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#!/usr/bin/env ruby
def runchain2dimvschain2dim(args,matchfile)
system "cat #{matchfile} | ../scripts/rf2of.rb > tmp.of"
system "../bin/gt chain2dim " + args + " -m tmp.of > gtchain.out"
system "chain2dim.x " + args + " tmp.of > vschain.out"
system "cmp -s gtchain.out vschain.out"
end
params = ["-global",
"-silent -global",
"-local -wf 1.8",
"-local -wf 0.5",
"-local -maxgap 20",
"-local 2b",
"-local 55p -silent",
"-global gc",
"-global ov",
"-global gc -wf 1.5",
"-global ov -wf 1.8",
"-global -maxgap 10",
"-global gc -wf 1.5 -maxgap 10",
"-global ov -wf 1.8 -maxgap 10",
"-local",
"-local 2p",
"-local 20",
"-local 2p -wf 1.8",
"-local 2b -wf 1.8",
"-local 20 -wf 1.8",
"-local -wf 1.8 -maxgap 20",
"-local 2p -wf 1.8 -maxgap 10",
"-local 2b -wf 1.8 -maxgap 10",
"-local 20 -wf 1.8 -maxgap 10"]
resultdir="#{ENV['GTTESTDATA']}/repfind-result"
Dir.foreach("#{resultdir}") do |matchfile|
if matchfile.match(/^\S+\.fna-\S+\.fna.result$/)
params.each do |args|
runchain2dimvschain2dim(args,"#{resultdir}/#{matchfile}")
end
end
end
system "rm -f tmp.of gtchain.out vschain.out"
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