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#!/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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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", |
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x=[ -1.2 | |
-1.19868 | |
-1.1947 | |
-1.18809 | |
-1.17886 | |
-1.16703 | |
-1.15263 | |
-1.1357 | |
-1.11627 |
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