Autopkgtest: modified run-unit-test

cp -a /usr/share/doc/${pkg}/test-data/* .

tar -xzvf *.tar.gz; rm *.tar.gz

echo ">>>>>Starting soapdenovo test..."

for command in soapdenovo-31mer soapdenovo-63mer; do

	echo ">>>>>Starting $command test..."

	echo ">>>>>Step 1: pregraph"

soapdenovo-31mer pregraph -s example.config -o graph

	$command pregraph -s example.config -o graph

	[ -s graph.kmerFreq ]

	[ -s graph.edge ]

	[ -s graph.preArc ]

	[ -s graph.preGraphBasic ]

	echo ">>>>>Step 2: contig"

soapdenovo-31mer contig -g graph

	$command contig -g graph

	[ -s graph.contig ]

	[ -s graph.Arc ]

	[ -s graph.updated.edge ]

	[ -s graph.ContigIndex ]

	echo ">>>>>Step 3: map"

soapdenovo-31mer map -s example.config -g graph

	$command map -s example.config -g graph

	[ -s graph.peGrads ]

	[ -s graph.readOnContig ]

	[ -s graph.readInGap ]

	echo ">>>>>Step 4: scaff"

soapdenovo-31mer scaff -g graph

	$command scaff -g graph

	[ -s graph.newContigIndex ]

	[ -s graph.links ]

	[ -s graph.scaf_gap ]

	[ -e graph.gapSeq ]

	[ -s graph.scafSeq ]

echo ""; echo "PASS"; echo ""

	rm graph.*

	echo ""; echo "OK"; echo ""

done

# soapdenovo-127mer testing requires lots of memory->Skipped