#!/bin/bash                                                                                                                                          

# $1 = parameter file to impute data in parallel                                                                                       
# $2 = imputed data file name                                                                                                                     
# $3 = no. of processers to run in parallel                                                                                                           

RANDOM=$$
#run bayesnetty $3 times for X bootstraps each                                                                                                       
for i in $(seq 1 $3);
do

../../bayesnetty $1 -so -seed $i0$RANDOM -output-network-node-data-file-prefix $2$i-i -output-network-node-data-bed-file -output-network-node-data-job $i $3 -impute-network-data-job $i $3&

done

#wait for all processes to finish                                                                                                                    
wait

##collate files
if [ -f "$21-i-cts.dat" ]
then
 > $2-cts.dat
fi

if [ -f "$21-i-discrete.dat" ]
then
 > $2-discrete.dat
fi

for j in $(seq 1 $3);
do

#collate cts data
if [ -f "$2$j-i-cts.dat" ]
then
 cat $2$j-i-cts.dat >> $2-cts.dat
 rm $2$j-i-cts.dat
fi

#collate discrete data
if [ -f "$2$j-i-discrete.dat" ]
then
 cat $2$j-i-discrete.dat >> $2-discrete.dat
 rm $2$j-i-discrete.dat
fi

#collate SNP plink style data
if [ -f "$2$j-i.fam" ]
then

 if [ $j == 1 ]
 then
  cp $2$j-i.fam $2.fam
  cp $2$j-i.bim $2.bim
  cp $2$j-i.bed $2.bed
 else
  plink --noweb --silent --bfile $2 --bmerge $2$j-i.bed $2$j-i.bim $2$j-i.fam --make-bed --out $2-merge
  mv $2-merge.bed $2.bed
  mv $2-merge.bim $2.bim
  mv $2-merge.fam $2.fam
  rm $2-merge.log
 fi

 rm $2$j-i.fam
 rm $2$j-i.bim
 rm $2$j-i.bed
fi

done

