ts_res
{
	;Dataset configs

		;TSLR leftover
		tslr_dataset  ""

	;Barcode index construction configs

		;Barcodes are counted on the last edge_tail_len nucleotides of the edge
		edge_tail_len 100000000
		;Edge will be split up to segments of length frame_size
		frame_size 500

	;Filtering configs

		;edges with less than trimming_threshold barcodes will be deleted
		;trimming_threshold 1

		;clouds further than gap_threshold from the end\beginning of the edge will be deleted
		;gap_threshold 100000000

	;Configs for 10X repeat resolution
		read_cloud_resolution_on true
		read_cloud_gap_closer_on true

	statistics
	{
		;Genome file
		genome_path ""

		;Baseline SPAdes contigs
		base_contigs_path ""

		;CloudSPAdes contigs
		cloud_contigs_path ""
	}

	long_edge_length_max_upper_bound 20000
	long_edge_length_min_upper_bound 5000
	long_edge_length_lower_bound 3000

	min_training_edges 20
	min_training_total_length 5000000
	optimal_training_total_length 20000000

	gap_closer_connection_score_threshold 0.05
	gap_closer_relative_coverage_threshold 50.0
	gap_closer_connection_length_threshold 100

	scaffold_polisher {
		share_threshold 0.05
		read_count_threshold 2
		max_scaffold_distance 4
		path_cluster_linkage_distance 2500
		path_cluster_min_reads 1
		path_cluster_score_threshold 10.0
	}

	scaffold_graph_construction {
		score_percentile 0.005
		cluster_length_percentile 0.9
		count_threshold 1
	    relative_coverage_threshold 4.0
	    connection_length_threshold 50
	    connection_count_threshold 1
	    initial_distance 15000
	    split_strictness 0.95
	    transitive_distance_threshold 2
	    path_scaffolder_tail_threshold 20000
	    path_scaffolder_count_threshold 1
	    min_edge_length_for_barcode_collection 1000
	}

	path_scaffolding_on true
	debug_mode false
}
