schema-1.0.0.json

{
	// 'meta-schema' describing this JSON as a schema
	//
	"$schema" : "http://json-schema.org/schema#",
	
	"type" : "object",
	"required" :
	[
		"schema",
		"kmerSize",
		"alphabet",
		"preserveCase",
		"canonical",
		"sketchSize",
		"hashType",
		"hashBits",
		"hashSeed"
	],
	"properties" :
	{
		// URI of the appropriate version of this schema
		//
		"schema" : {"type" : "string"},
		
		// the number of characters in each overlapping 'shingle'
		//
		"kmerSize" : {"type" : "number"},
		
		// all letters a k-mer can have (others will be skipped) (see also
		// 'preserveCase')
		//
		"alphabet" : {"type" : "string"},
		
		// if true, letters in a k-mer must match the case of letters in
		// 'alphabet'
		//
		"preserveCase" : {"type" : "boolean"},
		
		// if true, use alphabetical minima of k-mers and their reverse
		// complements (only makes sense for nucleotide alphabet)
		//
		"canonical" : {"type" : "boolean"},
		
		// the (maximum) number of min-hashes each sketch can have (there can be
		// if a sequence does not have enough valid k-mers)
		//
		"sketchSize" : {"type" : "number"},
		
		// the hashing function used to hash each k-mer
		//
		"hashType" : {"type" : "string"},
		
		// the number of (least significant) bits taken from the result of the
		// hash function
		//
		"hashBits" : {"type" : "number"},
		
		// the seed of the hash function, if applicable
		//
		"hashSeed" : {"type" : ["number", "null"]},
		
		// a collection of sketches that share the above sketching parameters
		//
		"sketches" :
		{
			"type" : "array",
			"items" :
			{
				"type" : "object",
				"required" :
				[
					"name",
					"hashes"
				],
				"properties" :
				{
					// a sequence identifier, expected to be unique in the
					// collection
					//
					"name" : {"type" : "string"},
					
					// the length of the source sequence that was sketched,
					// which could be a sum of for concatenated sequences or an
					// estimate from k-mer content of reads
					//
					"seqLength" : {"type" : "number"},
					
					// an additional description of the source sequence not
					// captured by 'name' (e.g. after whitesapce in a fasta tag)
					//
					"comment" : {"type" : "string"},
					
					// the number of k-mers from the source sequence that
					// conformed to the letters in 'alphabet' and was thus
					// considered for min-hashing (including repeated k-mers)
					//
					"numValidKmers" : {"type" : "number"},
					
					"filters" :
					{
						"type" : "object",
						"properties" :
						{
							// the minimum number of times a k-mer must appear
							// in the source sequence to be considered for min-
							// hashing (for filtering out erroneous k-mers in
							// read sets)
							//
							"minCopies" : {"type" : "number"},
						}
					},
					
					// the min-hashes of this sketch, represented as unsigned
					// integers but quoted as strings to avoid overflow
					//
					"hashes" :
					{
						"type" : "array",
						"uniqueItems" : true,
						"items" :
						{
							"type" : "string",
							"pattern" : "^[0-9]+$"
						}
					},
					
					// the k-mers that correspond to the hashes in 'hashes' (in
					// the same order), used mainly for confirming the hash
					// function and not necessarily valid for Jaccard estimates
					// due to potential hash collisions
					//
					"kmers" :
					{
						"type" : "array",
						"items" : {"type" : "string"}
					},
					
					// the number of times each hash in 'hash' was derived from
					// k-mers in the source sequence (in the same order)
					//
					"counts" :
					{
						"type" : "array",
						"items" : {"type" : "number"}
					}
				}
			}
		}
	}
}