/usr/share/doc/staden-io-lib/test/scram.test is in staden-io-lib-examples 1.14.9-4.
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 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 | #!/bin/sh
$srcdir/generate_data.pl || exit 1
scramble="${VALGRIND} /usr/bin/scramble ${SCRAMBLE_ARGS}"
compare_sam=$srcdir/compare_sam.pl
#valgrind="valgrind --leak-check=full"
#scramble="$valgrind $scramble"
case $# in
0) files=`/bin/ls $srcdir/data/*.{sam,bam} | egrep -v '[._](full|\.sub|java)\.'`
;;
*) files=${@+"$@"}
;;
esac
for i in $files
do
ref=`echo $i | sed 's/#.*/.fa/'`
root=`echo $i | sed 's/\.[sb]am$//;s:.*/::'`
echo "=== testing $i ==="
# Create BAM from SAM or SAM from BAM
if [ ${i//.bam} == $i ]
then
echo "$scramble $i $outdir/$root.bam"
$scramble $i $outdir/$root.bam || exit 1
cmp_sam=$srcdir/data/$root.sam
in_bam=$outdir/$root.bam
else
echo "$scramble $i $outdir/$root.sam"
$scramble $i $outdir/$root.sam || exit 1
cmp_sam=$outdir/$root.sam
in_bam=$i
fi
# Create CRAM
echo "$scramble -r $ref $in_bam $outdir/$root.full.cram"
$scramble -r $ref $in_bam $outdir/$root.full.cram || exit 1
# Test conversion back to SAM
echo "$scramble $in_bam > $outdir/tmp.sam"
$scramble $in_bam > $outdir/tmp.sam || exit 1
$compare_sam $cmp_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 || exit 1
$compare_sam --nomd --unknownrg $cmp_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 || exit 1
echo "$scramble $outdir/$root.full.bam $outdir/tmp.sam"
$scramble $outdir/$root.full.bam $outdir/tmp.sam || exit 1
sed '/^@PG.*scramble\.3.*/d;s/^\(@PG.*scramble.*\) -O bam/\1/' $outdir/tmp.sam > $outdir/$root.full.bam.sam
rm $outdir/tmp.sam
echo "$compare_sam --nopg $outdir/$root.full.sam $outdir/$root.full.bam.sam"
$compare_sam --nopg $outdir/$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 -e -r $ref $in_bam $outdir/$root.full.cram"
$scramble -e -r $ref $in_bam $outdir/$root.full.cram || exit 1
echo "$scramble $outdir/$root.full.cram > $outdir/$root.full.sam"
$scramble $outdir/$root.full.cram > $outdir/tmp.sam || exit 1
sed '/^@PG.*scramble\.3.*/d;s/^\(@PG.*scramble.*\) -e /\1 /' $outdir/tmp.sam > $outdir/$root.full.bam.sam
$compare_sam --nomd --unknownrg $cmp_sam $outdir/$root.full.sam || exit 1
echo "$compare_sam --nopg $outdir/$root.full.sam $outdir/$root.full.bam.sam"
$compare_sam --nopg $outdir/$root.full.sam $outdir/$root.full.bam.sam || exit 1
;;
esac
# And again with no ref.
echo "$scramble -x -r $ref $in_bam $outdir/$root.full.cram"
$scramble -x -r $ref $in_bam $outdir/$root.full.cram || exit 1
echo "$scramble $outdir/$root.full.cram > $outdir/$root.full.sam"
$scramble $outdir/$root.full.cram > $outdir/tmp.sam || exit 1
sed '/^@PG.*scramble\.3.*/d;s/^\(@PG.*scramble.*\) -x /\1 /' $outdir/tmp.sam > $outdir/$root.full.bam.sam
$compare_sam --nomd --unknownrg $cmp_sam $outdir/$root.full.sam || exit 1
# need compare against original here as ce#5b.sam as "*" in seq.
echo "$compare_sam --unknownrg $cmp_sam $outdir/$root.full.bam.sam"
$compare_sam --noqual --unknownrg $cmp_sam $outdir/$root.full.bam.sam || exit 1
echo ""
done
|