#!/bin/bash
set -e

pkg=mcaller
CUR_DIR=`pwd`

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 ${CUR_DIR}/testdata "${AUTOPKGTEST_TMP}"

cd "${AUTOPKGTEST_TMP}"
mkdir -p model_data

cp -a ${CUR_DIR}/*.pkl .

mCaller -p testdata/test_positions_A.txt -r testdata/pb_ecoli_polished_assembly.fasta -e testdata/masonread1.eventalign.tsv -d r95_twobase_model_NN_6_m6A.pkl -f testdata/masonread1.fastq
mCaller -p testdata/test_positions_m6A.txt -r testdata/pb_ecoli_polished_assembly.fasta -e testdata/masonread1.eventalign.tsv -d r95_twobase_model_NN_6_m6A.pkl -f testdata/masonread1.fastq
mCaller -p testdata/test_positions.txt -r testdata/pb_ecoli_polished_assembly.fasta -d r95_twobase_model_NN_6_m6A.pkl -e testdata/masonread1.eventalign.tsv -t 4 --train -f testdata/masonread1.fastq

rm -rf model_data
rm -rf testdata

echo "PASS"
