This file is indexed.

/usr/share/doc/staden-io-lib/test/java.test is in staden-io-lib-examples 1.14.6-2.

This file is owned by root:root, with mode 0o755.

The actual contents of the file can be viewed below.

 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