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#!/bin/bash
set -e
pkg=shasta
export LC_ALL=C.UTF-8
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
# We first test /usr/bin/shasta binary
echo "Testing /usr/bin/shasta"
gunzip TinyTest.fasta.gz
shasta --config Nanopore-Dec2019 --input TinyTest.fasta
# Now, test Python3 binding via invocation
echo "Alignment compression test"
python3 -c 'import shasta;shasta.testAlignmentCompression();'
echo "Base test"
python3 -c 'import shasta;shasta.testBase();'
echo "Compact undirected graph 1 test"
python3 -c 'import shasta;shasta.testCompactUndirectedGraph1();'
echo "Compact undirected graph 2 test"
python3 -c 'import shasta;shasta.testCompactUndirectedGraph2();'
echo "De-duplicate and count test"
python3 -c 'import shasta;shasta.testDeduplicateAndCount();'
echo "Long base sequence test"
python3 -c 'import shasta;shasta.testLongBaseSequence();'
echo "Median consensus caller test"
python3 -c 'import shasta;shasta.testMedianConsensusCaller();'
echo "Multi-threaded object test"
python3 -c 'import shasta;shasta.testMultithreadedObject();'
echo "Short base sequence test"
python3 -c 'import shasta;shasta.testShortBaseSequence();'
echo "Simple bayesian consensus test using guppy-2.3.1-a model"
python3 -c 'import shasta;shasta.testSimpleBayesianConsensusCaller("guppy-2.3.1-a");'
echo "Spoa test"
python3 -c 'import shasta;shasta.testSpoa();'
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