#!/bin/sh
# autopkgtest check: Run simulated test data through REAPR
# Author: Sascha Steinbiss <sascha@steinbiss.name>
set -e

ORIGDIR=$(pwd)
DATADIR=$ORIGDIR/debian/tests/
WORKDIR=$(mktemp -d)

trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
cd $WORKDIR

zcat $DATADIR/foo1.fasta.gz > foo1.fasta
wgsim -d 2000 -N 10000 -1 120 -2 120 -S 42 \
  foo1.fasta \
  foofq.1.fastq \
  foofq.2.fastq
reapr smaltmap \
  foo1.fasta \
  foofq.1.fastq \
  foofq.2.fastq \
  out.bam
reapr pipeline \
  foo1.fasta \
  out.bam \
  result
