#!/bin/bash

infile=$1
outfile=$2

cat $infile |
    paste -d '\t' - - |
    sed 's/-/_/g' |
    awk 'BEGIN {FS="\t"; OFS="\t"} { if ($1 > $7) { print substr($4,1,length($4)-2),$12,$7,$8,"16",$6,$1,$2,"8",$11,$5 } else { print substr($4,1,length($4)-2),$6,$1,$2,"8",$12,$7,$8,"16",$5,$11} }' |
    tr '_+' '01' |
    awk 'NF==11' > $outfile