BioDataStructures.jl

Installation

Pkg.clone("https://github.com/ylxdzsw/BioDataStructures.jl")
using BioDataStructures

Currently works for Julia v0.5 only.

IntRangeSet

A tree based datastructure holds Integers. Ideally for bed in NGS.

Features

• use a cache to make inserting integer incrementally (eg. push!(t, 2, 3, 4, 6, 8, 9)) in O(1), even when the tree is not balanced.
• automatically balance the tree when performing quering.
• use a dense structure aiming to save high-scale, clustered integers (more specifically, bed-like data in NGS).

Example

a = IntRangeSet{Int}()

push!(a, 2)
push!(a, 4:5)
show(a)

# IntRangeSets{Int64}:
#  2:2
#  4:5

push!(a, 3)
show(a)

# IntRangeSets{Int64}:
#   2:5

3 in a # true

b = IntRangeSet{Int}()
push!(b, 4:8)
push!(b, 2)
foreach(println, b)

# 2:2
# 4:8

c = union(a, b)
show(c)

# IntRangeSets{Int64}:
#   2:8

c = intersect(a, b)
show(c)

# IntRangeSets{Int64}:
#   2:2
#   4:5

collect(c)

# 2-element Array{UnitRange{Int64},1}:
#  2:2
#  4:5

Benchmark

run test/benchmark.jl to get your local performance.