gemini gene_wise

            #if int($min_filters) > 0:
                --min-filters $min_filters
            #end if

            #for $filter in $filter_by_genotype:
                #set $multiline_sql_expr = str($filter.gt_filter)
                #if $filter.is_required:
                    #set $cmdln_param = "--gt-filter-required"
                #else:
                    #set $cmdln_param = "--gt-filter"
                #end if
                
        #set $sql_expr = str($multiline_sql_expr).strip()
        #if str($sql_expr):
            #set $sql_expr = $sql_expr.replace('\r\n', '\n')
            #set $sql_expr = $sql_expr.replace('\r', '\n')
            #set $sql_expr = $sql_expr.replace('\\\n', ' ')
            $cmdln_param '$sql_expr'
        #end if
    
            #end for

            #set $report = $oformat.report
            
        
        #if str($report.report_selector) == 'full':
            #set cols = "*"
        #else:
            #if $report.columns and str($report.columns) != '':
                #set $cols = str($report.columns)
            #else
                #set $cols = ''
            #end if
            #if str($report.extra_cols).strip():
                #if $cols:
                    #set $cols = $cols + ', ' + str($report.extra_cols)
                #else:
                    #set $cols = str($report.extra_cols)
                #end if
            #end if
            #if not $cols:
                #set $cols = "variant_id, gene"
            #end if
        #end if
    
        #if $cols != "*"
            --columns '$cols'
        #end if
    

            #set $where_clause_elements = []
            #set $filter_cmdln_param = '--filter'
            #for $cond in $constraint:
                #if str($cond.filter).strip():
                    #silent $where_clause_elements.append(str($cond.filter).strip())
                    #if $cond.overwrite_default_filter:
                        #set $filter_cmdln_param = '--where'
                    #end if
                #end if
            #end for

            
        #set $region_elements = []
        #for $r in $regions:
            ## The actual chromosome name needs to be single-quoted
            ## in SQL, so we need to quote the single quotes like the
            ## sanitize_query macro would if the whole was a parameter.
            #set $r_elements = ["chrom = '\"'\"'%s'\"'\"'" % str($r.chrom).strip()]
            #if str($r.start).strip():
                #silent $r_elements.append("start >= %d" % int($r.start))
            #end if
            #if str($r.stop).strip():
                #silent $r_elements.append("end <= %d" % int($r.stop))
            #end if
            #silent $region_elements.append("(%s)" % " AND ".join($r_elements))
        #end for
    
    
            #if $region_elements:
                #silent $where_clause_elements.append(" OR ".join($region_elements))
            #end if
            #set $filter = " AND ".join($where_clause_elements)
            #if str($filter):
                $filter_cmdln_param '$filter'
            #end if

            '$infile'
            > '$outfile'