#!/bin/sh -e

pkg=progressivemauve

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

cd $AUTOPKGTEST_TMP

cp -a /usr/share/doc/${pkg}/test_data/* .
gunzip -r *

progressiveMauve --output=threeway.xmfa genome_1.gbk genome_2.gbk genome_3.gbk

progressiveMauve --output=threeway.xmfa --output-guide-tree=threeway.tree --backbone-output=threeway.backbone genome_1.gbk genome_2.gbk genome_3.gbk

progressiveMauve --output=threeway_no_backbone.xmfa --disable-backbone genome_1.gbk genome_2.gbk genome_3.gbk

progressiveMauve --apply-backbone=threeway_no_backbone.xmfa --output=threeway.xmfa --backbone-output=threeway.backbone --hmm-p-go-homologous=0.001 --hmm-p-go-unrelated=0.000005

progressiveMauve --mums --output=threeway.mums genome_1.gbk genome_2.gbk genome_3.gbk

progressiveMauve --match-input=threeway.mums --output=threeway.xmfa genome_1.gbk genome_2.gbk genome_3.gbk

progressiveMauve --output=threeway.xmfa --weight=50000 genome_1.gbk genome_2.gbk genome_3.gb

progressiveMauve --min-scaled-penalty=5000 --output=threeway.xmfa genome_1.gbk genome_2.gbk genome_3.gbk

progressiveMauve --collinear --seed-family --disable-backbone --output=virus.xmfa all_virii.fasta
