dcjones

#!/usr/bin/env julia

using IntervalTrees
using Bio.Intervals: Interval

function random_interval(seqname, minlen, maxlen, minstart, maxstart)
    first = rand(minstart:maxstart)
    last = first + rand(minlen:maxlen) - 1
    return Interval(seqname[1:end], first, last)
end

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dcjones

module BGZF

using BufferedStreams, Libz


# compressed and decompressed blocks are <= this in BGZF
const MAX_SIZE = 65536

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using SQLite

# generate some random data
function binned_data(xbins, ybins, n)
    xs = rand(n)
    ys = rand(n)

    # bin data
    bins = zeros(Float64, (xbins, ybins))

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function main()
  if length(ARGS) < 2
      println(STDERR, "Usage: fastq_rnd_seek_proper.jl filename numsamples")
      exit()
  end
  filename = ARGS[1]
  numsamples = parse(Int, ARGS[2])

  pattern = r"@.+[\n\r]+[A-Z-]+[\n\r]+\+[\n\r]+.+[\n\r]{0,1}"

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# Note: This only works on julia-0.4 currently.

using Bio.Seq

include("fogsaa.jl")

scoring = AlignmentScoring(2, -1, -3, -1)

FOGSAA(
    dna"AACGTACGTACAATAGTTTTACGATAACCGATAGCGATACCCATTAGACTATA",

dcjones

x=[ -1.2
    -1.19868
    -1.1947
    -1.18809
    -1.17886
    -1.16703
    -1.15263
    -1.1357
    -1.11627

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