/usr/share/doc/staden-io-lib/test/java.test is in staden-io-lib-examples 1.14.8-2.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | #!/bin/sh
# Tests scramble compatibility with a simple cramtools.jar cram file.
# Minimal, but potentially useful compatibility test.
scramble="${VALGRIND} /usr/bin/scramble ${SCRAMBLE_ARGS}"
compare_sam=$srcdir/compare_sam.pl
for i in `/bin/ls $srcdir/data/*_java.cram`
do
echo "=== testing $i ==="
ref=`echo $i | sed 's/#.*/.fa/'`
root=`echo $i | sed 's/\.cram$//;s:.*/::'`
echo root=$root
echo "$scramble -r $ref $i $outdir/$root.scramble.sam"
$scramble -r $ref $i $outdir/$root.scramble.sam || exit 1
echo $compare_sam $srcdir/data/${root}.sam $outdir/$root.scramble.sam
$compare_sam $srcdir/data/${root}.sam $outdir/$root.scramble.sam || exit 1
done
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