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#! /bin/bash
set -e
readonly tmpdir=$(mktemp -d)
tar -xf /usr/share/doc/gmap/examples/tests.tar.xz -C $tmpdir
readonly srcdir=${tmpdir}/tests
echo "align.test"
gmap -A -g ${srcdir}/ss.chr17test ${srcdir}/ss.her2 > align.test.out
diff align.test.out ${srcdir}/align.test.ok
rm -f align.test.out
echo "coords1.test"
/usr/lib/gmap/fa_coords -o coords.chr17test ${srcdir}/ss.chr17test
diff coords.chr17test ${srcdir}/coords1.test.ok
rm -f coords.chr17test
echo "iit.test"
/usr/lib/gmap/iit_store -o iittest ${srcdir}/fa.iittest
diff iittest.iit ${srcdir}/iittest.iit.ok
/usr/lib/gmap/iit_get iittest.iit 20000 > iit_get.out
diff iit_get.out ${srcdir}/iit_get.out.ok
/usr/lib/gmap/iit_dump iittest.iit > iit_dump.out
diff iit_dump.out ${srcdir}/fa.iittest
rm -f iit_get.out
rm -f iittest.iit
rm -f iit_dump.out
echo "setup1.test"
gmap_build -k 15 -B /usr/lib/gmap -D . -d chr17test ${srcdir}/ss.chr17test
rm -rf chr17test/
rm -rf $tmpdir
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