[ 
{"function": "optimizerSetting", "lambdaL2": 1e-6, "pseudocount": 20, 
        "nThreads": 20 },
{"function": "addTable", "leftFlank": "", "rightFlank": "", 
    "variableRegionLength": 200, "nColumns":2, "modeledColumns":[0,1],
	"countTableFile":"countTable.0.IMR90_GR_chip-seq_rep1.tsv.gz", "inputFileType":"tsv.gz" },
{"function": "addSELEX", "modelType": "SELEX", "cumulativeEnrichment": true },
{"function": "addNS" }, 
{"function": "addBindingMode", "size": 15, "flankLength": 0, 
        "dinucleotideDistance": 0, "positionBias": true }, 
{"function": "addBindingMode", "size": 10, "flankLength": 0, 
        "dinucleotideDistance": 0, "positionBias": true }, 
{"function": "addBindingMode", "size": 10, "flankLength": 0, 
        "dinucleotideDistance": 0, "positionBias": true }, 
{"function": "addBindingMode", "size": 10, "flankLength": 0, 
        "dinucleotideDistance": 0, "positionBias": true }, 
{"function": "bindingModeSeed"       , "index": 1, 
        "mononucleotideString": "AG.ACA...TGT.CT" }, 
{"function": "symmetry",               "index": 1, 
        "symmetryString": "abcdefg1GFEDCBA" }, 
{"function": "bindingModeConstraints", "index": 1, 
        "positionBiasBinWidth": 5 }, 
{"function": "bindingModeConstraints", "index": 2, "maxSize": 18, 
        "positionBiasBinWidth": 5, "fittingStages": [ 
                { "optimizeMotifShiftHeuristic": true }, 
                { "optimizeSize": true } ] }, 
{"function": "bindingModeConstraints", "index": 3, "maxSize": 18, 
        "positionBiasBinWidth": 5, "fittingStages": [ 
                { "optimizeMotifShiftHeuristic": true }, 
                { "optimizeSize": true } ] }, 
{"function": "bindingModeConstraints", "index": 4, "maxSize": 18, 
        "positionBiasBinWidth": 5, "fittingStages": [ 
                { "optimizeMotifShiftHeuristic": true }, 
                { "optimizeSize": true } ] },
{"function": "output", "outputPath": "", "baseName": "fit", "verbose": true }
]