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#!/bin/bash
#
# This script tests whether dose data without a MaCH/minimac-style
# arrow is read correctly by palinear (and by palogist, since reading
# genetic data is done using the same code).
echo "Checking palinear with dose data without '->'"
# Exit with error when one of the steps in the script fails
set -e
if [ -z ${srcdir} ]; then
srcdir="."
fi
inputdir="${srcdir}/inputfiles/"
results="${srcdir}/verified_results/"
outfile="height_base_add.out.txt"
sed 's/^[[:digit:]]*->//' $inputdir/test.mldose > test.mldose
../src/palinear \
-p ${inputdir}/height.txt \
-d test.mldose \
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 \
-o height_base > /dev/null
blanks=" "
echo -n " Verifying "
if diff $outfile $results/$outfile; then
echo -e "${outfile}${blanks:${#outfile}} OK"
else
echo -e "${outfile}${blanks:${#outfile}} FAILED"
exit 1
fi
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