{
    "queries":[
        {
            "feature":"transcript",
            "feature.anchor":"start",
            "distance":${TSS_flanking},
            "filter.attribute":"transcript_type",
            "attribute.value":["IG_C_gene","IG_D_gene","IG_J_gene","IG_V_gene","IG_LV_gene","TR_C_gene","TR_D_gene","TR_J_gene","TR_V_gene","lncRNA","protein_coding"],
            "show.attributes":["transcript_type","gene_id","gene_name","hgnc_id","transcript_id","transcript_name"],
            "name": "TSS"
        },
        {
            "feature":"transcript",
            "feature.anchor":"start",
            "distance":[${TSS_proximal_upstream},${TSS_proximal_downstream}],
            "filter.attribute":"transcript_type",
            "attribute.value":["IG_C_gene","IG_D_gene","IG_J_gene","IG_V_gene","IG_LV_gene","TR_C_gene","TR_D_gene","TR_J_gene","TR_V_gene","lncRNA","protein_coding"],
            "show.attributes":["transcript_type","gene_id","gene_name","hgnc_id","transcript_id","transcript_name"],
            "name": "TSS_proximal"
        },
         {
            "feature":"transcript",
            "feature.anchor":"start",
            "distance":${distal_distance},
            "filter.attribute":"transcript_type",
            "relative_location":["OverlapStart"],
            "attribute.value":["IG_C_gene","IG_D_gene","IG_J_gene","IG_V_gene","IG_LV_gene","TR_C_gene","TR_D_gene","TR_J_gene","TR_V_gene","lncRNA","protein_coding"],
            "show.attributes":["transcript_type","gene_id","gene_name","hgnc_id","transcript_id","transcript_name"],
            "name": "TSS_overlap"
        },
        {
            "feature":"transcript",
            "feature.anchor":"start",
            "distance":${distal_distance},
            "filter.attribute":"transcript_type",
            "relative_location":["FeatureInsidePeak"],
            "attribute.value":["IG_C_gene","IG_D_gene","IG_J_gene","IG_V_gene","IG_LV_gene","TR_C_gene","TR_D_gene","TR_J_gene","TR_V_gene","lncRNA","protein_coding"],
            "show.attributes":["transcript_type","gene_id","gene_name","hgnc_id","transcript_id","transcript_name"],
            "name": "TSS_FIP"
        },
         {
            "feature":"gene",
            "feature.anchor":"start",
            "distance":${distal_distance},
            "filter.attribute":"gene_type",
            "relative_location":["OverlapStart"],
            "attribute.value":["IG_C_gene","IG_D_gene","IG_J_gene","IG_V_gene","IG_LV_gene","TR_C_gene","TR_D_gene","TR_J_gene","TR_V_gene","lncRNA","protein_coding"],
            "show.attributes":["gene_type","gene_id","gene_name","hgnc_id"],
            "name": "gene_body_overlap_start"
        },
         {
            "feature":"gene",
            "feature.anchor":"start",
            "distance":${distal_distance},
            "filter.attribute":"gene_type",
            "relative_location":["FeatureInsidePeak"],
            "attribute.value":["IG_C_gene","IG_D_gene","IG_J_gene","IG_V_gene","IG_LV_gene","TR_C_gene","TR_D_gene","TR_J_gene","TR_V_gene","lncRNA","protein_coding"],
            "show.attributes":["gene_type","gene_id","gene_name","hgnc_id"],
            "name": "gene_body_FIP"
        },              
        {
            "feature":"gene",
            "feature.anchor": ["start", "center", "end"],
            "distance":10,
            "internals":"True",
            "filter.attribute":"gene_type",
            "relative_location":["PeakInsideFeature"],
            "attribute.value":["IG_C_gene","IG_D_gene","IG_J_gene","IG_V_gene","IG_LV_gene","TR_C_gene","TR_D_gene","TR_J_gene","TR_V_gene","lncRNA","protein_coding"],
            "show.attributes":["gene_type","gene_id","gene_name","hgnc_id"],
            "name": "gene_body"
        },
        {
            "feature":"gene",
            "feature.anchor":"end",
            "distance":${distal_distance},
            "filter.attribute":"gene_type",
            "relative_location":["OverlapEnd"],
            "attribute.value":["IG_C_gene","IG_D_gene","IG_J_gene","IG_V_gene","IG_LV_gene","TR_C_gene","TR_D_gene","TR_J_gene","TR_V_gene","lncRNA","protein_coding"],
            "show.attributes":["gene_type","gene_id","gene_name","hgnc_id"],
            "name": "gene_body_overlap_end"
        },      
        {
            "feature":"gene",
            "feature.anchor":"start",
            "distance":${distal_distance},
            "filter.attribute":"gene_type",
            "relative_location":["Upstream","Downstream"],
            "attribute.value":["IG_C_gene","IG_D_gene","IG_J_gene","IG_V_gene","IG_LV_gene","TR_C_gene","TR_D_gene","TR_J_gene","TR_V_gene","lncRNA","protein_coding"],
            "show.attributes":["gene_type","gene_id","gene_name","hgnc_id"],
            "name": "distal"
        },
        {
            "feature":"gene",
            "feature.anchor":"start",
            "distance":5000000,
            "relative_location":["Upstream","Downstream"],
            "filter.attribute":"gene_type",
            "attribute.value":["IG_C_gene","IG_D_gene","IG_J_gene","IG_V_gene","IG_LV_gene","TR_C_gene","TR_D_gene","TR_J_gene","TR_V_gene","lncRNA","protein_coding"],
            "show.attributes":["gene_type","gene_id","gene_name","hgnc_id"],
            "name": "intergenic"
        }
    ],
    "priority":"Yes",
    "gtf":${gtf_file},
    "bed":${bed_file}
}