#!/bin/bash

#set -Eeuo pipefail


if [ $# -lt 2 ]
  then
        echo "par1 is vcf,par2 is pvalue,sample_size=297"
        exit
fi



#vcftools --vcf $1 --freq --out ${1}maf1
sed -i 's/:/\t/g' ${1}maf1.frq
awk '$6<=$8 {print $0," ",$6} $6>$8 {print $0," ",$8}' ${1}maf1.frq>${1}maf1.frq1
awk '{print $1"-"$2,$0}' ${1}maf1.frq1>${1}maf1.frq2
##################################### create ld file
touch master.file
echo 'z;ld;snp;config;cred;log;n_samples'>master.file

for file in `find ./ -name "*LD2*"`
do

sed -i '$a '"$file"'.z;'"$file"'.ld;'"$file"'.snp;'"$file"'.config;'"$file"'.cred;'"$file"'.log;297' master.file

vcftools --vcf $1 --positions $file --recode --out $file
plink --vcf ${file}.recode.vcf --r2 --matrix
mv plink.ld ${file}.ld
#rm *recode*
rm *log*  
rm *nosex*
################################### create .z file

             
awk '{print $1"-"$2}' $file >${file}_id

awk 'NR==FNR{lee[$1]=$0;next}NR>FNR{if($1 in lee){print $0 "\t" lee[$1]} else {print $0 "\t" "None"}}' $2 ${file}_id >${file}_id.extracted
awk 'NR==FNR{lee[$1]=$0;next}NR>FNR{if($1 in lee){print $0 "\t" lee[$1]} else {print $0 "\t" "None"}}' ${1}maf1.frq2 ${file}_id.extracted >${file}_id.extracted.maf
awk '{print $3,$4,$5,$6,$7,$NF,$8,$9}' ${file}_id.extracted.maf>${file}.z
sed -i 's/"//g' ${file}.z
sed -i '1i rsid chromosome position allele1 allele2 maf beta se' ${file}.z
    
done

for i in `awk '{print NR-1}' master.file`;do ../finemap_v1.4.1_x86_64/finemap_v1.4.1_x86_64 --sss --in-files master.file dataset $i;done