#!/bin/bash


# This script is for IBD>0.05 with very many individuals
# It shows how individuals could be remover sequentially
# Result is in files RES_*
# It incorporates functions from LFE64


#####You need to change filenames on the left:

cp IBDPAIRS_name.txt FILENAME
cp PFILE_name.txt PFILENAME
wait

#####This is assuming that the file names are space delimited

for limvalue in 0.5 0.4 0.3 0.2 0.1 0.09 0.08 0.07 0.06 0.055; do

ppp=15000

ALLELE -M relout5 -file FILENAME -pfile PFILENAME -out RES_${limvalue}.txt -limit ${limvalue} -delim space -mode 2 -pdefault zero -pidsize $ppp > RES_${limvalue}.log

wait

LFE64 -M extractcolumns -columns 2 -delim space -file RES_${limvalue}.txt -out list.txt

wait

LFE64 -M listselection -file FILENAME -header no -column 1 -delim space -list list.txt -in-or-out out -out FILENAME_inter
wait

LFE64 -M listselection -file FILENAME_inter -header no -column 2 -delim space -list list.txt -in-or-out out -out FILENAME_temp
wait

rm FILENAME_inter

LFE64 -M listselection -file PFILENAME -header no -column 1 -delim space -list list.txt -in-or-out out -out PFILENAME_temp

wait

mv FILENAME_temp FILENAME
mv PFILENAME_temp PFILENAME
wait

done

################################



limvalue=0.05;

ALLELE -M relout5 -file FILENAME -pfile PFILENAME -out RES_${limvalue}.txt -limit ${limvalue} -delim space -mode 2 -pdefault zero -pidsize 1 > RES_${limvalue}.log


rm FILENAME
rm PFILENAME