from VcfFilter import VcfFilter

import argparse
import os

#get command line arguments

parser = argparse.ArgumentParser(description='Script to select a certain variant type from a VCF file')

#parameters
parser.add_argument('--bcftools_folder', type=str, required=True, help='Folder containing the Bcftools binary' )
parser.add_argument('--filename', type=str, required=True, help='Name (without the fullpath) of the VCF file that will be analysed. It assumes that the filename format is for example lc_bams.gatk.xxxx.vcf.gz, where lc_bams is the analysis group and gatk is the method used' )
parser.add_argument('--type', type=str, required=False, help='Type of variant to select. i.e. snps/indels etc' )

args = parser.parse_args()

if __name__ == '__main__':
    
    vcf_f=VcfFilter(vcf=args.filename,bcftools_folder=args.bcftools_folder)
    
    vcf_f.filter_by_variant_type(type=args.type)
    

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