TransGirlCodes

##  ABBA BABA tests
##  Heath Blackmon
##  coleoguy@gmail.com
##  28 July 2013
##  This file has algorithms found in:

##  Durand, Eric Y., et al. "Testing for ancient admixture between 
##  closely related populations." Molecular biology and evolution 
##  28.8 (2011): 2239-2252.

TransGirlCodes

authors:
  hanzou:
    name: Hanzou Hattori
    display_name: Hanzou
    gravatar: c66919cb194f96c696c1da0c47354a6a
    email: hanzou@company.com
    web: http://company.com
    twitter: company
    github: hhattori
  jorgen:

TransGirlCodes

# From this:
type MinHashSketch
    sketch::Vector{UInt64}
    kmersize::Int

    function MinHashSketch(sketch::Vector, kmersize::Int)
        length(sketch) > 0 || error("Sketch cannot be empty")
        kmersize > 0 || error("Kmersize must be greater than 0")
        new(sketch, kmersize)
    end

TransGirlCodes

function scan(T, filename)
    reader = open(T, filename)
    record = eltype(reader)()
    n = 0
    try
        while true
            read!(reader, record)
            n += 1
        end
    catch ex

TransGirlCodes

#!/usr/bin/env julia
######################################################################
# Overwrite REQUIRE using dependency information from Project.toml.
#
# Call from the root of the package repository.
#
# Has some basic sanity checks, but **use at your own risk**, `REQUIRE`
# will be overwritten.
#
# The purpose of this script is to appease attobot, until

TransGirlCodes

Keybase proof

I hereby claim:

• I am BenJWard on github.
• I am benjward (https://keybase.io/benjward) on keybase.
• I have a public key whose fingerprint is 612E 4FB8 FF0A 78DB 5917 A2A8 ACF2 1E71 286A CAFB

To claim this, I am signing this object:

TransGirlCodes

using BioSequences, BenchmarkTools

# In BioSequences.jl kmers are called Mer, not Kmer so there is no name clash.
struct Kmer{A<:NucleicAcidAlphabet{2},K,N}
    data::NTuple{N,UInt64}
end

const DNAKmer{K,N} = Kmer{DNAAlphabet{2},K,N}

###

TransGirlCodes

Keybase proof

I hereby claim:

• I am SabrinaJaye on github.
• I am sabrinajaye (https://keybase.io/sabrinajaye) on keybase.
• I have a public key whose fingerprint is 1B61 8245 FD24 5F98 36B9 C8CD 328B 9904 045A 2D7E

To claim this, I am signing this object:

TransGirlCodes

### A Pluto.jl notebook ###
# v0.17.7

using Markdown
using InteractiveUtils

# ╔═╡ 47e088e3-00ae-46b2-b0ba-325e52156381
import Pkg; Pkg.activate("/Users/bward/repos/github/BioJulia/Kmers.jl")

# ╔═╡ ead5355a-0262-4617-8551-d6b1d21c62bc

TransGirlCodes

### A Pluto.jl notebook ###
# v0.17.7

using Markdown
using InteractiveUtils

# ╔═╡ 47e088e3-00ae-46b2-b0ba-325e52156381
import Pkg; Pkg.activate("/Users/bward/repos/github/BioJulia/Kmers.jl")

# ╔═╡ ead5355a-0262-4617-8551-d6b1d21c62bc