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#!/usr/bin/env ruby
require 'gtruby'
if ARGV.length != 2
STDERR.puts "Usage #{$0} <indexname> <matchfile>"
exit 1
end
indexname=ARGV[0]
matchfile=ARGV[1]
el = GT::EncseqLoader.new
encseq = el.load(indexname)
mirrored=false
File.new(indexname + ".prj","r").each_line do |line|
m = line.match(/^mirrored=(\d+)/)
if m
if m[1].to_i == 0
mirrored=false
else
mirrored=true
end
end
end
if mirrored
encseq.mirror()
end
File.new(matchfile,"r").each_line do |line|
if not line.match(/^#/)
m = line.split
seqnum1 = m[1].to_i
relpos1 = m[2].to_i
seqnum2 = m[5].to_i
relpos2 = m[6].to_i
matchlen = m[0].to_i
#puts "sn1=#{seqnum1} rp1=#{relpos1} " +
#"sn2=#{seqnum2} rp2=#{relpos2} ml=#{matchlen}"
if relpos1 == 0
seqlen2 = encseq.seqlength(seqnum2)
if relpos2 + matchlen == seqlen2
puts "#{seqnum2} #{seqnum1} #{matchlen}"
end
elsif relpos2 == 0
seqlen1 = encseq.seqlength(seqnum1)
if relpos1 + matchlen == seqlen1
puts "#{seqnum1} #{seqnum2} #{matchlen}"
end
end
end
end
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