--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plink.sh	Fri Aug 05 09:46:55 2016 -0400
@@ -0,0 +1,49 @@
+#!/bin/bash
+
+
+tool_path=$(dirname $0)
+
+filein=$1
+fileout_label=$(date "+%Y%m%d%H%M%S")
+fileout=$2
+filelog=$3
+frequency=$4
+max_freq=$5
+allow_missing=$6
+type=${7}
+bound_start=${8}
+bound_end=${9}
+
+cp -rf $filein input$$.vcf
+
+if [ "${10}" != "None" ]
+then samples="--samples ${10}"
+fi
+
+if [ "${11}" != "None" ]
+then chromosomes="--chromosomes ${11}"
+fi
+
+if [ "$bound_start" -gt "$bound_end" ]
+then tmp=$bound_start ; bound_start=$bound_end ; bound_end=$tmp ; echo "Warning : Lower bound must be lower than greater bound!" >&2
+fi
+
+
+export="VCF"
+
+perl $tool_path/Plink.pl --input input$$.vcf --out $fileout_label --export $export --frequency $frequency --max_freq $max_freq --allow_missing $allow_missing --type $type --bounds $bound_start','$bound_end $samples $chromosomes
+
+
+#echo ${16} >>$fileout_label.log
+#echo ${15} >>$fileout_label.log
+#echo ${17} >>$fileout_label.log
+#echo ${18} >>$fileout_label.log
+
+if [ "$export" = "VCF" ]
+then cp  $fileout_label.vcf $fileout ; rm $fileout_label.vcf
+else cp  $fileout_label.bed $fileout; cp $fileout_label.bed ${15} ; cp $fileout_label.bim ${18} ;rm $fileout_label.bed $fileout_label.fam $fileout_label.bim
+fi
+
+cp $fileout_label.log $filelog
+rm $fileout_label.log
+