# Processing the binary annotation matrix
mkdir variant_overlap
cd paintor_files
for i in `ls -v out_*.annotation | cut -d "." -f1-3`; do paste -d ' ' $i ${i}.annotation > ../variant_overlap/${i}_overlap.txt; done
cd ../variant_overlap
mkdir mod
for i in `ls -v *overlap.txt`; do tail -n +2 $i > mod/mod_${i}; done
cd mod
cat *overlap.txt > all.overlap.txt
head -1 ../out_chrX.rs12009217.processed_overlap.txt | cat - all.overlap.txt > final.all.overlap.txt

# Processing the null results
cd null_mcmc
mkdir mod
for i in `ls -v *processed*`; do tail -n +2 $i > mod/mod_${i}; done
cd mod
cat * > all.null.results.txt
head -1 ../out_chrX.rs12009217.processed.null.mcmc.results | cat - all.null.results.txt > final.all.null.results.txt

# Processing the annotation results
cd anno_mcmc
mkdir mod
 for i in `ls -v *processed*`; do tail -n +2 $i > mod/mod_${i}; done
cd mod
cat * > all.anno.results.txt
head -1 ../out_chrX.rs12009217.processed.anno.mcmc.results | cat - all.anno.results.txt > final.all.anno.results.txt 

# Putting everything in a nice results directory
mkdir results
cp variant_overlap/mod/final.all.overlap.txt results/
cp anno_mcmc/mod/final.all.anno.results.txt results/
cp null_mcmc/mod/final.all.null.results.txt results/
