/usr/share/bedtools/test/bamtofastq/test-bamtofastq.sh is in bedtools-test 2.25.0-1.
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/bash
BT=${BT-../../bin/bedtools}
check()
{
if diff $1 $2; then
echo ok
else
echo fail
fi
}
samtools view -Sb test.sam > test.bam 2> /dev/null
$BT bamtofastq -i test.bam -fq test.fq -fq2 test.fq2 2> /dev/null
check test.fq golden.fq
check test.fq2 golden.fq2
rm test.bam test.fq test.fq2
|