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#!/bin/sh -e
# https://dep-team.pages.debian.net/deps/dep8/
# Autopkgtest: Test if SHAPEIT4 run analysis correctly
# Author: Dylan Aïssi <daissi@debian.org>
# Based on https://odelaneau.github.io/shapeit4/#documentation
pkg=shapeit4
if [ "$AUTOPKGTEST_TMP" = "" ] ; then
AUTOPKGTEST_TMP=`mktemp -d /tmp/${debname}-test.XXXXXX`
trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
fi
cd $AUTOPKGTEST_TMP
cp -a /usr/share/doc/${pkg}/examples/test/* $AUTOPKGTEST_TMP
gunzip *.bcf.gz
set -x
# 2. Phasing a chunk of data
shapeit4 --input unphased.vcf.gz \
--map chr20.b37.gmap.gz \
--region 20:2000000-3000000 \
--thread 4 \
--output phased.vcf.gz
# 12. Complex run
shapeit4 --input unphased.bcf \
--map chr20.b37.gmap.gz \
--region 20 \
--reference reference.bcf \
--scaffold scaffold.bcf \
--use-PS 0.0001 \
--thread 4 \
--log phased.log\
--output phased.bcf
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