#!/bin/bash
set -e

pkg=bamkit
examplepkg=samtools

export LC_ALL=C.UTF-8
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi

cp -a /usr/share/doc/${examplepkg}/examples/toy.sam "${AUTOPKGTEST_TMP}"


cd "${AUTOPKGTEST_TMP}"
mv -f toy.sam read.sam

cat read.sam| samtools view -Sb > reads.bam
samtools index reads.bam 
samtools addreplacerg -r ID:S1 -r LB:L1 -r SM:SAMPLE1 -o output reads.bam

bamlibs.py reads.bam 
bamcleanheader.py reads.bam > output
bamfilterrg.py -i reads.bam > filter
[ -s "output" ] && [ -s "filter" ] || exit 1
echo "PASS Tests"
