#!/bin/sh -e

pkg="soapdenovo2"

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

echo ">>>>>Starting soapdenovo2-63mer test..."
echo ">>>>>Step 1: pregraph"
soapdenovo2-63mer pregraph -s example.config -o graph
[ -s graph.kmerFreq ]
[ -s graph.edge.gz ]
[ -s graph.preArc ]
[ -s graph.vertex ]
[ -s graph.preGraphBasic ]

echo ">>>>>Step 2: contig"
soapdenovo2-63mer contig -g graph
[ -s graph.contig ]
[ -s graph.Arc ]
[ -s graph.updated.edge ]
[ -s graph.ContigIndex ]

echo ">>>>>Step 3: map"
soapdenovo2-63mer map -s example.config -g graph
[ -s graph.peGrads ]
[ -s graph.readOnContig.gz ]
[ -s graph.readInGap.gz ]

echo ">>>>>Step 4: scaff"
soapdenovo2-63mer scaff -g graph
[ -s graph.newContigIndex ]
[ -s graph.links ]
[ -s graph.scaf_gap ]
[ -s graph.scaf ]
[ -e graph.gapSeq ]
[ -s graph.scafSeq ]

# soapdenovo2-127mer testing requires lots of memory->Skipped

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