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#!/bin/bash
set -e
pkg=idba
export LC_ALL=C.UTF-8
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
# Double quote below to expand the temporary directory variable now versus
# later is on purpose.
# shellcheck disable=SC2064
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 *
cd ud
echo "=== Generate sample data for ud ==="
sim_reads 220668.fa 220668.reads-10 --paired --depth 10
sim_reads 321956.fa 321956.reads-100 --paired --depth 100
sim_reads 557433.fa 557433.reads-1000 --paired --depth 1000
cat 220668.reads-10 321956.reads-100 557433.reads-1000 > meta.reads
echo
echo "=== Testing idba_ud ==="
idba_ud -r meta.reads -o out1
echo
echo "=== Testing idba_ud with second level scaffolds ==="
idba_ud -r 321956.reads-100 --read_level_2 321956.reads-100 -o out2
echo
cd ../hybrid
echo "=== Generate sample data for hybrid ==="
sim_reads ecoli_target.fa reads-4 --depth 4 --paired
sim_reads ecoli_target.fa reads-8 --depth 8 --paired
sim_reads ecoli_target.fa reads-12 --depth 12 --paired
sim_reads ecoli_target.fa reads-16 --depth 16 --paired
sim_reads ecoli_target.fa reads-20 --depth 20 --paired
cat reads-4 reads-8 reads-12 reads-16 reads-20 > meta.reads
echo
echo "=== Testing idba_hybrid with simulated E. coli reads ==="
idba_hybrid -r meta.reads -o out1
echo
echo "=== Testing idba_hybrid with simulated E. coli reads wrt E. coli ==="
idba_hybrid -r meta.reads --reference ecoli_ref.fa -o out2
echo
echo "=== Testing idba_hybrid with simulated E. coli reads wrt E. fergusonii ==="
idba_hybrid -r meta.reads --reference efergusonii_ref.fa -o out3
echo
cd ../tran
echo "=== Generate sample data for tran ==="
sim_reads_tran found-transcripts.fa reads.fa
echo
echo "=== Testing idba_tran ==="
idba_tran -r reads.fa -o out
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