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#! @SHELL@
if test -z "$srcdir"; then
srcdir=.
fi
. ${srcdir}/defs
cp ${top_builddir}/util/fa_coords.pl ${top_builddir}/src/fa_coords
chmod +x ${top_builddir}/src/fa_coords
cp ${top_builddir}/util/gmap_process.pl ${top_builddir}/src/gmap_process
chmod +x ${top_builddir}/src/gmap_process
# Not sure if 12-mers work with new version
#${top_builddir}/util/gmap_build -k 12 -B ${top_builddir}/src -D . -d chr17test ${srcdir}/ss.chr17test
${top_builddir}/util/gmap_build -k 15 -B ${top_builddir}/src -D . -d chr17test ${srcdir}/ss.chr17test
#${top_builddir}/util/gmap_setup -k 12 -B ${top_builddir}/src -D . -d chr17test ${srcdir}/ss.chr17test
#make -f Makefile.chr17test coords
#make -f Makefile.chr17test gmapdb
#make -f Makefile.chr17test install
if diff ./chr17test/chr17test.genomecomp ${srcdir}/setup.genomecomp.ok; then
:
else
echo "Difference found between chr17test.genomecomp and setup.genomecomp.ok" >& 2
exit 1
fi
# Would need to check against ref153positions
#if diff ./chr17test/chr17test.ref123positions ${srcdir}/setup.ref123positions.ok; then
# :
#else
# echo "Difference found between chr17test.ref123positions and setup.ref123positions.ok" >& 2
# exit 1
#fi
# Need to debug uninitialized variables
#${top_builddir}/src/gmap -D . -d chr17test ${srcdir}/ss.her2 > map.test.out
#if diff map.test.out ${srcdir}/map.test.ok; then
# :
#else
# echo "Difference found between map.test.out and map.test.ok" >& 2
# exit 1
#fi
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