def run(options):
merger = simple_vcf_merger.SimpleVcfMerger(
options.samtools_vcf,
options.cortex_vcf,
options.output_vcf,
options.ref_fasta,
homozygous_only=not options.include_homozygous,
max_REF_len=None,
min_SNP_qual=options.min_SNP_qual,
min_dp4=options.min_dp4,
min_GT_conf=options.min_GT_conf,
)
merger.run()
def _test_run(self):
'''test run'''
samtools_vcf = os.path.join(data_dir, 'samtools.vcf')
cortex_vcf = os.path.join(data_dir, 'cortex.vcf')
ref_fasta = os.path.join(data_dir, 'NC_000962.3.fa')
expected_vcf = os.path.join(data_dir, 'expect.vcf')
tmp_vcf = 'tmp.simple_vcf_merger.out.vcf'
# ... run the merging ...
merger = simple_vcf_merger.SimpleVcfMerger(samtools_vcf,
cortex_vcf,
tmp_vcf,
ref_fasta,
homozygous_only=True,
min_SNP_qual=30.0,
min_dp4=5.0,
min_GT_conf=5.0)
merger.run()
self.assertTrue(filecmp.cmp(expected_vcf, tmp_vcf, shallow=False))
os.unlink(tmp_vcf)