Revision d3f213f733f5d80a62f00d4967b26edb7a06ba72 authored by Mikhail Kolmogorov on 22 March 2015, 19:11:36 UTC, committed by Mikhail Kolmogorov on 22 March 2015, 19:11:36 UTC
1 parent 4bf798f
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config.py
#(c) 2013-2014 by Authors
#This file is a part of Ragout program.
#Released under the BSD license (see LICENSE file)

"""
This module stores some configuration parameters
"""

vals =  {
            "overlap" :
            {
                "min_overlap" : 33,
                "max_overlap" : 200,
                "max_path_len" : 30,
                "detect_kmer" : True
            },

            "maf2synteny" :
            [
                (30, 10),
                (100, 100),
                (500, 1000),
                (1000, 5000),
                (5000, 15000)
            ],

            "sibelia" :
            [
                (30, 150),
                (100, 500),
                (500, 1500)
            ],

            "blocks" :
            {
                "small" : [5000, 500, 100],
                "large" : [10000, 5000, 500, 100]
            },

            "big_genome_threshold" : 500 * 1024 * 1024,

            "min_synteny_coverage" : 0.6,
            "min_overlap_rate" : 0.5,

            "detect_chimera" : True
        }
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