#!/bin/bash
set -e

pkg=gasic

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}"

gunzip -r *

echo -e "\e[93m\e[1mTest 0: Create Genome Indices\e[0m"
cd genomes
bwa index dwv.fasta
bwa index vdv1.fasta            
bwa index vdv1dwv9.fasta
bwa index vdv1dwv5.fasta
cd ..
echo -e "\e[92m\e[1mPassed\e[0m"
echo

echo -e "\e[93m\e[1mTest 1: run_mappers\e[0m"
run_mappers names reads/SRR059298_subset.fastq -i ./genomes/%s.fasta -o ./SAM/mapped_%s.sam -m bwa
echo -e "\e[92m\e[1mPassed\e[0m"
echo

echo -e "\e[93m\e[1mTest 2: create_matrix\e[0m"
create_matrix names -s mason_illumina -m bwa -r genomes/%s.fasta -i genomes/%s.fasta -t ./SAM
echo -e "\e[92m\e[1mPassed\e[0m"
echo

echo -e "\e[93m\e[1mTest 3: correct_abundances\e[0m"
correct_abundances names -s ./SAM/mapped_%s.sam -m similarity_matrix.npy -o results.txt
echo -e "\e[92m\e[1mPassed\e[0m"
echo

echo -e "\e[93m\e[1mTest 4: quality_check\e[0m"
quality_check ./SAM/mapped_vdv1.sam
echo -e "\e[92m\e[1mPassed\e[0m"
echo

