src/

Package bitvector contains types and methods for working with bit vectors

Package countmin is an implementation of the CountMin Sketch (https://sites.google.com/site/countminsketch/cm-latin.pdf?attredirects=0)

Package distances contains the distance calculations for several common metrics

Package helpers contains some helper functions which the HULK CL program needs

Package histosketch is a Go implementation of HistoSketch: Fast Similarity-Preserving Sketching of Streaming Histograms with Concept Drift (https://exascale.info/assets/pdf/icdm2017_HistoSketch.pdf) I've made some changes in my implementation compared to the paper: - Instead of providing the number of histogram bins (Dimensions) and the number of countmin hash tables (d), I have decided to use epsilon and delta values to calculate CMS Dimensions.

Package kmerspectrum uses a Go implementation of the jump consistent hash algorithm to bin hashed k-mers into k-mer spectrum bins (ala histogram)

Package minhash contains implementations of KMV and KHF MinHash algorithms

Package minimizer takes a sequence and finds the minimizers (for w consecutive k-mers) NOTE: currently it uses mapset to store the minimizers - this is unordered, which is fine for HULK but the minimizer sketch isn't that useful for anything else yet

Package pipeline contains a streaming pipeline implementation based on the Gopher Academy article by S. Lampa - Patterns for composable concurrent pipelines in Go (https://blog.gopheracademy.com/advent-2015/composable-pipelines-improvements/)

Package queue implements a simple queue for uint64s - it is not thread safe (uncomment the mutex lines if you need thread safety)

Package seqio contains custom types and methods for holding and processing sequence data

Package sketchio is used to read and write HULK sketches