#! /usr/local/bin/bash -f
#
#Copyright (c) 2000 Jeff Lessem, Institute for Behavioral Genetics,
#    University of Colorado; and Stacey Cherny, Wellcome Trust Centre
#    for Human Genetics, University of Oxford
#
# http://ibgwww.Colorado.EDU/~lessem/software/qms2.html#license for the
# terms under which this software may be used.
#
# Convert a genehunter ibd file to something that SAS software can easily
# read
#
# The file to read in
# IBDFILE=dump.ibd
if [ "$1" = "" ]; then
    cat <<EOF
Usage: pre-sas.sh inputfile [outputfile]
EOF
exit 0
fi
IBDFILE=$1
# The file to create
if [ "$2" = "" ]; then
    OUTFILE=${1%.*}-sas.ibd
else
    OUTFILE=$2
fi
echo -n "Converting \"$IBDFILE\" to \"$OUTFILE\"..."
# Cut out the top line of text
grep -v pos $IBDFILE | \
# Replace tabs with spaces
expand | \
# Replace , with space and write to $OUTFILE
sed -e "s/,/ /" > $OUTFILE
echo done.
exit 0