Module Expr Str Import alias Import alias Assign NameStore Call AttributeLoad NameLoad attr NameLoad FunctionDef arguments args NameParam NameParam defaults body Expr Str Return Call NameLoad Call NameLoad NameLoad Call AttributeLoad Call AttributeLoad NameLoad attr attr Str decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Dict For NameStore Call AttributeLoad NameLoad attr Str body Assign NameStore Call AttributeLoad NameLoad attr Str If CompareEq Call NameLoad NameLoad Num body Assign SubscriptStore NameLoad Index SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num orelse Assign SubscriptStore NameLoad Index SubscriptLoad NameLoad Index Num ListLoad Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore SubscriptLoad NameLoad Index Str Assign NameStore SubscriptLoad NameLoad Index Str Assign NameStore SubscriptLoad NameLoad Index Str Assign NameStore Str Assign NameStore Call AttributeLoad Str attr GeneratorExp NameLoad comprehension NameStore SubscriptLoad NameLoad Index Str CompareNotIn NameLoad NameLoad Return Call AttributeLoad Str attr ListLoad NameLoad NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults NameLoad body Expr Str Assign NameStore Dict For NameStore Call AttributeLoad NameLoad attr Str body Assign NameStore Call NameLoad Call NameLoad NameLoad Call AttributeLoad NameLoad attr Str If CompareIn Str NameLoad body Assign NameStore SubscriptLoad NameLoad Index Str If CompareIn NameLoad NameLoad body Expr Call AttributeLoad SubscriptLoad NameLoad Index NameLoad attr NameLoad orelse Assign SubscriptStore NameLoad Index NameLoad ListLoad NameLoad Return NameLoad decorator_list
N/A N/A Parse a variant line in different ways N/A string N/A logging N/A logging N/A N/A logging getLogger __name__ get_variant_dict N/A N/A variant_line header_line N/A N/A N/A Parse a variant line
        
        Split a variant line and map the fields on the header columns
        
        Args:
            variant_line (str): A vcf variant line
            header_line (list): A list with the header columns
        Returns:
            variant_dict (dict): A variant dictionary
     N/A N/A dict N/A zip header_line N/A N/A N/A N/A variant_line rstrip split N/A get_info_dict N/A N/A info_line N/A N/A N/A Parse a info field of a variant
        
        Make a dictionary from the info field of a vcf variant.
        Keys are the info keys and values are the raw strings from the vcf
        
        Args:
            info_line (str): The info field of a vcf variant
        Returns:
            info_dict (dict): A INFO dictionary
     N/A variant_info N/A N/A raw_info N/A N/A info_line split ; N/A N/A splitted_info N/A N/A raw_info split = N/A N/A N/A len splitted_info 2 N/A N/A N/A variant_info N/A N/A splitted_info N/A 0 N/A splitted_info N/A 1 N/A N/A N/A variant_info N/A N/A splitted_info N/A 0 N/A N/A variant_info N/A get_variant_id N/A N/A variant_dict N/A N/A N/A Build a variant id
    
        The variant id is a string made of CHROM_POS_REF_ALT
        
        The alt field for svs needs some massage to work downstream.
        
        Args:
            variant_dict (dict): A variant dictionary
        
        Returns:
            variant_id (str)
     N/A chrom N/A variant_dict N/A CHROM N/A pos N/A variant_dict N/A POS N/A ref N/A variant_dict N/A REF N/A bad_chars <>[]: N/A alt N/A N/A join N/A c N/A c N/A variant_dict N/A ALT N/A c bad_chars N/A N/A N/A _ join N/A chrom pos ref alt N/A get_vep_dict N/A N/A vep_string vep_header allele N/A None N/A N/A Make the vep annotation into a dictionary
    
        This dictionary will have the alleles as keys and a list of 
        dictionaries with vep annotations as values.
        
        Args:
            vep_list (string): A string with the CSQ annotation
            vep_header (list): A list with the vep header
            allele (str): The allele that is annotated
        
        Return:
            vep_dict (dict): A vep dict as described above
    
     N/A vep_dict N/A N/A vep_annotation N/A N/A vep_string split , N/A N/A inner_dict N/A dict N/A zip vep_header N/A N/A vep_annotation split | N/A N/A Allele inner_dict N/A N/A allele N/A inner_dict N/A Allele N/A N/A allele vep_dict N/A N/A N/A N/A N/A vep_dict N/A allele append inner_dict N/A N/A N/A vep_dict N/A allele N/A inner_dict N/A vep_dict N/A