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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,68 +1,75 @@ | ||
| // the minhash package contains a MinHash implementation that is adapted from go-minhash (https://godoc.org/github.com/dgryski/go-minhash) | ||
| // the minhash package contains a minHash implementation that uses the ntHash rolling hash function | ||
| package minhash | ||
|
|
||
| import ( | ||
| "errors" | ||
| "math" | ||
|
|
||
| "github.com/will-rowe/ntHash" | ||
| ) | ||
|
|
||
| // if set true, ntHash will return the canonical k-mer (inspects both strands for each k-mer and returns the lowest hash value) | ||
| const CANONICAL = false | ||
|
|
||
| /* | ||
| The MinHash struct contains all the minimum hash values for a sequence | ||
| The minHash struct contains all the minimum hash values for a sequence | ||
| */ | ||
| type MinHash struct { | ||
| type minHash struct { | ||
| kSize int | ||
| signature []uint64 | ||
| hashFunc1 Hash64 | ||
| hashFunc2 Hash64 | ||
| } | ||
| type Hash64 func([]byte) uint64 | ||
|
|
||
| /* | ||
| A method to hash a k-mer and add signature to the MinHash struct | ||
| */ | ||
| func (self *MinHash) Add(kmer []byte) { | ||
| hashValue1, hashValue2 := self.hashFunc1(kmer), self.hashFunc2(kmer) | ||
| for i, minVal := range self.signature { | ||
| newVal := hashValue1 + uint64(i)*hashValue2 | ||
| if newVal < minVal { | ||
| self.signature[i] = newVal | ||
| // Add a sequence to the minHash | ||
| func (minHash *minHash) Add(sequence []byte) error { | ||
| // initiate the rolling hash | ||
| hasher, err := ntHash.New(&sequence, minHash.kSize) | ||
| if err != nil { | ||
| return err | ||
| } | ||
| } | ||
| // get hashed kmers from read | ||
| for hash := range hasher.Hash(CANONICAL) { | ||
| // for each hashed k-mer, try adding it to the sketch | ||
| for i, minVal := range minHash.signature { | ||
| // split the hashed k-mer (uint64) into two uint32 | ||
| h1, h2 := uint32(hash), uint32(hash>>32) | ||
| // get the new hash value for this signature position | ||
| newVal := uint64(h1 + uint32(i)*h2) | ||
| // evaluate and add to the signature if it is a minimum | ||
| if newVal < minVal { | ||
| minHash.signature[i] = newVal | ||
| } | ||
| } | ||
| } | ||
| return nil | ||
| } | ||
|
|
||
| /* | ||
| A method to dump the MinHash signature | ||
| */ | ||
| func (self *MinHash) Signature() []uint64 { | ||
| return self.signature | ||
| // Signature returns the current minHash signature (set of minimums) | ||
| func (minHash *minHash) Signature() []uint64 { | ||
| return minHash.signature | ||
| } | ||
|
|
||
| /* | ||
| A method to estimate Jaccard Similarity between a MinHash struct and a query MH signature | ||
| */ | ||
| func (self *MinHash) Similarity(querySig []uint64) (float64, error) { | ||
| if len(self.signature) != len(querySig) { | ||
| // Similarity is a method to estimate the Jaccard Similarity using to minHash signatures | ||
| func (minHash *minHash) Similarity(querySig []uint64) (float64, error) { | ||
| if len(minHash.signature) != len(querySig) { | ||
| return 0, errors.New("length of minhash signatures do not match\n") | ||
| } | ||
| intersect := 0 | ||
| for i := range self.signature { | ||
| if self.signature[i] == querySig[i] { | ||
| for i := range minHash.signature { | ||
| if minHash.signature[i] == querySig[i] { | ||
| intersect++ | ||
| } | ||
| } | ||
| return float64(intersect) / float64(len(self.signature)), nil | ||
| return float64(intersect) / float64(len(minHash.signature)), nil | ||
| } | ||
|
|
||
| /* | ||
| A function to create a new MinHash struct | ||
| */ | ||
| func NewMinHash(h1, h2 Hash64, size int) *MinHash { | ||
| signature := make([]uint64, size) | ||
| // NewminHash initiates a minHash struct and populates the signature with max values | ||
| func NewMinHash(kSize, sigSize int) *minHash { | ||
| signature := make([]uint64, sigSize) | ||
| for i := range signature { | ||
| signature[i] = math.MaxUint64 | ||
| } | ||
| newMinHash := new(MinHash) | ||
| newMinHash.hashFunc1 = h1 | ||
| newMinHash.hashFunc2 = h2 | ||
| newMinHash.signature = signature | ||
| return newMinHash | ||
| return &minHash{ | ||
| kSize: kSize, | ||
| signature: signature, | ||
| } | ||
| } |
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