/usr/share/doc/staden-io-lib/test/scram.test is in staden-io-lib-examples 1.13.7-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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$srcdir/generate_data.pl || exit 1
scramble="${VALGRIND} /usr/bin/scramble ${SCRAMBLE_ARGS}"
compare_sam=$srcdir/compare_sam.pl
#valgrind="valgrind --leak-check=full"
#scramble="$valgrind $scramble"
# fast cmp that does large blocks to avoid disk thrashing
#cmp=fcmp
cmp=cmp
case $# in
0) files=`/bin/ls $srcdir/data/*.sam | egrep -v '\.(full|sub)\.'`
;;
*) files=${@+"$@"}
;;
esac
for i in $files
do
ref=`echo $i | sed 's/#.*/.fa/'`
root=`echo $i | sed 's/\.sam$//;s:.*/::'`
echo "=== testing $root.sam ==="
# Create BAM
echo "$scramble $i $outdir/$root.bam"
$scramble $i $outdir/$root.bam
# Create CRAM
echo "$scramble -r $ref $outdir/$root.bam $outdir/$root.full.cram"
$scramble -r $ref $outdir/$root.bam $outdir/$root.full.cram
# Test conversion back to SAM
echo "$scramble $outdir/$root.bam > $outdir/tmp.sam"
$scramble $outdir/$root.bam > $outdir/tmp.sam
$compare_sam $srcdir/data/$root.sam $outdir/tmp.sam || exit 1
echo "$scramble $outdir/$root.full.cram > $outdir/$root.full.sam"
$scramble $outdir/$root.full.cram > $outdir/$root.full.sam
$compare_sam --nomd --unknownrg $srcdir/data/$root.sam $outdir/$root.full.sam || exit 1
echo "$scramble -O bam $outdir/$root.full.cram > $outdir/$root.full.bam"
$scramble -O bam $outdir/$root.full.cram > $outdir/$root.full.bam
echo "$scramble $outdir/$root.full.bam $outdir/tmp.sam"
$scramble $outdir/$root.full.bam $outdir/tmp.sam;
sed '/^@PG.*scramble\.3.*/d;s/\(^@PG.*scramble.*\) -O bam/\1/' $outdir/tmp.sam > $outdir/$root.full.bam.sam
rm $outdir/tmp.sam
echo "$cmp $outdir/$root.full.sam $outdir/$root.full.bam.sam"
$cmp $outdir/$root.full.sam $outdir/$root.full.bam.sam || exit 1
# Try again with embedded ref; skip for unsorted sams
case "$root" in
*"unsorted") #skip
;;
*)
echo "$scramble -X -r $ref $outdir/$root.bam $outdir/$root.full.cram"
$scramble -r $ref $outdir/$root.bam $outdir/$root.full.cram
echo "$scramble $outdir/$root.full.cram > $outdir/$root.full.sam"
$scramble $outdir/$root.full.cram > $outdir/$root.full.sam
$compare_sam --nomd --unknownrg $srcdir/data/$root.sam $outdir/$root.full.sam || exit 1
echo "$cmp $outdir/$root.full.sam $outdir/$root.full.bam.sam"
$cmp $outdir/$root.full.sam $outdir/$root.full.bam.sam || exit 1
;;
esac
# And again with no ref.
echo "$scramble -x -r $ref $outdir/$root.bam $outdir/$root.full.cram"
$scramble -r $ref $outdir/$root.bam $outdir/$root.full.cram
echo "$scramble $outdir/$root.full.cram > $outdir/$root.full.sam"
$scramble $outdir/$root.full.cram > $outdir/$root.full.sam
$compare_sam --nomd --unknownrg $srcdir/data/$root.sam $outdir/$root.full.sam || exit 1
echo "$cmp $outdir/$root.full.sam $outdir/$root.full.bam.sam"
$cmp $outdir/$root.full.sam $outdir/$root.full.bam.sam || exit 1
echo ""
done
|