#!/bin/sh -e

pkg=pirs
testbin=pirs

if [ "$ADTTMP" = "" ] ; then
  ADTTMP=$(mktemp -d /tmp/${pkg}-${testbin}-test.XXXXXX)
  # trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
fi

cd $ADTTMP

cp -a /usr/share/doc/${pkg}/examples/${testbin}/* .
find . -type f -name "*.gz" -exec gunzip \{\} \;

pirs diploid ref_seq.fa -s 0.001 -R 2 -d 0.0001 -v 0.000001 -c gzip -o ref22 >SimDiploid.out 2>SimDiploid.err
pirs simulate -A dist ref_seq.fa ref22.snp.indel.inversion.fa.gz -d -M lowercase -m 800 -l 100 -x 10 -v 40 -o Illumina >SimReads.out 2>SimReads.err
pirs simulate ref_seq.fa ref22.snp.indel.inversion.fa.gz -d -M lowercase -m 800 -l 100 -x 10 -v 40 -o EAMSS2 >SimReadsEAMSS2.out 2>SimReadsEAMSS2.err
