID', "lowQUAL"),
('Description', "Low variant call quality")]
header.add_meta(key='FILTER', items=items)
items = [('ID', "conflictPos"), ('Description', "Overlapping record")]
header.add_meta(key='FILTER', items=items)
items = [('ID', "GT"), ('Number', 1), ('Type', 'String'),
('Description', "Genotype")]
header.add_meta(key='FORMAT', items=items)
items = [('ID', "GQ"), ('Number', 1), ('Type', 'Float'),
('Description', "Genotype Quality")]
header.add_meta(key='FORMAT', items=items)
bam_sqs = self.bam_handler.get_header_sq()
for sq in bam_sqs:
id = sq['SN']
ln = sq['LN']
items = [('ID', id), ('length', ln)]
header.add_meta(key='contig', items=items)
header.add_sample(sample_name)
return header