#!/bin/sh -e

pkg="soapdenovo"

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

for command in soapdenovo-31mer soapdenovo-63mer; do
	echo ">>>>>Starting $command test..."
	echo ">>>>>Step 1: pregraph"
	$command pregraph -s example.config -o graph
	[ -s graph.kmerFreq ]
	[ -s graph.edge ]
	[ -s graph.preArc ]
	[ -s graph.vertex ]
	[ -s graph.preGraphBasic ]

	echo ">>>>>Step 2: contig"
	$command contig -g graph
	[ -s graph.contig ]
	[ -s graph.Arc ]
	[ -s graph.updated.edge ]
	[ -s graph.ContigIndex ]
	
	echo ">>>>>Step 3: map"
	$command map -s example.config -g graph
	[ -s graph.peGrads ]
	[ -s graph.readOnContig ]
	[ -s graph.readInGap ]
	
	echo ">>>>>Step 4: scaff"
	$command scaff -g graph
	[ -s graph.newContigIndex ]
	[ -s graph.links ]
	[ -s graph.scaf_gap ]
	[ -s graph.scaf ]
	[ -e graph.gapSeq ]
	[ -s graph.scafSeq ]
	
	rm graph.*
	echo ""; echo "OK"; echo ""
done

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

